Mercurial > repos > galaxyp > mqppep_anova
annotate mqppep_anova_script.Rmd @ 5:514afed1f40d draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit aa5f4a19e76ec636812865293b8ee9b196122121
| author | galaxyp |
|---|---|
| date | Fri, 17 Feb 2023 22:38:51 +0000 |
| parents | 2d9f216c1048 |
| children |
| rev | line source |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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1 --- |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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2 title: "MaxQuant Phosphoproteomic Enrichment Pipeline ANOVA/KSEA" |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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3 author: |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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4 - "Nick Graham^[ORCiD 0000-0002-6811-1941, University of Southern California: Los Angeles, CA, US]" |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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5 - "Larry Cheng^[ORCiD 0000-0002-6922-6433, Rutgers School of Graduate Studies: New Brunswick, NJ, US]" |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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6 - "Art Eschenlauer^[ORCiD 0000-0002-2882-0508, University of Minnesota: Minneapolis, Minnesota, US]" |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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7 date: |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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8 - "May 28, 2018" |
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2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
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9 - "; revised December 7, 2022" |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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10 lot: true |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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11 output: |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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12 pdf_document: |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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13 toc: true |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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14 toc_depth: 2 |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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15 keep_tex: true |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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16 dev: pdf |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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17 includes: |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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18 in_header: mqppep_anova_preamble.tex |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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19 latex_macros: false |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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20 raw_tex: true |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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21 urlcolor: blue |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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22 params: |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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23 alphaFile: "test-data/alpha_levels.tabular" |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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24 inputFile: "test-data/test_input_for_anova.tabular" |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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25 preprocDb: "test-data/test_input_for_anova.sqlite" |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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26 kseaAppPrepDb: !r c(":memory:", "test-data/mqppep.sqlite")[2] |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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27 regexSampleNames: "\\.\\d+[A-Z]$" |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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28 regexSampleGrouping: "\\d+" |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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29 groupFilterPatterns: ".+" |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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30 groupFilter: !r c("none", "exclude", "include")[1] |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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31 imputationMethod: !r c("group-median", "median", "mean", "random")[4] |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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32 kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5, 0.9)[5] |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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33 #imputationMethod: !r c("group-median", "median", "mean", "random")[1] |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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34 |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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35 # how should sample groups be interpreted? |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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36 # - "f": fixed patterns (like `grep -F`) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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37 # - "p": PERL-compatible (like `grep -P`) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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38 # - "r": extended grep patterns (like `grep -E`) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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39 # use what case sensitivity? |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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40 # - "i": case insensitive matching (like `grep -i`) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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41 groupFilterMode: !r c("r", "ri", "p", "pi", "f", "fi")[1] |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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42 # what pattern should be used for the first column |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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43 # (extended grep pattern, case sensitive) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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44 firstDataColumn: "^Intensity[^_]" |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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45 # for small random value imputation, what percentile should be center? |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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46 meanPercentile: 50 |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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47 #meanPercentile: 1 |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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48 # for small random value imputation, what should `s / mean(x)` ratio be? |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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49 sdPercentile: 1.0 |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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50 # output path for imputed data file |
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dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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51 imputedDataFilename: "test-data/imputedDataFilename.txt" |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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52 # output path for imputed/quantile-normalized/log-transformed data file |
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dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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53 imputedQNLTDataFile: "test-data/imputedQNLTDataFile.txt" |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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54 # output path for contents of `stats_metadata_v` table |
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dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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55 anovaKseaMetadata: "test-data/anovaKseaMetadata.txt" |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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56 # how to test one variable with > 2 categories (e.g., aov or kruskal.test) |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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57 oneWayManyCategories: !r c("aov", "kruskal.test", "oneway.test")[1] |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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58 # how to test one variable with 2 categories (e.g., oneway.test) |
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dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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59 oneWayTwoCategories: !r c("aov", "kruskal.test", "oneway.test")[3] |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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60 # what should be the minimum quality for consideration in both |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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61 minQuality: 0 |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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62 # correct KSEA with FDR (recommended) or raw p-value |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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63 kseaCutoffStatistic: !r c("FDR", "p.value")[1] |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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64 # correct KSEA threshold 0.05 (conventional) or higher (perhaps better) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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65 # "perhaps better" meaning that KSEA is an hypothesis-generator, not -test |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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66 #kseaCutoffThreshold: !r c(0.05, 0.1, 0.25, 0.5)[1] |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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67 # minimum number of substrates required for a kinase to be considered in KSEA |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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68 kseaMinSubstrateCount: 1 |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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69 # Should KSEA be performed aggregating signed log2FC or absolute? |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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70 # FALSE use raw log2FC for KSEA as for KSEAapp::KSEA.Scores |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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71 # TRUE use abs(log2FC) for KSEA as Justin Drake requested; this is a |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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72 # justifiable deviation from the KSEAapp::KSEA.Scores algorithm. |
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73 kseaUseAbsoluteLog2FC: TRUE |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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74 #kseaUseAbsoluteLog2FC: FALSE |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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75 # minimum number of observed values per sample-group |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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76 intensityMinValuesPerGroup: 1 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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77 # maximum number of heatmap rows (result are poor when > 50) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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78 intensityHeatmapRows: 50 |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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79 # what should be the primary criterion to eliminate excessive heatmap rows |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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80 intensityHeatmapCriteria: !r c("quality", "na_count", "p_value")[1] |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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81 # should correlation among substrates be used (rather than covariance) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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82 correlateSubstrates: TRUE |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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83 # only show covariance among variables having variance > 1 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 1c1dbc5a9838e5cd45724b6e53246eb80437e1f1
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84 filterCovVarGT1: FALSE |
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1
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85 # maximum number of residues to display for ppeps in rownames or columnames |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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86 ppepTruncN: 10 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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87 # maximum number of characters of subgenes to display in rownames or columnames |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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88 subgeneTruncN: 10 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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89 # maximum number of characters for paste(subgene, ppep) for enrichment plots |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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90 substTruncN: 20 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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91 # should boxplots use variable-width boxes to reflect # of samples |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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92 boxPlotVarWidth: TRUE |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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93 # should boxplots use notched boxes to reflect difference between samples |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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94 boxPlotNotch: TRUE |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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95 # look-up tables for kinase descriptions |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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96 kinaseNameUprtLutBz2: "./kinase_name_uniprot_lut.tabular.bz2" |
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97 kinaseUprtDescLutBz2: "./kinase_uniprot_description_lut.tabular.bz2" |
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98 # should debugging trace messages be printed? |
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99 showEnrichedSubstrates: FALSE |
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3
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100 # should row-scaling be applied to heatmaps: "none" or "row" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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101 defaultHeatMapRowScaling: !r c("none", "row")[1] |
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102 # how missing values be displayed on heat maps: "NA" or " " |
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103 heatMapNAcellNote: !r c(" ", "NA")[1] |
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104 # how missing values be displayed on heat maps: "NA" or " " |
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105 heatMapNAgrey: "#D8D8D8" |
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106 # temporary hack |
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107 heatMapNAsubstitute: TRUE |
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108 # what color should be used for missing values be displayed on heat maps |
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109 heatMapNAcellColor: "grey15" |
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110 # should debugging trace messages be printed? |
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111 printTraceMsgs: FALSE |
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112 # when debugging files are needed, set debugFileBasePath to the path |
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113 # to the directory where they should be written |
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114 debugFileBasePath: !r if (TRUE) NULL else "test-data" |
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4
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115 # should debugging nb/nbe messages be printed? |
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116 printNBMsgs: FALSE |
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117 #printNBMsgs: TRUE |
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118 --- |
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119 |
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120 ```{r setup, include = FALSE, results = 'asis'} |
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121 |
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122 # simple debug messaging |
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123 print_nb_messages <- params$printNBMsgs |
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124 |
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125 nb <- if (!print_nb_messages) { |
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126 function(...) invisible() |
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127 } else { |
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128 function(..., f = cat) f("\n$\\exists{}\\supset\\forall{}$", ...) |
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129 } |
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130 |
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131 nbe <- if (!print_nb_messages) { |
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132 function(...) invisible() |
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133 } else { |
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134 function(..., f = cat, file = stderr()) { |
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135 cat( |
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3
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136 stringi::stri_unescape_unicode("\nN.B. \\u2203\\u2283\\u2200"), |
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1
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137 ..., |
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138 file = file |
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139 ) |
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140 } |
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141 } |
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142 |
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0
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143 #ref for debugging: https://yihui.org/tinytex/r/#debugging |
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144 options(tinytex.verbose = TRUE) |
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145 |
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146 # ref for parameterizing Rmd document: https://stackoverflow.com/a/37940285 |
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147 # ref for top and bottom struts: https://tex.stackexchange.com/a/50355 |
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1
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148 knitr::opts_chunk$set(echo = FALSE, fig.dim = c(9, 10), dpi = 300) |
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0
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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149 |
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150 # freeze the random number generator so the same results will be produced |
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151 # from run to run |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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152 set.seed(28571) |
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153 |
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154 ### LIBRARIES |
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155 |
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156 if (print_nb_messages) nbe("library(gplots)") |
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157 library(gplots) |
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158 if (print_nb_messages) nbe("library(caret)") |
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159 # load caret for nearZeroVar |
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3
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160 if (print_nb_messages) nbe("Please ignore any messages about systemd.\n") |
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161 library(caret) |
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162 if (print_nb_messages) nbe("library(DBI)") |
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163 library(DBI) |
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164 if (print_nb_messages) nbe("library(RSQLite)") |
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165 library(RSQLite) |
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166 if (print_nb_messages) nbe("library(sqldf)\n") |
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167 # Suppress "Warning: no DISPLAY variable so Tk is not available" |
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168 suppressWarnings(suppressMessages(library(sqldf))) |
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169 |
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170 # required but not added to search list: |
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171 # - DBI |
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172 # - RSQLite |
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173 # - ggplot2 |
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174 # - knitr |
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175 # - latex2exp |
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176 # - preprocessCore |
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177 # - reshape2 |
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178 # - vioplot |
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179 |
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180 ### CONSTANTS |
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181 |
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182 const_boxplot_fill <- "grey94" |
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183 const_ksea_astrsk_kinases <- 1 |
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184 const_ksea_nonastrsk_kinases <- 2 |
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185 const_ksea_all_kinases <- 3 |
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186 const_log10_e <- log10(exp(1)) |
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187 const_stripchart_cex <- 0.5 |
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188 const_stripchart_jitter <- 0.3 |
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189 const_table_anchor_bp <- "bp" |
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190 const_table_anchor_ht <- "ht" |
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191 const_table_anchor_p <- "p" |
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192 const_table_anchor_t <- "t" |
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193 const_table_anchor_tbp <- "tbp" |
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194 |
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195 |
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196 ### GLOBAL VARIABLES (params) |
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197 |
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198 ## functions to process params |
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199 |
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200 is_string_null_or_empty <- function(x) { |
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201 # N. B. non-strings are intentionally treated as NULL |
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202 if (is.null(x)) |
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203 TRUE |
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204 else if (!is.character(x)) |
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205 TRUE |
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206 else x == "" |
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207 } |
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208 |
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209 ##' Catch *and* save both errors and warnings, and in the case of |
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210 ##' a warning, also keep the computed result. |
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211 ##' return result as list(value = ..., warning = ...) |
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212 ##' - value will be: |
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213 ##' - the result if no exception is thrown |
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214 ##' - the exception if an exception is caught |
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215 ##' - warning will be a string except perhaps when warning argument is not NULL |
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216 ##' |
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217 ##' adapted from `demo(error.catching)` |
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218 ##' |
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219 ##' @title tryCatch both warnings (with value) and errors |
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220 ##' @param expr an \R expression to evaluate |
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221 ##' @return a list with 'value' and 'warning', where |
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222 ##' 'value' may be an error caught. |
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223 ##' @author Martin Maechler; |
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224 ##' Copyright (C) 2010-2012 The R Core Team |
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1
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225 try_catch_w_e <- |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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226 function(expr, error = function(e) e, warning = NULL) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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227 wrn <- NULL |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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228 # warning handler |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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229 w_handler <- |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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230 if (is.function(warning)) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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231 warning |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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232 else |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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233 function(w) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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234 wrn <<- w |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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235 invokeRestart("muffleWarning") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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236 } |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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237 e_handler <- |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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238 if (is.function(error)) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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239 error |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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240 else |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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241 function(e) e |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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242 # return result as list(value = ..., warning = ...) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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243 # - value will be: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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244 # - the result if no exception is thrown |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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245 # - the exception if an exception is caught |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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246 list( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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247 value = withCallingHandlers( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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248 tryCatch( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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249 expr, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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250 error = e_handler |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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251 ), |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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252 warning = w_handler |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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253 ), |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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254 warning = wrn |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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255 ) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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256 } |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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257 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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258 see_kvp <- |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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259 function(format, key, value, suffix = "") { |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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260 if ( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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261 !all( |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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262 is.character(format), |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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263 is.character(key), |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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264 is.character(value), |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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265 is.character(suffix) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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266 ) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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267 ) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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268 cat("all arguments to see_kvp should be character") |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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269 knitr::knit_exit() |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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270 } |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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271 result <- sprintf(format, value) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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272 if (length(result) > 1) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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273 sprintf( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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274 "%s = c(%s)%s", |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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275 whack_underscores(key), |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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276 paste(result, collapse = ", "), |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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277 suffix |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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278 ) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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279 } else { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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280 sprintf( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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281 "%s = %s%s", |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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282 key, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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283 result, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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284 suffix |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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285 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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286 } |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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287 } |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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288 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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289 see_logical <- |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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290 function(x, suffix = "", xprssn = deparse1(substitute(x))) { |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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291 result <- as.character(as.logical(x)) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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292 # handle NAs and NaNs |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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293 result[is.na(result)] <- "NA" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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294 see_kvp( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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295 format = "%s", |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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296 key = xprssn, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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297 value = result, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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298 suffix = suffix |
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299 ) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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300 } |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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301 |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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302 see_numeric <- |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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303 function(x, suffix = "", digits = 3, xprssn = deparse1(substitute(x))) { |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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304 if (is.numeric(digits) && is.numeric(x)) { |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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305 digits <- as.integer(digits) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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306 digits <- min(16, max(0, digits)) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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307 format <- paste0("%0.", as.character(digits), "g") |
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308 result <- sprintf(format, x) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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309 see_kvp( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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310 format = "%s", |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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311 key = xprssn, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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312 value = result, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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313 suffix = suffix |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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314 ) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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315 } |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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316 } |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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317 |
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318 see_character <- |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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319 function(x, suffix = "", xprssn = deparse1(substitute(x))) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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320 if (is.character(x)) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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321 see_kvp( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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322 format = "%s", |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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323 key = xprssn, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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324 value = sprintf("\"%s\"", x), |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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325 suffix = suffix |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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326 ) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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327 } |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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328 } |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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329 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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330 see_variable <- |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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331 function(x, suffix = "", digits = 3, xprssn = deparse1(substitute(x))) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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332 if (is.character(x)) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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333 see_character(x, suffix, xprssn) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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334 } else if (is.numeric(x)) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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335 see_numeric(x, suffix, digits, xprssn) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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336 } else if (is.logical(x)) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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337 see_logical(x, suffix, xprssn) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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338 } else { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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339 f <- file("") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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340 sink(f) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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341 str(x) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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342 msg <- paste(readLines(f), collapse = "\n") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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343 sink() |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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344 close(f) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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345 paste0( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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346 "see_variable - str(", |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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347 xprssn, |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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348 "):\n", |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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349 msg, "\n" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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350 ) |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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351 } |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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352 } |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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353 |
|
3
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354 divert_warnings <- |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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355 function(expr, classes = "warning") { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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356 withCallingHandlers( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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357 expr, |
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358 warning = function(w) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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359 cat(" divert_warnings: ", w$message, "\n", file = stderr()) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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360 if (inherits(w, classes)) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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361 tryInvokeRestart("muffleWarning") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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362 } |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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363 ) |
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dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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364 } |
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dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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365 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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366 # ref: https://tug.org/texinfohtml/latex2e.html |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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367 # LaTeX sets aside the following characters for special purposes. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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368 # For example, the percent sign % is for comments. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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369 # They are called reserved characters or special characters. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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370 # They are all discussed elsewhere in this manual. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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371 # |
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372 # $ % & { } _ ~ ^ \ # |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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373 # |
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374 # If you want a reserved character to be printed as itself, in the text body |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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375 # font, for all but the final three characters in that list simply put |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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376 # a backslash \ in front of the character. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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377 # Thus, typing \$1.23 will produce $1.23 in your output. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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378 # |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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379 # As to the last three characters, to get a tilde in the text body font, |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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380 # use \~{} (omitting the curly braces would result in the next character |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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381 # receiving a tilde accent). |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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382 # Similarly, to get a text body font circumflex use \^{}. |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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383 # To get a backslash in the font of the text body enter \textbackslash{}. |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
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changeset
|
384 whack_math <- if (TRUE) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
385 function(v) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
386 v <- as.character(v) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
387 w <- v |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
388 w <- gsub("\\", "\\textbackslash ", v, fixed = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
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389 w <- Reduce( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
390 f = function(l, r) { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
391 ptrn <- paste0("\\", r) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
392 for (i in seq_along(l)) { |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
393 if (!grepl(ptrn, l[i], fixed = TRUE)) { |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
394 l[i] <- gsub(r, ptrn, l[i], fixed = TRUE) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
395 } |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
396 } |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
397 l |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
398 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
399 x = c("#", "$", "%", "&", "{", "}", "_"), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
400 init = w |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
401 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
402 w <- gsub("^", "\\^{}", w, fixed = TRUE) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
403 w <- gsub("\\textbackslash \\_", "\\_", w, fixed = TRUE) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
404 return(w) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
405 } |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
406 } else { |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
407 function(v) { |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
408 v <- as.character(v) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
409 w <- v |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
410 w <- gsub("\\", "\\textbackslash ", v, fixed = TRUE) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
411 w <- Reduce( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
412 f = function(l, r) { |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
413 if (length(l) > 1) { |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
414 cat("whack_math: deparse1(v) = `", deparse1(v), "`\n", |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
415 file = stderr()) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
416 cat("whack_math: v = `", v, "`\n", file = stderr()) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
417 cat(" Reduce f: l = `", l, |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
418 "` r = `", r, |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
419 "`\n", file = stderr() |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
420 ) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
421 divert_warnings(grepl(r, l, fixed = TRUE)) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
422 } |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
423 ptrn <- paste0("\\", r) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
424 cat("ptrn: `", ptrn, "`\n", file = stderr()) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
425 for (i in seq_along(l)) { |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
426 cat(" before l[i] = ", l[i], "\n", file = stderr()) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
427 if (!grepl(ptrn, l[i], fixed = TRUE)) { |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
428 l[i] <- gsub(r, ptrn, l[i], fixed = TRUE) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
429 } |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
430 cat(" after l[i] = ", l[i], "\n", file = stderr()) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
431 } |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
432 l |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
433 }, |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
434 x = c("#", "$", "%", "&", "{", "}", "_"), |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
435 init = w |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
436 ) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
437 w <- gsub("^", "\\^{}", w, fixed = TRUE) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
438 w <- gsub("\\textbackslash \\_", "\\_", w, fixed = TRUE) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
439 return(w) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
440 if (all(v == w)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
441 v |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
442 else |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
443 paste0("\\texttt{", w, "}") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
444 } |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
445 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
446 whack_underscores <- whack_math |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
447 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
448 ## dump params to stderr (remove this eventually) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
449 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
450 if (FALSE) nbe(see_variable(params)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
451 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
452 ## unlist params for eventual output |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
453 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
454 param_unlist <- unlist(as.list(params)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
455 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
456 # no need to whack underscores and dollars because this is verbatim |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
457 param_df <- data.frame( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
458 parameter = paste0("\\verb@", names(param_unlist), "@"), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
459 value = paste0( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
460 "\n\\begin{tiny}\n\\verb@", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
461 param_unlist, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
462 "@\n\\end{tiny}" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
463 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
464 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
465 param_df <- data.frame( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
466 parameter = names(param_unlist), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
467 value = param_unlist |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
468 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
469 param_df <- param_df[order(param_df$parameter), ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
470 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
471 ## general output control |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
472 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
473 debug_file_base_path <- params$debugFileBasePath |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
474 print_trace_messages <- params$printTraceMsgs |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
475 show_enriched_substrates <- params$showEnrichedSubstrates |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
476 boxplot_varwidth <- params$boxPlotVarWidth |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
477 boxplot_notch <- params$boxPlotNotch |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
478 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
479 ## parameters for static data |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
480 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
481 kinase_name_uprt_lut_bz2 <- params$kinaseNameUprtLutBz2 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
482 kinase_uprt_desc_lut_bz2 <- params$kinaseUprtDescLutBz2 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
483 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
484 ## parameters for input file |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
485 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
486 preproc_db <- params$preprocDb |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
487 alpha_file <- params$alphaFile |
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08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
488 input_file <- params$inputFile |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
489 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
490 # First data column - ideally, this could be detected via |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
491 # regexSampleNames, but for now leave it as is. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
492 first_data_column <- params$firstDataColumn |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
493 fdc_is_integer <- is.integer(first_data_column) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
494 if (fdc_is_integer) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
495 first_data_column <- as.integer(params$firstDataColumn) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
496 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
497 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
498 ## parameters for output files |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
499 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
500 ksea_app_prep_db <- params$kseaAppPrepDb |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
501 imputed_data_filename <- params$imputedDataFilename |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
502 imp_qn_lt_data_filenm <- params$imputedQNLTDataFile |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
503 anova_ksea_mtdt_file <- params$anovaKseaMetadata |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
504 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
505 ## parameters for imputation |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
506 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
507 # Imputation method, should be one of |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
508 # "random", "group-median", "median", or "mean" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
509 imputation_method <- params$imputationMethod |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
510 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
511 # Selection of percentile of logvalue data to set the mean for random number |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
512 # generation when using random imputation |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
513 mean_percentile <- params$meanPercentile / 100.0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
514 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
515 # deviation adjustment-factor for random values; real number. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
516 sd_percentile <- params$sdPercentile |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
517 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
518 ## parameters for group parsing and filtering |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
519 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
520 # Regular expression of Sample Names, e.g., "\\.(\\d+)[A-Z]$" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
521 regex_sample_names <- params$regexSampleNames |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
522 # Regular expression to extract Sample Grouping from Sample Name; |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
523 # if error occurs, compare smpl_trt vs. sample_name_matches |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
524 # to see if groupings/pairs line up |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
525 # e.g., "(\\d+)" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
526 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
527 regex_sample_grouping <- params$regexSampleGrouping |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
528 # What are the patterns for filtering sample groups? |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
529 # How should sample groups be filtered? |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
530 # - none: do not filter |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
531 # - include: include sample groups matching filter |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
532 # - exclude: include sample groups not matching filter |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
533 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
534 sample_group_filter <- params$groupFilter |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
535 if (grepl("f", params$groupFilterMode, fixed = TRUE)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
536 sample_group_filter_perl <- FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
537 sample_group_filter_fixed <- TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
538 } else if (grepl("p", params$groupFilterMode, fixed = TRUE)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
539 sample_group_filter_perl <- TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
540 sample_group_filter_fixed <- FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
541 } else { # normal regex |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
542 sample_group_filter_perl <- FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
543 sample_group_filter_fixed <- FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
544 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
545 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
546 sample_group_filter_nocase <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
547 grepl("i", params$groupFilterMode, fixed = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
548 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
549 # What PCRE patterns should be included or excluded |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
550 group_filter_patterns_csv <- params$groupFilterPatterns |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
551 sample_group_filter_patterns <- strsplit( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
552 x = group_filter_patterns_csv, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
553 split = ",", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
554 fixed = TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
555 )[[1]] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
556 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
557 ## parameters for hypothesis testing |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
558 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
559 one_way_all_categories_fname <- params$oneWayManyCategories |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
560 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
561 one_way_all_categories <- try_catch_w_e( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
562 match.fun(one_way_all_categories_fname)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
563 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
564 if (!is.function(one_way_all_categories$value)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
565 write("fatal error for parameter oneWayManyCategories:", stderr()) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
566 write(one_way_all_categories$value$message, stderr()) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
567 if (sys.nframe() > 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
568 cat("Cannot continue and quit() failed. Goodbye.") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
569 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
570 quit(save = "no", status = 1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
571 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
572 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
573 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
574 one_way_all_categories <- one_way_all_categories$value |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
575 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
576 one_way_two_categories_fname <- params$oneWayManyCategories |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
577 one_way_two_categories <- try_catch_w_e( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
578 match.fun(one_way_two_categories_fname)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
579 if (!is.function(one_way_two_categories$value)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
580 cat("fatal error for parameter oneWayTwoCategories: \n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
581 cat(one_way_two_categories$value$message, fill = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
582 if (sys.nframe() > 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
583 cat("Cannot continue and quit() failed. Goodbye.") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
584 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
585 quit(save = "no", status = 1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
586 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
587 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
588 one_way_two_categories <- one_way_two_categories$value |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
589 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
590 ## parameters for KSEA |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
591 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
592 ksea_cutoff_statistic <- params$kseaCutoffStatistic |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
593 ksea_cutoff_threshold <- params$kseaCutoffThreshold |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
594 ksea_min_substrate_count <- params$kseaMinSubstrateCount |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
595 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
596 ## parameters for global variables consumed by functions |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
597 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
598 # intensityHeatmapCriteria: !r c("na_count", "p_value")[2] # TODO switch to 1 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
599 # TODO Validate within list |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
600 g_intensity_hm_criteria <- params$intensityHeatmapCriteria |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
601 if (is_string_null_or_empty(g_intensity_hm_criteria)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
602 cat("invalid intensityHeatmapCriteria parameter (must be string)") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
603 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
604 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
605 switch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
606 g_intensity_hm_criteria, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
607 "quality" = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
608 "na_count" = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
609 "p_value" = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
610 { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
611 with( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
612 params, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
613 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
614 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
615 "invalid %s (must be %s)", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
616 see_variable(intensityHeatmapCriteria), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
617 "one of quality or na_count or p_value" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
618 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
619 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
620 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
621 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
622 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
623 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
624 |
|
2
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
625 g_default_heatmap_row_scaling <- |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
626 params$defaultHeatMapRowScaling |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
627 if ( |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
628 !is.character(g_default_heatmap_row_scaling) || |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
629 !(g_default_heatmap_row_scaling %in% c("row", "none")) |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
630 ) { |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
631 cat("invalid defaultHeatMapRowScaling (must be 'row' or 'none')") |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
632 knitr::knit_exit() |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
633 } |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
634 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
635 # intensityHeatmapRows: 50 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
636 # TODO Validate >> 0 < 75 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
637 g_intensity_hm_rows <- params$intensityHeatmapRows |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
638 if (!is.integer(g_intensity_hm_rows) || g_intensity_hm_rows < 1) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
639 cat("invalid intensityHeatmapRows (must be integer > 0)") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
640 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
641 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
642 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
643 g_intensity_min_per_class <- params$intensityMinValuesPerGroup |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
644 if (!is.integer(g_intensity_min_per_class) || g_intensity_min_per_class < 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
645 cat("invalid intensityMinValuesPerGroup (must be integer > -1") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
646 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
647 } |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
648 g_correlate_substrates <- params$correlateSubstrates |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
649 if (is.na(as.logical(g_correlate_substrates))) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
650 cat("invalid correlateSubstrates (must be TRUE or FALSE)") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
651 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
652 } |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
653 g_filter_cov_var_gt_1 <- params$filterCovVarGT1 |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
654 if (is.na(as.logical(g_filter_cov_var_gt_1))) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
655 cat("invalid filterCovVarGT1 parameter (must be TRUE or FALSE)") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
656 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
657 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
658 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
659 # TODO Validate >> 0 < 30 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
660 g_ppep_trunc_n <- params$ppepTruncN |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
661 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
662 # TODO Validate >> 0 < 30 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
663 g_subgene_trunc_n <- params$subgeneTruncN |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
664 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
665 # TODO Validate >> 0 < 30 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
666 g_sbstr_trunc_n <- params$substTruncN |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
667 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
668 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
669 ### OPERATORS |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
670 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
671 # Test for exclusion |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
672 # ref: https://www.reneshbedre.com/blog/in-operator-r.html |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
673 `%notin%` <- Negate(`%in%`) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
674 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
675 # Augmented assignment |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
676 # ref: https://www2.cs.arizona.edu/icon/refernce/infix2.htm#aug_assign |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
677 `%||:=%` <- function(lvalue, ...) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
678 pf <- parent.frame() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
679 rvalue <- Reduce(paste0, x = ..., init = lvalue) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
680 assign( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
681 x = as.character(substitute(lvalue)), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
682 value = rvalue, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
683 pos = pf |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
684 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
685 invisible(rvalue) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
686 } |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
687 # Infix concatenation |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
688 `%||%` <- function(lvalue, rvalue) paste0(lvalue, rvalue) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
689 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
690 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
691 ### FUNCTIONS |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
692 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
693 no_op <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
694 function() { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
695 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
696 # this function is not used in this file and should be removed while |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
697 # factoring out reusable code |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
698 all_apply <- function(f, v, na_rm = TRUE, ...) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
699 Reduce( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
700 f = function(l, r) if (na_rm && is.na(r)) TRUE else l && r, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
701 x = sapply(X = v, FUN = f, ...), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
702 init = TRUE |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
703 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
704 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
705 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
706 write_debug_file <- function(data_frame) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
707 if (!is.null(debug_file_base_path)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
708 s_path <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
709 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
710 "%s/%s.txt", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
711 debug_file_base_path, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
712 deparse(substitute(data_frame)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
713 ) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
714 write.table( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
715 data_frame, |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
716 file = s_path, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
717 sep = "\t", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
718 col.names = TRUE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
719 row.names = TRUE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
720 quote = FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
721 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
722 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
723 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
724 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
725 # ref: http://adv-r.had.co.nz/Environments.html |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
726 # "When creating your own environment, note that you should set its parent |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
727 # environment to be the empty environment. This ensures you don't |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
728 # accidentally inherit objects from somewhere else." |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
729 # Caution: this prevents `with(my_env, expr)` from working when `expr` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
730 # contains anything from the global environment, even operators! |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
731 # Hence, `x <- 1; get("x", new_env())` fails by design. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
732 new_env <- function() { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
733 new.env(parent = emptyenv()) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
734 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
735 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
736 # make apply readable for rows |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
737 row_apply <- function(x, fun, ..., simplify = TRUE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
738 apply(x, MARGIN = 1, fun, ..., simplify = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
739 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
740 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
741 # make apply readable for columns |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
742 column_apply <- function(x, fun, ..., simplify = TRUE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
743 apply(x, MARGIN = 2, fun, ..., simplify = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
744 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
745 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
746 ##' Produce a vector of boolean values whose i-th value is TRUE when any |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
747 ##' member of v matches the i-th membr of s, where i in 1:seq_len(length(s)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
748 ##' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
749 ##' @title Search multiple strings for matches of multiple substrings |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
750 ##' @param v a vector of substrings to match |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
751 ##' @param s a vector of strings to search for matches |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
752 ##' @param ... additional arguments to grepl |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
753 ##' @return a list with keys in s and valuse that are vectors of elements of v |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
754 ##' @author Art Eschenlauer |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
755 ##' Copyright (C) 2022 Art Eschenlauer; |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
756 ##' MIT License; https://en.wikipedia.org/wiki/MIT_License#License_terms |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
757 mgrepl <- function(v, s, ...) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
758 grpl_rslt <- rep_len(0, length(s)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
759 for (vi in v) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
760 grpl_rslt_v <- sapply( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
761 X = s, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
762 FUN = function(t) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
763 Reduce( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
764 f = function(l, r) if (is.null(l)) r else c(l, r), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
765 x = sapply( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
766 X = vi, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
767 FUN = function(f) grepl(f, t, ...) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
768 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
769 init = c() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
770 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
771 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
772 simplify = "array" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
773 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
774 grpl_rslt <- grpl_rslt + grpl_rslt_v |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
775 } |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
776 unname(grpl_rslt > 0) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
777 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
778 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
779 ##' Produce positions in a vector where succeeding value != current valus |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
780 ##' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
781 ##' @title Search vector for neighboring positions having different values |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
782 ##' @param v a vector of comparable numeric values (e.g. integers) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
783 ##' @return a vector of positions i where v[i] != v[i + 1] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
784 ##' @author Art Eschenlauer |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
785 ##' Copyright (C) 2022 Art Eschenlauer; |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
786 ##' MIT License; https://en.wikipedia.org/wiki/MIT_License#License_terms |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
787 transition_positions <- function(v) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
788 Reduce( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
789 f = function(l, i) if ((i != 1) && (v[i - 1] != v[i])) c(l, i - 1) else l, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
790 x = seq_along(v)[-1:0], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
791 init = c() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
792 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
793 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
794 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
795 ### figure debug functions |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
796 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
797 cat_par_vector <- function(par_name, lbl = "", newlines = TRUE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
798 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
799 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
800 "%spar(%s) = c(%s)%s", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
801 lbl, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
802 par_name, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
803 paste(par(par_name), collapse = ", "), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
804 if (newlines) "\n\n" else "" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
805 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
806 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
807 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
808 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
809 cat_margins <- function(lbl = NULL) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
810 for (p in c("fig", "fin", "mar", "mai", "omd", "omi", "oma")) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
811 cat_par_vector(p, if (!is.null(lbl)) paste0(lbl, " ") else NULL) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
812 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
813 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
814 cat_variable <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
815 function(x, suffix = "", digits = 3, force_str = FALSE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
816 xprssn <- deparse1(substitute(x)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
817 if (force_str || is.matrix(x) || is.list(x) || is.data.frame(x)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
818 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
819 paste0( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
820 "\n\\texttt{\\textbf{", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
821 whack_underscores(xprssn), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
822 "}} [", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
823 typeof(x), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
824 ",", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
825 mode(x), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
826 "] =\n" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
827 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
828 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
829 cat("\n\\begin{verbatim}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
830 str(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
831 cat("\n\\end{verbatim}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
832 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
833 cat("\n", see_variable(x, suffix, digits, xprssn)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
834 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
835 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
836 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
837 ### structure helper functions |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
838 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
839 # ref: staque.R - Icon-oriented stack and queue operations |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
840 # - https://gist.github.com/eschen42/917690355e53918b9e7ba7138a02d1f8 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
841 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
842 # sq_get(v):x produces the leftmost element of v and removes it from v, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
843 # but produces NA if v is empty |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
844 sq_get <- function(v) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
845 if (length(v) == 0) return(NA) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
846 assign(as.character(substitute(v)), v[-1], parent.frame()) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
847 return(v[1]) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
848 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
849 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
850 # sq_put(v,x1,...,xn):v puts x1, x2, ..., xn onto the right end of v, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
851 # producing v. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
852 # Values are pushed in order from left to right, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
853 # so xn becomes the last (rightmost) value on v. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
854 # sq_put(v) with no second argument does nothing. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
855 sq_put <- function(v, x = NA, ...) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
856 pf <- parent.frame() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
857 if (is.null(x)) return(pf$v) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
858 if ( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
859 !(length(x) > 1) && |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
860 !rlang::is_closure(x) && |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
861 is.na(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
862 ) return(pf$v) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
863 assign(as.character(substitute(v)), c(v, x, ...), pf) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
864 pf[[as.character(substitute(v))]] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
865 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
866 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
867 ### numerical/statistical helper functions |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
868 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
869 any_nan <- function(x) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
870 !any(x == "NaN") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
871 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
872 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
873 # determine standard deviation of quantile to impute |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
874 sd_finite <- function(x) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
875 ok <- is.finite(x) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
876 sd(x[ok]) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
877 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
878 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
879 # compute anova raw p-value |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
880 anova_func <- function(x, grouping_factor, one_way_f) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
881 subject <- data.frame( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
882 intensity = x |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
883 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
884 x_aov <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
885 one_way_f( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
886 formula = intensity ~ grouping_factor, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
887 data = subject |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
888 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
889 pvalue <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
890 if (identical(one_way_f, aov)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
891 summary(x_aov)[[1]][["Pr(>F)"]][1] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
892 else |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
893 pvalue <- x_aov$p.value |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
894 pvalue |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
895 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
896 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
897 # This code adapted from matrixcalc::is.positive.definite |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
898 # Notably, this simply tests without calling stop() |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
899 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
900 # squash un-actionable cyclomatic_complexity warning |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
901 is_positive_definite <- function(x, tol = 1e-08) { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
902 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
903 if (!is.matrix(x)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
904 return(FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
905 if (!is.numeric(x)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
906 return(FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
907 if (nrow(x) < 1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
908 return(FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
909 if (ncol(x) < 1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
910 return(FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
911 if (nrow(x) != ncol(x)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
912 return(FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
913 sum_symm <- sum(x == t(x), na.rm = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
914 value_count <- Reduce("*", dim(x)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
915 if (sum_symm != value_count) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
916 return(FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
917 eigenvalues <- eigen(x, only.values = TRUE)$values |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
918 n <- nrow(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
919 for (i in 1:n) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
920 if (abs(eigenvalues[i]) < tol) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
921 eigenvalues[i] <- 0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
922 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
923 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
924 if (any(eigenvalues <= 0)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
925 return(FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
926 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
927 return(TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
928 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
929 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
930 ### LaTeX functions |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
931 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
932 # Use this like print.data.frame, from which it is adapted: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
933 data_frame_table_latex <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
934 function( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
935 x, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
936 # digits to pass to format.data.frame |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
937 digits = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
938 # TRUE -> right-justify columns; FALSE -> left-justify |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
939 right = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
940 # maximumn number of rows to print |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
941 max = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
942 # string with justification of each column |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
943 justification = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
944 # TRUE to center on page |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
945 centered = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
946 # optional caption |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
947 caption = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
948 # h(inline); b(bottom); t (top) or p (separate page) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
949 anchor = "h", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
950 # set underscore_whack to TRUE to escape underscores |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
951 underscore_whack = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
952 # how to emit results |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
953 emit = cat |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
954 ) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
955 if (is.null(justification)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
956 justification <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
957 Reduce( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
958 f = paste, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
959 x = rep_len(if (right) "r" else "l", length(colnames(x))) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
960 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
961 n <- length(rownames(x)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
962 if (length(x) == 0L) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
963 emit( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
964 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
965 # if n is one, use singular 'row', else use plural 'rows' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
966 ngettext( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
967 n, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
968 "data frame with 0 columns and %d row", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
969 "data frame with 0 columns and %d rows" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
970 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
971 n |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
972 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
973 "\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
974 sep = "" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
975 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
976 } else if (n == 0L) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
977 emit("0 rows for:\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
978 latex_itemized_list( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
979 v = names(x), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
980 underscore_whack = underscore_whack |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
981 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
982 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
983 if (is.null(max)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
984 max <- getOption("max.print", 99999L) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
985 if (!is.finite(max)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
986 cat("Abend because: invalid 'max' / getOption(\"max.print\"): ", max) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
987 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
988 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
989 omit <- (n0 <- max %/% length(x)) < n |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
990 m <- as.matrix( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
991 format.data.frame( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
992 if (omit) x[seq_len(n0), , drop = FALSE] else x, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
993 digits = digits, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
994 na.encode = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
995 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
996 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
997 emit( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
998 # h(inline); b(bottom); t (top) or p (separate page) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
999 paste0("\\begin{table}[", anchor, "]"), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1000 "\\leavevmode", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1001 sep = "\n" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1002 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1003 if (!is.null(caption)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1004 emit(paste0(" \\caption{", caption, "}")) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1005 if (centered) emit("\\centering\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1006 emit( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1007 paste( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1008 " \\begin{tabular}{", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1009 justification, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1010 "}\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1011 sep = "" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1012 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1013 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1014 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1015 # ref for top and bottom struts (\T and \B): |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1016 # https://tex.stackexchange.com/a/50355 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1017 if (!is.null(caption)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1018 emit("\\B \\\\\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1019 latex_table_row( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1020 v = colnames(m), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1021 extra = " \\T \\B", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1022 underscore_whack = underscore_whack |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1023 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1024 emit("\\hline \\\\\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1025 for (i in seq_len(length(m[, 1]))) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1026 latex_table_row( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1027 v = m[i, ], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1028 underscore_whack = underscore_whack |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1029 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1030 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1031 emit( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1032 paste( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1033 " \\end{tabular}", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1034 "\\end{table}", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1035 sep = "\n" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1036 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1037 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1038 if (omit) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1039 emit(" [ reached 'max' / getOption(\"max.print\") -- omitted", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1040 n - n0, "rows ]\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1041 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1042 invisible(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1043 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1044 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1045 # Use this like print.data.frame, from which it is adapted: |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1046 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1047 # squash un-actionable cyclomatic_complexity warning |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1048 # squash un-actionable "no visible global for ..." |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1049 data_frame_tabbing_latex <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1050 function( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1051 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1052 x, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1053 # vector of tab stops, in inches |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1054 tabstops, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1055 # vector of headings, registered with tab-stops |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1056 headings = colnames(x), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1057 # digits to pass to format.data.frame |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1058 digits = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1059 # maximumn number of rows to print |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1060 max = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1061 # optional caption |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1062 caption = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1063 # set underscore_whack to TRUE to escape underscores |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1064 underscore_whack = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1065 # flag for landscape mode |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1066 landscape = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1067 # flag indicating that subsubsection should be used for caption |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1068 # rather than subsection |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1069 use_subsubsection_header = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1070 # character-size indicator; for possible values, see: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1071 # https://tug.org/texinfohtml/latex2e.html#Font-sizes |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1072 charactersize = "small", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1073 # set verbatim to TRUE to debug output |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1074 verbatim = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1075 ) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1076 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1077 hlinport <- if (landscape) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1078 function() cat("\\hlinlscp \\\\\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1079 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1080 function() cat("\\hlinport \\\\\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1081 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1082 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1083 tabstops_tex <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1084 Reduce( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1085 f = function(l, r) paste0(l, r), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1086 x = sprintf("\\hspace{%0.2fin}\\=", tabstops), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1087 init = "" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1088 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1089 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1090 n <- length(rownames(x)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1091 if (length(x) == 0L) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1092 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1093 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1094 # if n is one, use singular 'row', else use plural 'rows' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1095 ngettext( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1096 n, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1097 "data frame with 0 columns and %d row", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1098 "data frame with 0 columns and %d rows" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1099 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1100 n |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1101 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1102 "\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1103 sep = "" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1104 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1105 } else if (n == 0L) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1106 cat("0 rows for:\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1107 latex_itemized_list( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1108 v = names(x), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1109 underscore_whack = underscore_whack |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1110 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1111 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1112 if (is.null(max)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1113 max <- getOption("max.print", 99999L) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1114 if (!is.finite(max)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1115 cat("Abend because: invalid 'max' / getOption(\"max.print\"): ", max) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1116 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1117 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1118 omit <- (n0 <- max %/% length(x)) < n |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1119 m <- as.matrix( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1120 format.data.frame( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1121 if (omit) x[seq_len(n0), , drop = FALSE] else x, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1122 digits = digits, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1123 na.encode = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1124 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1125 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1126 if (landscape) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1127 cat("\n\\begin{landscape}") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1128 tex_caption <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1129 if (!is.null(caption)) sprintf("\\captionof{table}{%s}\n", caption) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1130 else "\n" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1131 # build the column names, which have multiple lines when |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1132 # length(headings) is a multiple of the number of columns |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1133 column_names <- "" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1134 while (length(headings) > 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1135 my_row <- c() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1136 for (i in 1:(1 + length(tabstops))) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1137 my_field <- sq_get(headings) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1138 sq_put(my_row, if (is.na(my_field)) "" else my_field) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1139 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1140 column_names %||:=% latex_tabbing_row( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1141 v = my_row, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1142 underscore_whack = underscore_whack, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1143 action = paste0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1144 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1145 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1146 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1147 # Begin tabbing environment after beginning charactersize environment |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1148 if (verbatim) cat("\n\\begin{verbatim}") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1149 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1150 paste0( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1151 "\n\\begin{", charactersize, "}", tex_caption, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1152 "\\begin{tabwrap}{", tabstops_tex, "}\n" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1153 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1154 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1155 # emit column names |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1156 cat(column_names) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1157 # emit hline |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1158 hlinport() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1159 for (i in seq_len(length(m[, 1]))) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1160 my_row <- latex_tabbing_row( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1161 v = m[i, ], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1162 underscore_whack = underscore_whack, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1163 action = paste0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1164 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1165 if (FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1166 cat(my_row) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1167 else |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1168 cat(my_row) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1169 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1170 hlinport() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1171 if (omit) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1172 cat(" [ reached 'max' / getOption(\"max.print\") -- omitted", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1173 n - n0, "rows ]\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1174 # End charactersize environment after ending tabbing environment |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1175 cat(paste0("\\end{tabwrap}\n\\end{", charactersize, "}\n")) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1176 if (verbatim) cat("\\end{verbatim}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1177 if (landscape) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1178 cat("\\end{landscape}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1179 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1180 invisible(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1181 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1182 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1183 param_df_noexit <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1184 function(e = NULL) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1185 data_frame_tabbing_latex( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1186 x = param_df, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1187 tabstops = c(1.75), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1188 underscore_whack = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1189 caption = "Input parameters", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1190 verbatim = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1191 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1192 if (!is.null(e)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1193 sink(stderr()) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1194 cat("Caught fatal error:\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1195 str(e) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1196 sink() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1197 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1198 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1199 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1200 param_df_exit <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1201 function(e = NULL) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1202 param_df_noexit(e) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1203 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1204 exit(-1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1205 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1206 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1207 # exit with exit code (default 0) and optional msg |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1208 exit <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1209 function(code = 0, msg = NULL, use_stderr = FALSE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1210 if (!is.null(msg)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1211 if (use_stderr) sink(stderr()) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1212 cat("\n\n", msg, "\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1213 if (use_stderr) sink() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1214 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1215 q(save = "no", status = code) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1216 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1217 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1218 # make control sequences into printable latex sequences |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1219 latex_printable_control_seqs <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1220 function(s) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1221 s <- gsub("[\\]", "xyzzy_plugh", s) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1222 s <- gsub("[$]", "\\\\$", s) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1223 s <- gsub("xyzzy_plugh", "$\\\\backslash$", s) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1224 return(s) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1225 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1226 nolatex_verbatim <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1227 function(expr) eval(expr) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1228 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1229 error_knitrexit_stop <- |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1230 function(e) { |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1231 cat("Caught error:\n\n") |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1232 str(e) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1233 knitr::knit_exit() |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1234 stop(e) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1235 } |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1236 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1237 latex_verbatim <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1238 function(expr) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1239 cat("\n\\begin{verbatim}\n___\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1240 tryCatch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1241 expr = expr, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1242 error = param_df_exit, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1243 finally = cat("...\n\\end{verbatim}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1244 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1245 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1246 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1247 latex_samepage <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1248 function(expr) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1249 cat("\n\\begin{samepage}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1250 tryCatch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1251 expr = expr, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1252 error = param_df_exit, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1253 finally = cat("\n\\end{samepage}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1254 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1255 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1256 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1257 # return the result of invocation after showing parameters |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1258 # ref: https://www.r-bloggers.com/2013/08/a-new-r-trick-for-me-at-least/ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1259 latex_show_invocation <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1260 function(f, f_name = deparse1(substitute(f)), head_patch = FALSE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1261 function(...) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1262 va <- list(...) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1263 my_rslt <- new_env() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1264 my_rslt$rslt <- NULL |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1265 latex_verbatim( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1266 expr = { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1267 cat(sprintf("\n .. Local variables for '%s':\n\n", f_name)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1268 str(va) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1269 if (!head_patch) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1270 # return this result |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1271 # ref: |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1272 # https://www.r-bloggers.com/2013/08/a-new-r-trick-for-me-at-least/ |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1273 cat(sprintf("\n .. Invoking '%s'\n", f_name)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1274 tryCatch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1275 { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1276 cat("\n\\end{verbatim}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1277 rslt <- do.call(f, va) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1278 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1279 error = param_df_exit, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1280 finally = cat("\n\\begin{verbatim}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1281 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1282 cat(sprintf("\n .. '%s' returned:\n", f_name)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1283 str(rslt) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1284 my_rslt$rslt <- rslt |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1285 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1286 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1287 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1288 # return the result of invocation with the shown parameters |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1289 # ref: https://www.r-bloggers.com/2013/08/a-new-r-trick-for-me-at-least/ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1290 if (head_patch) my_rslt$rslt <- do.call(f, va) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1291 (my_rslt$rslt) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1292 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1293 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1294 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1295 latex_collapsed_vector <- function( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1296 collapse_string, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1297 v, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1298 underscore_whack = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1299 action = cat0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1300 ) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1301 v_sub <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1302 if (underscore_whack) whack_underscores(v) else v |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1303 action( |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1304 paste0( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1305 v_sub, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1306 collapse = collapse_string |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1307 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1308 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1309 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1310 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1311 latex_itemized_collapsed <- |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1312 function(collapse_string, v, underscore_whack = TRUE) { |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1313 cat("\\begin{itemize}\n\\item ") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1314 latex_collapsed_vector(collapse_string, v, underscore_whack) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1315 cat("\n\\end{itemize}\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1316 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1317 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1318 latex_itemized_list <- function(v, underscore_whack = TRUE) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1319 latex_itemized_collapsed("\n\\item ", v, underscore_whack) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1320 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1321 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1322 latex_enumerated_collapsed <- |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1323 function(collapse_string, v, underscore_whack = TRUE) { |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1324 cat("\\begin{enumerate}\n\\item ") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1325 latex_collapsed_vector(collapse_string, v, underscore_whack) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1326 cat("\n\\end{enumerate}\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1327 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1328 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1329 latex_enumerated_list <- function(v) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1330 latex_enumerated_collapsed("\n\\item ", v) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1331 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1332 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1333 latex_table_row <- function(v, extra = "", underscore_whack = TRUE) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1334 latex_collapsed_vector(" & ", v, underscore_whack) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1335 cat(extra) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1336 cat(" \\\\\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1337 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1338 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1339 latex_tabbing_row <- function( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1340 v, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1341 extra = "", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1342 underscore_whack = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1343 action = cat0 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1344 ) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1345 # latex_collapsed_vector applies action to result of paste0; |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1346 # by default, action = cat; |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1347 # hence, a scalar string is assigned to v_collapsed |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1348 v_collapsed <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1349 latex_collapsed_vector( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1350 "} \\> \\tabfill{", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1351 v, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1352 underscore_whack, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1353 action = paste0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1354 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1355 action( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1356 "\\tabfill{", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1357 v_collapsed, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1358 "}", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1359 extra, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1360 " \\\\\n" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1361 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1362 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1363 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1364 # N.B. use con = "" to emulate regular cat |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1365 fcat0 <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1366 function(..., sprtr = " ", cnnctn = file()) { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1367 gsubfn::cat0(..., sep = sprtr, file = cnnctn) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1368 invisible(cnnctn) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1369 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1370 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1371 hypersub <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1372 function(s) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1373 hyper <- tolower(s) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1374 hyper <- gsub("[^a-z0-9]+", "-", hyper) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1375 hyper <- gsub("[-]+", "-", hyper) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1376 hyper <- gsub("[_]+", "-", hyper) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1377 hyper <- sub("^[-]", "", hyper) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1378 hyper <- sub("[-]$", "", hyper) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1379 return(hyper) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1380 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1381 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1382 table_href <- function(s = "offset", caption = "") { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1383 paste0("\\hyperlink{table.\\arabic{", s, "}}{Table \\arabic{", s, "}}") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1384 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1385 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1386 table_offset <- function(i = 0, s = "offset", new = FALSE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1387 paste0( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1388 if (new) paste0("\\newcounter{", s, "}\n") else "", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1389 "\\setcounter{", s, "}{\\value{table}}\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1390 paste0(if (i > 0) rep(paste0("\\stepcounter{", s, "}"), i), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1391 ) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1392 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1393 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1394 a_section_header <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1395 function(s, prefix = "") { |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1396 hyper <- hypersub(s) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1397 my_subsection_header <- sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1398 "\\hypertarget{%s}{\\%ssection{%s}\\label{%s}}\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1399 hyper, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1400 prefix, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1401 gsub("_", "\\_", s, fixed = TRUE), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1402 hyper |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1403 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1404 my_subsection_header |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1405 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1406 section_header <- function(s) a_section_header(s, "") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1407 subsection_header <- function(s) a_section_header(s, "sub") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1408 subsubsection_header <- function(s) a_section_header(s, "subsub") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1409 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1410 ### SQLite functions |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1411 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1412 ddl_exec <- function(db, sql) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1413 discard <- DBI::dbExecute(conn = db, statement = sql) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1414 if (FALSE && discard != 0) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1415 need_newpage <- TRUE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1416 if (need_newpage) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1417 need_newpage <<- FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1418 cat("\\newpage\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1419 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1420 o_file <- stdout() |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1421 cat("\n\\begin{verbatim}\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1422 cat(sql, file = o_file) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1423 cat(sprintf("\n%d rows affected by DDL\n", discard), file = o_file) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1424 cat("\n\\end{verbatim}\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1425 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1426 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1427 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1428 dml_no_rows_exec <- function(db, sql) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1429 discard <- DBI::dbExecute(conn = db, statement = sql) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1430 if (discard != 0) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1431 need_newpage <- TRUE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1432 if (need_newpage) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1433 need_newpage <<- FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1434 cat("\\newpage\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1435 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1436 cat("\n\\begin{verbatim}\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1437 o_file <- stdout() |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1438 cat(sql, file = o_file) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1439 cat(sprintf("\n%d rows affected by DML\n", discard), file = o_file) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1440 cat("\n\\end{verbatim}\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1441 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1442 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1443 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1444 ### KSEA functions and helpers |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1445 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1446 #' The KSEA App Analysis (KSEA Kinase Scores Only) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1447 #' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1448 #' Compute KSEA kinase scores and statistics from phoshoproteomics data input |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1449 #' Adapted from KSEAapp::KSEA.Scores to allow retrieval of maximum log2(FC) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1450 #' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1451 #' Result is an R data.frame with column names |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1452 #' "Kinase.Gene", "mS", "Enrichment", "m", "z.score", "p.value", "FDR" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1453 #' "Please refer to the original Casado et al. publication for detailed |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1454 #' description of these columns and what they represent: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1455 #' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1456 #' - Kinase.Gene indicates the gene name for each kinase. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1457 #' - mS represents the mean log2(fold change) of all the |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1458 #' kinase's substrates. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1459 #' - Enrichment is the background-adjusted value of the kinase's mS. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1460 #' - m is the total number of detected substrates |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1461 #' from the experimental dataset for each kinase. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1462 #' - z.score is the normalized score for each kinase, weighted by |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1463 #' the number of identified substrates. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1464 #' - p.value represents the statistical assessment for the z.score. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1465 #' - FDR is the p-value adjusted for multiple hypothesis testing |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1466 #' using the Benjamini & Hochberg method." |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1467 #' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1468 #' @param ksdata the Kinase-Substrate dataset uploaded from the file |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1469 #' prefaced with "PSP&NetworKIN_" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1470 #' available from github.com/casecpb/KSEA/ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1471 #' @param px the experimental data file formatted as described in |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1472 #' the KSEA.Complete() documentation |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1473 #' @param networkin a binary input of TRUE or FALSE, indicating whether |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1474 #' or not to include NetworKIN predictions, where |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1475 #' \code{NetworKIN = TRUE} |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1476 #' means include NetworKIN predictions |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1477 #' @param networkin_cutoff a numeric value between 1 and infinity setting |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1478 #' the minimum NetworKIN score |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1479 #' (this can be omitted if NetworKIN = FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1480 #' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1481 #' @return creates a new R data.frame with all the KSEA kinase |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1482 #' scores, along with each one's statistical |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1483 #' assessment, as described herein. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1484 #' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1485 #' @references |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1486 #' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1487 #' Casado et al. (2013) Sci Signal. 6(268):rs6 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1488 #' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1489 #' Hornbeck et al. (2015) Nucleic Acids Res. 43:D512-20 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1490 #' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1491 #' Horn et al. (2014) Nature Methods 11(6):603-4 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1492 #' |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1493 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1494 # squash un-actionable cyclomatic_complexity warning |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1495 ksea_scores <- function( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1496 # nolint end |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1497 # For human data, typically, ksdata = KSEAapp::ksdata |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1498 ksdata, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1499 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1500 # Input data file having columns: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1501 # - Protein : abbreviated protein name |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1502 # - Gene : HUGO gene name |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1503 # - Peptide : peptide sequence without indications of phosphorylation |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1504 # - Reside.Both : position(s) of phosphorylation within Gene sequence |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1505 # - First letter designates AA that is modified |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1506 # - Numbers indicate position within Gene |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1507 # - Multiple values are separated by semicolons |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1508 # - p : p-value |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1509 # - FC : fold-change |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1510 px, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1511 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1512 # A binary input of TRUE or FALSE, indicating whether or not to include |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1513 # NetworKIN predictions |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1514 networkin, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1515 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1516 # A numeric value between 1 and infinity setting the minimum NetworKIN |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1517 # score (can be left out if networkin = FALSE) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1518 networkin_cutoff, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1519 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1520 # Minimum substrate count, necessary to adjust the p-value appropriately. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1521 minimum_substrate_count |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1522 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1523 ) { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1524 if (FALSE) { |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1525 if (print_nb_messages) nbe("Output contents of `ksdata` table\n") |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1526 cat_variable(ksdata) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1527 cat("\n\\clearpage\n") |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1528 data_frame_tabbing_latex( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1529 x = ksdata[order(ksdata$GENE, ksdata$SUB_GENE), ], |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1530 tabstops = c(0.3, 0.3, 1.2, 0.3, 0.3, 0.3, 0.3, |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1531 0.8, 0.3, 0.8, 0.3, 0.3, 0.3), |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1532 caption = "ksdata dump", |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1533 use_subsubsection_header = FALSE |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1534 ) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1535 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1536 # no px$FC should be <= 0, but abs(px$FC) is used below as a precaution. |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1537 if (length(grep(";", px$Residue.Both)) == 0) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1538 # There are no Residue.Both entries having semicolons, so new is |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1539 # simply px except two columns are renamed and a column is added |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1540 # for log2(abs(fold-change)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1541 new <- px |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1542 colnames(new)[c(2, 4)] <- c("SUB_GENE", "SUB_MOD_RSD") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1543 new$log2_fc <- log2(abs(as.numeric(as.character(new$FC)))) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1544 new <- new[complete.cases(new$log2_fc), ] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1545 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1546 # Split each row having semicolons in Residue.Both into rows that are |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1547 # duplicated in all respects except that each row has a single |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1548 # member of the set "split-on-semicolon-Residue.Both" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1549 px_double <- px[grep(";", px$Residue.Both), ] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1550 residues <- as.character(px_double$Residue.Both) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1551 residues <- as.matrix(residues, ncol = 1) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1552 split <- strsplit(residues, split = ";") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1553 # x gets count of residues in each row, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1554 # i.e., 1 + count of semicolons |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1555 x <- sapply(split, length) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1556 # Here is the set of split rows |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1557 px_single <- data.frame( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1558 Protein = rep(px_double$Protein, x), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1559 Gene = rep(px_double$Gene, x), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1560 Peptide = rep(px_double$Peptide, x), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1561 Residue.Both = unlist(split), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1562 p = rep(px_double$p, x), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1563 FC = rep(px_double$FC, x) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1564 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1565 # new first gets the split rows |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1566 new <- px[-grep(";", px$Residue.Both), ] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1567 # to new, append the rows that didn't need splitting in the first place |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1568 new <- rbind(new, px_single) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1569 # map Gene to SUB_GENE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1570 # map Residue.Both to SUB_MOD_RSD |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1571 colnames(new)[c(2, 4)] <- c("SUB_GENE", "SUB_MOD_RSD") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1572 # Eliminate any non-positive values to prevent introduction of |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1573 # infinite or NaN values |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1574 new[(0 <= new$log2_fc), "log2_fc"] <- NA |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1575 # Because of preceding step, there is no need for abs in the next line |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1576 new$log2_fc <- log2(as.numeric(as.character(new$FC))) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1577 # Convert any illegal values from NaN to NA |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1578 new[is.nan(new$log2_fc), "log2_fc"] <- NA |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1579 # Eliminate rows having missing values (e.g., non-imputed data) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1580 new <- new[complete.cases(new$log2_fc), ] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1581 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1582 # At this point, new$log2_fc is signed according to which contrast has |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1583 # the greater intensity |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1584 # To take the magnitude into account without taking the direction into |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1585 # account, set params$kseaUseAbsoluteLog2FC to TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1586 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1587 # Should KSEA be performed aggregating signed log2FC or absolute? |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1588 # FALSE use raw log2FC for KSEA as for KSEAapp::KSEA.Scores |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1589 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1590 # squash un-actionable "no visible global for ..." |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1591 if (params$kseaUseAbsoluteLog2FC) { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1592 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1593 # TRUE use abs(log2FC) for KSEA as Justin requested; this is a |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1594 # justifiable deviation from the KSEAapp::KSEA.Scores algorithm. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1595 new$log2_fc <- abs(new$log2_fc) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1596 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1597 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1598 monitor_filtration_on_stderr <- TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1599 if (monitor_filtration_on_stderr) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1600 # set to TRUE to monitor filtration on stderr |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1601 sink(stderr()) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1602 cat(see_variable(networkin, "\n")) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1603 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1604 ksdata_filtered <- |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1605 sqldf::sqldf( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1606 sprintf("%s %s", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1607 "select * from ksdata where not Source = 'NetworKIN'", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1608 if (networkin) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1609 sprintf("or networkin_score >= %d", networkin_cutoff) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1610 else |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1611 "" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1612 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1613 ) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1614 if (FALSE) write.csv(x = ksdata_filtered, file = "ksdata_filtered.csv") |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1615 if (monitor_filtration_on_stderr) { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1616 cat(see_variable(sqldf::sqldf( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1617 "select count(*), Source from ksdata group by Source"), "\n")) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1618 cat(see_variable(sqldf::sqldf( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1619 "select count(*), Source from ksdata_filtered group by Source"), "\n")) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1620 sink() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1621 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1622 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1623 ############################################################################ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1624 # Line numbers below refer to lines of: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1625 # https://github.com/casecpb/KSEAapp/blob/master/R/KSEA.Scores.R |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1626 # I would put the original line in a comment but then lint would complain... |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1627 # - Indeed, I had to rename all the variables because lint didn't like names |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1628 # containing periods or capital letters. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1629 # ACE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1630 ############################################################################ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1631 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1632 # (1) Join the two data.frames on common columns SUB_GENE and SUB_MOD_RSD |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1633 # colnames of ksdata_filtered: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1634 # "KINASE" "KIN_ACC_ID" "GENE" "KIN_ORGANISM" "SUBSTRATE" "SUB_GENE_ID" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1635 # "SUB_ACC_ID" "SUB_GENE" "SUB_ORGANISM" "SUB_MOD_RSD" "SITE_GRP_ID" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1636 # "SITE_...7_AA" "networkin_score" "Source" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1637 # colnames of new: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1638 # "Protein" "SUB_GENE" "Peptide" "SUB_MOD_RSD" "p" "FC" "log2_fc" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1639 # Equivalent to: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1640 # SELECT a.*. b.Protein, b.Peptide, b.p, b.FC, b.log2_fc |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1641 # FROM ksdata_filtered a |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1642 # INNER JOIN new b |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1643 # ON a.SUB_GENE = b.SUB_GENE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1644 # AND a.SUB_MOD_RSD = b.SUB_MOD_RSD |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1645 # (KSEA.Scores.R line # 105) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1646 # "Extract KSData.filtered annotations that are only found in new" |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1647 ksdata_dataset <- base::merge(ksdata_filtered, new) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1648 # colnames of ksdata_dataset: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1649 # "KINASE" "KIN_ACC_ID" "GENE" "KIN_ORGANISM" "SUBSTRATE" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1650 # "SUB_GENE_ID" "SUB_ACC_ID" "SUB_GENE" "SUB_ORGANISM" "SUB_MOD_RSD" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1651 # "SITE_GRP_ID" "SITE_...7_AA" "networkin_score" "Source" "Protein" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1652 # "Peptide" "p" "FC" "log2_fc" (uniprot_no_isoform) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1653 # Re-order dataset; prior to accounting for isoforms |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1654 # (KSEA.Scores.R line # 106) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1655 ksdata_dataset <- ksdata_dataset[order(ksdata_dataset$GENE), ] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1656 # Extract non-isoform accession in UniProtKB |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1657 # (KSEA.Scores.R line # 107) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1658 ksdata_dataset$uniprot_no_isoform <- sapply( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1659 ksdata_dataset$KIN_ACC_ID, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1660 function(x) unlist(strsplit(as.character(x), split = "-"))[1] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1661 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1662 # "last expression collapses isoforms ... for easy processing" |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1663 # Discard previous results while selecting interesting columns ... |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1664 # (KSEA.Scores.R line # 110) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1665 ksdata_dataset_abbrev <- ksdata_dataset[, c(5, 1, 2, 16:19, 14)] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1666 # Column names are now: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1667 # "GENE" "SUB_GENE" "SUB_MOD_RSD" "Peptide" "p" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1668 # "FC" "log2_fc" "Source" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1669 # Make column names human-readable |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1670 # (KSEA.Scores.R line # 111) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1671 colnames(ksdata_dataset_abbrev) <- c( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1672 "Kinase.Gene", "Substrate.Gene", "Substrate.Mod", "Peptide", "p", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1673 "FC", "log2FC", "Source" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1674 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1675 # SELECT * FROM ksdata_dataset_abbrev |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1676 # ORDER BY Kinase.Gene, Substrate.Gene, Substrate.Mod, p |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1677 # (KSEA.Scores.R line # 112) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1678 # "Extract KSData.filtered annotations that are only found in new" |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1679 ksdata_dataset_abbrev <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1680 ksdata_dataset_abbrev[ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1681 order( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1682 ksdata_dataset_abbrev$Kinase.Gene, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1683 ksdata_dataset_abbrev$Substrate.Gene, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1684 ksdata_dataset_abbrev$Substrate.Mod, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1685 ksdata_dataset_abbrev$p), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1686 ] |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1687 if (print_nb_messages) nbe(see_variable(ksdata_dataset_abbrev)) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1688 if (FALSE) write.csv( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1689 x = ksdata_dataset_abbrev, |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1690 file = "ksdata_dataset_abbrev_no_aggregation.csv", |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1691 row.names = FALSE |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1692 ) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1693 |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1694 # For some kinases, the only difference between kinase names in two databases |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1695 # is the case of the the letters; dedup to eliminate this false distinction |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1696 # The only imperfection with this approach is when the NetworKIN-only fliter |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1697 # is in force and there is a duplication between NetworKIN and HPRD (which |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1698 # outranks NetworKIN). Presently, the script does not invoke with this |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1699 # function with the NetworKIN-only filter active. |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1700 dedup_sql <- " |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1701 select |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1702 r.'Kinase.Gene', r.'Substrate.Gene', r.'Substrate.Mod', |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1703 r.Peptide, r.p, r.FC, r.log2FC, r.Source |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1704 from |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1705 ( select |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1706 rowid, |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1707 rank() over |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1708 (partition by |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1709 lower(k.'Kinase.Gene'), k.p, k.FC |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1710 order by |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1711 k.Source |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1712 ) as rank, |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1713 * |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1714 from |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1715 ksdata_dataset_abbrev k |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1716 ) as r |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1717 where r.rank = 1 |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1718 " |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1719 ksdata_dataset_abbrev <- sqldf::sqldf(x = dedup_sql) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1720 if (FALSE) write.csv( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1721 x = ksdata_dataset_abbrev, |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1722 file = "ksdata_dataset_abbrev_no_aggregation_dedup.csv", |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1723 row.names = FALSE |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1724 ) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1725 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1726 # First aggregation step to account for multiply phosphorylated peptides |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1727 # and differing peptide sequences; the goal here is to combine results |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1728 # for all measurements of the same substrate. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1729 # SELECT `Kinase.Gene`, `Substrate.Gene`, `Substrate.Mod`, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1730 # `Source`, avg(log2FC) AS log2FC |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1731 # FROM ksdata_dataset_abbrev |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1732 # GROUP BY `Kinase.Gene`, `Substrate.Gene`, `Substrate.Mod`, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1733 # `Source` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1734 # ORDER BY `Kinase.Gene`; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1735 # in two steps: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1736 # (1) compute average log_2(fold-change) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1737 # "take the mean of the log2FC amongst phosphosite duplicates" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1738 # (KSEA.Scores.R line # 115) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1739 ksdata_dataset_abbrev <- aggregate( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1740 log2FC ~ Kinase.Gene + Substrate.Gene + Substrate.Mod + Source, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1741 data = ksdata_dataset_abbrev, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1742 FUN = mean |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1743 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1744 if (print_nb_messages) nbe(see_variable(ksdata_dataset_abbrev)) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1745 # (2) order by Kinase.Gene |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1746 # (KSEA.Scores.R line # 117) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1747 ksdata_dataset_abbrev <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1748 ksdata_dataset_abbrev[order(ksdata_dataset_abbrev$Kinase.Gene), ] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1749 # SELECT `Kinase.Gene`, count(*) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1750 # FROM ksdata_dataset_abbrev |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1751 # GROUP BY `Kinase.Gene`; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1752 # in two steps: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1753 # (1) Extract the list of Kinase.Gene names |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1754 # "@@@@@@@@@@@@@@@@@@@@" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1755 # "Do analysis for KSEA" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1756 # "@@@@@@@@@@@@@@@@@@@@" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1757 # (KSEA.Scores.R line # 124) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1758 kinase_list <- as.vector(ksdata_dataset_abbrev$Kinase.Gene) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1759 # (2) Convert to a named list of counts of kinases in ksdata_dataset_abrev, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1760 # named by Kinase.Gene |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1761 # (KSEA.Scores.R line # 125) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1762 kinase_list <- as.matrix(table(kinase_list)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1763 # Second aggregation step to account for all substrates per kinase |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1764 # CREATE TABLE mean_fc |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1765 # AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1766 # SELECT `Kinase.Gene`, avg(log2FC) AS log2FC |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1767 # FROM ksdata_dataset_abbrev |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1768 # GROUP BY `Kinase.Gene` |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1769 # (KSEA.Scores.R line # 127) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1770 if (print_nb_messages) nb(see_variable(ksdata_dataset_abbrev), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1771 mean_fc <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1772 aggregate( |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1773 log2FC ~ Kinase.Gene, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1774 data = ksdata_dataset_abbrev, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1775 FUN = mean |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1776 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1777 if (print_nb_messages) nbe(see_variable(mean_fc), "\n") |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1778 if (FALSE) write.csv(x = mean_fc, file = "mean_fc.csv") |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1779 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1780 # for contrast j |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1781 # for each kinase i |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1782 # extract log2 of fold-change (from `new` above) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1783 # (used in KSEA.Scores.R lines # 130 & 132) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1784 log2_fc_j_each_i <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1785 new$log2_fc |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1786 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1787 # for contrast j |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1788 # for all kinases i |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1789 # compute mean of abs(log2 of fold-change) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1790 # (used in KSEA.Scores.R lines # 130) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1791 mean_abs_log2_fc_j_all_i <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1792 mean(abs(log2_fc_j_each_i), na.rm = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1793 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1794 # for contrast j |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1795 # for all kinases i |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1796 # compute mean of log2 of fold-change |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1797 # (used in KSEA.Scores.R lines # 132) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1798 mean_log2_fc_j_all_i <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1799 mean(log2_fc_j_each_i, na.rm = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1800 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1801 # Reorder mean_fc, although I don't see why |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1802 # (KSEA.Scores.R line 128 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1803 mean_fc <- mean_fc[order(mean_fc[, 1]), ] |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1804 if (FALSE) write.csv(x = mean_fc, file = "mean_fc.csv") |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1805 # mean_fc columns so far: "Kinase.Gene", "log2FC" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1806 # - Kinase.Gene |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1807 # indicates the gene name for each kinase. |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1808 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1809 # Create column 3: mS |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1810 # - mS |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1811 # represents the mean log2(fold change) of all the |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1812 # kinase's substrates. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1813 # (KSEA.Scores.R line # 129) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1814 mean_fc$m_s <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1815 mean_fc_m_s <- mean_fc[, 2] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1816 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1817 # Create column 4: Enrichment |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1818 # - Enrichment |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1819 # is the background-adjusted value of the kinase's mS. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1820 # (KSEA.Scores.R line # 130) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1821 mean_fc$enrichment <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1822 mean_fc_m_s / mean_abs_log2_fc_j_all_i |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1823 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1824 # Create column 5: m, count of substrates of kinase (count of j for i) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1825 # - m |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1826 # is the total number of detected substrates |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1827 # from the experimental dataset for each kinase. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1828 # (KSEA.Scores.R line # 131) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1829 mean_fc$m <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1830 mean_fc_m <- kinase_list |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1831 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1832 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1833 # Create column 6: z-score |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1834 # - z.score |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1835 # is the normalized score for each kinase, weighted by |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1836 # the number of identified substrates. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1837 # (KSEA.Scores.R line # 132) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1838 mean_fc$z_score <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1839 (mean_fc_m_s - mean_log2_fc_j_all_i) * sqrt(mean_fc_m) / |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1840 sd(log2_fc_j_each_i, na.rm = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1841 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1842 # Create column 7: p-value, deduced from z-score |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1843 # - p.value |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1844 # represents the statistical assessment for the z.score. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1845 # (KSEA.Scores.R line # 133) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1846 # "one-tailed p-value" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1847 mean_fc$p_value <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1848 pnorm(-abs(mean_fc$z_score)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1849 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1850 # zap excluded kinases; this must be done before adjusting p-value |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1851 if (TRUE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1852 mean_fc <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1853 mean_fc[ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1854 mean_fc$m >= minimum_substrate_count, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1855 , |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1856 drop = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1857 ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1858 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1859 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1860 # Create column 8: FDR, deduced by Benjamini-Hochberg adustment from p-value |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1861 # - FDR |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1862 # is the p-value adjusted for multiple hypothesis testing |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1863 # using the Benjamini & Hochberg method." |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1864 # (KSEA.Scores.R line # 134) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1865 mean_fc$fdr <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1866 p.adjust(mean_fc$p_value, method = "fdr") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1867 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1868 # It makes no sense to leave Z-scores negative when using |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1869 # absolute value of fold-change |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1870 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1871 # squash un-actionable "no visible global for ..." |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1872 if (params$kseaUseAbsoluteLog2FC) { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
1873 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1874 mean_fc$z_score <- abs(mean_fc$z_score) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1875 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1876 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1877 # Remove second column (log2FC), which is duplicated as mS |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1878 # (KSEA.Scores.R line # 136) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1879 mean_fc <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1880 mean_fc[order(mean_fc$Kinase.Gene), -2] |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1881 # Correct the column names which we had to hack because of the linter... |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1882 colnames(mean_fc) <- c( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1883 "Kinase.Gene", "mS", "Enrichment", "m", "z.score", "p.value", "FDR" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1884 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1885 # (KSEA.Scores.R line # 138) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1886 return(mean_fc) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1887 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1888 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1889 ksea_low_fdr_barplot_factory <- function( |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1890 rslt, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1891 i_cntrst, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1892 i, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1893 a_level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1894 b_level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1895 fold_change, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1896 caption |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1897 ) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1898 rslt_score_list_i <- rslt$score_list[[i]] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1899 if (!is.null(rslt_score_list_i)) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1900 rslt_score_list_i_nrow <- nrow(rslt_score_list_i) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1901 k <- data.frame( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1902 contrast = as.integer(i_cntrst), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1903 a_level = rep.int(a_level, rslt_score_list_i_nrow), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1904 b_level = rep.int(b_level, rslt_score_list_i_nrow), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1905 kinase_gene = rslt_score_list_i$Kinase.Gene, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1906 mean_log2_fc = rslt_score_list_i$mS, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1907 enrichment = rslt_score_list_i$Enrichment, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1908 substrate_count = rslt_score_list_i$m, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1909 z_score = rslt_score_list_i$z.score, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1910 p_value = rslt_score_list_i$p.value, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1911 fdr = rslt_score_list_i$FDR |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1912 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1913 selector <- switch( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1914 ksea_cutoff_statistic, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1915 "FDR" = { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1916 k$fdr |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1917 }, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1918 "p.value" = { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1919 k$p_value |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1920 }, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1921 { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1922 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1923 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1924 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1925 ksea_cutoff_statistic |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1926 ) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1927 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1928 param_df_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1929 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1930 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1931 ) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1932 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1933 k <- k[selector < ksea_cutoff_threshold, ] |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1934 nrow_k <- nrow(k) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1935 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1936 if (nrow_k > 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1937 max_nchar_rowname <- max(nchar(rownames(k))) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1938 my_cex_names <- 1.0 / (1 + nrow_k / 50) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1939 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1940 if (print_trace_messages) cat_margins("Initially") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1941 if (print_trace_messages) cat_variable(nrow_k, "\n\n", 0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1942 if (print_trace_messages) cat_variable(my_cex_names, "\n\n", 0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1943 if (print_trace_messages) cat_variable(max_nchar_rowname, "\n\n", 0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1944 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1945 # fin: The figure region dimensions, (width, height), in inches. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1946 # mar: A numerical vector of the form c(bottom, left, top, right) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1947 # that gives the number of lines of margin to be specified |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1948 # on the four sides of the plot; default: c(5, 4, 4, 2) + 0.1 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1949 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1950 # mar: The figure region dimensions, (width, height), in inches. |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1951 numeric_z_score <- as.numeric(k$z_score) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1952 bar_order <- order(-as.numeric(k$p_value)) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1953 kinase_name <- k$kinase_gene |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1954 long_caption <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1955 sprintf( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1956 "Kinase z-score, %s, KSEA %s < %s", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1957 caption, |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1958 ksea_cutoff_statistic, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1959 ksea_cutoff_threshold |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1960 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1961 my_cex_caption <- 65.0 / max(65.0, nchar(long_caption)) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1962 # return a function that draws the plot |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1963 function() { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1964 par_fin <- par("fin") # vector of width_in_inches and height_in_inches) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1965 op <- par( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1966 bg = if (print_trace_messages) "yellow" else "white", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1967 fin = c(par_fin[1], min(par_fin[2], 2.5 + nrow_k / 6)), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1968 mar = par("mar") + |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1969 c(3 / nrow_k, (1 + max_nchar_rowname * my_cex_names) / 2, 0, 0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1970 # bottom, left, top, right |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1971 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1972 on.exit(par(op)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1973 if (print_trace_messages) cat_margins("Eventually") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1974 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1975 barplot( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1976 height = numeric_z_score[bar_order], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1977 border = NA, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1978 xpd = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1979 cex.names = my_cex_names, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1980 main = long_caption, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1981 cex.main = my_cex_caption, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1982 names.arg = kinase_name[bar_order], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1983 horiz = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1984 srt = 45, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1985 las = 1, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1986 cex.axis = 0.9 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1987 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1988 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1989 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1990 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1991 no_op |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1992 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1993 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1994 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1995 # note that this adds elements to the global variable `ksea_asterisk_hash` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1996 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1997 ksea_low_fdr_print <- function( |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1998 rslt, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1999 i_cntrst, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2000 i, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2001 a_level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2002 b_level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2003 fold_change, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2004 caption, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2005 write_db = TRUE, # if TRUE, write to DB, else print table |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2006 anchor = c(const_table_anchor_p, const_table_anchor_t) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2007 ) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2008 rslt_score_list_i <- rslt$score_list[[i]] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2009 if (!is.null(rslt_score_list_i)) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2010 rslt_score_list_i_nrow <- nrow(rslt_score_list_i) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2011 k <- contrast_ksea_scores <- data.frame( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2012 contrast = as.integer(i_cntrst), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2013 a_level = rep.int(a_level, rslt_score_list_i_nrow), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2014 b_level = rep.int(b_level, rslt_score_list_i_nrow), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2015 kinase_gene = rslt_score_list_i$Kinase.Gene, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2016 mean_log2_fc = rslt_score_list_i$mS, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2017 enrichment = rslt_score_list_i$Enrichment, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2018 substrate_count = rslt_score_list_i$m, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2019 z_score = rslt_score_list_i$z.score, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2020 p_value = rslt_score_list_i$p.value, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2021 fdr = rslt_score_list_i$FDR |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2022 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2023 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2024 selector <- switch( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2025 ksea_cutoff_statistic, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2026 "FDR" = { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2027 k$fdr |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2028 }, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2029 "p.value" = { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2030 k$p_value |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2031 }, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2032 { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2033 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2034 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2035 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2036 ksea_cutoff_statistic |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2037 ) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2038 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2039 param_df_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2040 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2041 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2042 ) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2043 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2044 k <- k[selector < ksea_cutoff_threshold, ] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2045 # save kinase names to ksea_asterisk_hash |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2046 for (kinase_name in k$kinase_gene) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2047 ksea_asterisk_hash[[kinase_name]] <- 1 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2048 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2049 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2050 if (write_db) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2051 db_write_table_overwrite <- (i_cntrst < 2) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2052 db_write_table_append <- !db_write_table_overwrite |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2053 RSQLite::dbWriteTable( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2054 conn = db, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2055 name = "contrast_ksea_scores", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2056 value = contrast_ksea_scores, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2057 append = db_write_table_append |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2058 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2059 "" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2060 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2061 selector <- switch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2062 ksea_cutoff_statistic, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2063 "FDR" = { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2064 contrast_ksea_scores$fdr |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2065 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2066 "p.value" = { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2067 contrast_ksea_scores$p_value |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2068 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2069 { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2070 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2071 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2072 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2073 ksea_cutoff_statistic |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2074 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2075 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2076 param_df_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2077 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2078 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2079 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2080 if (print_nb_messages) nbe(see_variable(contrast_ksea_scores)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2081 output_df <- contrast_ksea_scores[ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2082 selector < ksea_cutoff_threshold, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2083 c("kinase_gene", "mean_log2_fc", "enrichment", "substrate_count", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2084 "z_score", "p_value", "fdr") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2085 ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2086 output_df$kinase_gene <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2087 gsub( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2088 "_", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2089 "\\\\_", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2090 output_df$kinase_gene |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2091 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2092 colnames(output_df) <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2093 c( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2094 colnames(output_df)[1], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2095 colnames(output_df)[2], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2096 "enrichment", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2097 "m_s", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2098 "z_score", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2099 "p_value", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2100 "fdr" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2101 ) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2102 |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2103 # nolint start |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2104 output_order <- with(output_df, order(p_value)) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2105 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2106 output_df <- output_df[output_order, ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2107 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2108 output_df[, 2] <- sprintf("%0.3g", output_df[, 2]) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2109 output_df$fdr <- sprintf("%0.4f", output_df$fdr) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2110 output_df$p_value <- sprintf("%0.2e", output_df$p_value) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2111 output_df$z_score <- sprintf("%0.2f", output_df$z_score) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2112 output_df$m_s <- sprintf("%d", output_df$m_s) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2113 output_df$enrichment <- sprintf("%0.3g", output_df$enrichment) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2114 colnames(output_df) <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2115 c( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2116 "Kinase or motif", |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2117 "\\(\\overline{{\\lvert}\\log_2 (\\text{fold-change}){\\rvert}}\\)", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2118 "Enrichment", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2119 "Substrates", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2120 "z-score", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2121 "p-value", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2122 "FDR" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2123 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2124 selector <- switch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2125 ksea_cutoff_statistic, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2126 "FDR" = { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2127 rslt$score_list[[i]]$FDR |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2128 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2129 "p.value" = { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2130 rslt$score_list[[i]]$p.value |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2131 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2132 { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2133 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2134 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2135 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2136 ksea_cutoff_statistic |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2137 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2138 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2139 param_df_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2140 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2141 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2142 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2143 if (sum(selector < ksea_cutoff_threshold) > 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2144 if (print_nb_messages) nbe(see_variable(output_df)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2145 math_caption <- gsub("{", "\\{", caption, fixed = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2146 math_caption <- gsub("}", "\\}", math_caption, fixed = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2147 if (TRUE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2148 data_frame_tabbing_latex( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2149 x = output_df, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2150 # vector of tab stops, in inches |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2151 tabstops = c(1.8, 1.2, 0.8, 0.8, 0.8, 0.8, 0.8), |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2152 # vector of headings, registered with tab-stops |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2153 headings = colnames(output_df), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2154 # digits to pass to format.data.frame |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2155 digits = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2156 # maximumn number of rows to print |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2157 max = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2158 # optional caption |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2159 caption = sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2160 "\\text{%s}, KSEA %s < %s", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2161 math_caption, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2162 ksea_cutoff_statistic, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2163 ksea_cutoff_threshold |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2164 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2165 # set underscore_whack to TRUE to escape underscores |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2166 underscore_whack = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2167 # flag for landscape mode |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2168 landscape = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2169 # flag indicating that subsubsection should be used for caption |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2170 # rather than subsection |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2171 use_subsubsection_header = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2172 # character-size indicator; for possible values, see: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2173 # https://tug.org/texinfohtml/latex2e.html#Font-sizes |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2174 charactersize = "small", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2175 # set verbatim to TRUE to debug output |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2176 verbatim = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2177 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2178 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2179 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2180 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2181 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2182 "\\break |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2183 No kinases had |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2184 \\(\\text{KSEA %s}_\\text{enrichment} < %s\\) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2185 for contrast %s\\hfill\\break\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2186 ksea_cutoff_statistic, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2187 ksea_cutoff_threshold, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2188 caption |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2189 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2190 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2191 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2192 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2193 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2194 "" |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2195 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2196 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2197 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2198 # create_breaks is a helper for ksea_heatmap |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2199 create_breaks <- function(merged_scores) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2200 if (sum(!is.na(merged_scores)) < 2) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2201 return(NULL) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2202 if (min(merged_scores, na.rm = TRUE) < -1.6) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2203 breaks_neg <- seq(-1.6, 0, length.out = 30) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2204 breaks_neg <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2205 append( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2206 seq(min(merged_scores, na.rm = TRUE), -1.6, length.out = 10), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2207 breaks_neg |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2208 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2209 breaks_neg <- sort(unique(breaks_neg)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2210 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2211 breaks_neg <- seq(-1.6, 0, length.out = 30) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2212 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2213 if (max(merged_scores, na.rm = TRUE) > 1.6) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2214 breaks_pos <- seq(0, 1.6, length.out = 30) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2215 breaks_pos <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2216 append( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2217 breaks_pos, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2218 seq(1.6, max(merged_scores, na.rm = TRUE), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2219 length.out = 10) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2220 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2221 breaks_pos <- sort(unique(breaks_pos)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2222 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2223 breaks_pos <- seq(0, 1.6, length.out = 30) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2224 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2225 breaks_all <- unique(append(breaks_neg, breaks_pos)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2226 mycol_neg <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2227 gplots::colorpanel(n = length(breaks_neg), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2228 low = "blue", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2229 high = "white") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2230 mycol_pos <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2231 gplots::colorpanel(n = length(breaks_pos) - 1, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2232 low = "white", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2233 high = "red") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2234 mycol <- unique(append(mycol_neg, mycol_pos)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2235 color_breaks <- list(breaks_all, mycol) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2236 return(color_breaks) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2237 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2238 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2239 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2240 # squash un-actionable cyclomatic_complexity warning |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2241 hm2plus <- function( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2242 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2243 x, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2244 mat = matrix( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2245 c( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2246 c(0, 4, 0), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2247 c(0, 3, 3), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2248 c(2, 1, 1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2249 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2250 nrow = 3, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2251 ncol = 3, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2252 byrow = TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2253 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2254 denwid = 0.5, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2255 denhgt = 0.15, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2256 widths = c(0.5, 2.5, 1.5), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2257 heights = c(0.4, 0.15, 3.95), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2258 divergent = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2259 notecol = "grey50", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2260 trace = "none", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2261 margins = c(6, 20), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2262 srtcol = 90, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2263 srtrow = 0, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2264 density_info = "none", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2265 key_xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2266 key_par = list(), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2267 hclustfun = hclust, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2268 ... |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2269 ) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2270 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2271 if (FALSE) # this is to avoid commenting out code to pass linting... |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2272 my_hm2 <- latex_show_invocation(gplots::heatmap.2, head_patch = FALSE) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2273 else |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2274 my_hm2 <- gplots::heatmap.2 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2275 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2276 x <- as.matrix(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2277 if (sum(!is.na(x)) < 1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2278 return(NULL) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2279 color_count <- 1 + max(64, length(as.vector(x))) # 8 was not enough |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2280 break_count <- 1 + color_count |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2281 min_nonax <- min(x, na.rm = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2282 max_nonax <- max(x, na.rm = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2283 if (print_nb_messages) nb("within hm2plus", see_variable(divergent), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2284 if (divergent) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2285 zlim <- max(abs(min_nonax), abs(max_nonax)) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2286 if (print_nb_messages) nb(see_variable(zlim, "\n")) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2287 breaks <- (zlim) / (break_count:1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2288 if (print_nb_messages) nb(see_variable(breaks, "\n")) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2289 breaks <- breaks - median(breaks) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2290 zlim <- c(-zlim, zlim) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2291 if (print_nb_messages) nb(see_variable(zlim, "\n")) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2292 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2293 zlim <- max(abs(min_nonax), abs(max_nonax)) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2294 if (print_nb_messages) nb(see_variable(zlim, "\n")) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2295 breaks <- zlim / (break_count:1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2296 if (print_nb_messages) nb(see_variable(breaks, "\n")) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2297 if (max_nonax < 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2298 breaks <- breaks - zlim |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2299 zlim <- c(-zlim, 0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2300 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2301 zlim <- c(0, zlim) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2302 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2303 if (print_nb_messages) nb(see_variable(zlim, "\n")) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2304 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2305 nonax <- x |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2306 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2307 # squash un-actionable "no visible global for ..." |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2308 if (params$heatMapNAsubstitute) nonax[is.na(x)] <- min_nonax |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2309 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2310 if (is.null(widths)) widths <- c(denwid, 4 - denwid, 1.5) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2311 if (is.null(heights)) heights <- c(0.4, denhgt, 4.0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2312 colors <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2313 if (divergent && min_nonax < 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2314 # divergent colors on both sides of zero |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2315 colorRampPalette(c("red", "white", "blue"))(color_count) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2316 } else if (divergent && min_nonax > 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2317 # "divergent" colors > zero |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2318 colorRampPalette(c("white", "blue"))(color_count) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2319 } else if (divergent && max_nonax < 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2320 # "divergent" colors < zero |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2321 colorRampPalette(c("red", "white"))(color_count) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2322 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2323 # "non-divergent" colors including zero |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2324 tmp <- hcl.colors(color_count, "YlOrRd", rev = TRUE) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2325 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2326 # squash un-actionable "no visible global for ..." |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2327 tmp[1] <- params$heatMapNAgrey |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2328 # nolint end |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2329 tmp |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2330 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2331 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2332 nbe("There are ", sum(is.na(x)), " NA values") |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2333 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2334 suppressWarnings( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2335 my_hm2( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2336 x = x, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2337 col = colors, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2338 density.info = density_info, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2339 srtCol = srtcol, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2340 srtRow = srtrow, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2341 margins = margins, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2342 lwid = widths, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2343 lhei = heights, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2344 key.title = NA, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2345 key.xlab = key_xlab, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2346 key.par = key_par, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2347 lmat = mat, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2348 notecol = notecol, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2349 trace = trace, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2350 bg = "yellow", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2351 hclustfun = hclustfun, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2352 oldstyle = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2353 ... # varargs |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2354 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2355 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2356 # implicitly returning value returned by heatmap.2 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2357 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2358 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2359 # draw_kseaapp_summary_heatmap is a helper function for ksea_heatmap |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2360 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2361 # squash un-actionable cyclomatic_complexity warning |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2362 draw_kseaapp_summary_heatmap <- function( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2363 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2364 x, # matrix with row/col names already formatted |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2365 sample_cluster, # a binary input of TRUE or FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2366 # indicating whether or not to perform |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2367 # hierarchical clustering of the sample columns |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2368 merged_asterisk, # matrix having dimensions of x, values "*" or "" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2369 color_breaks, # breaks for color gradation, from create_breaks |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2370 # passed to `breaks` argument of `image` |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2371 margins = c(8, 15), # two integers setting the bottom and right margins |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2372 # to accommodate row and column labels |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2373 master_cex = 0.7, # basis for text sizes |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2374 ... |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2375 ) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2376 merged_scores <- x |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2377 if (!is.matrix(x)) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2378 cat( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2379 paste0( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2380 "No plot because \\texttt{typeof(x)} is '", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2381 typeof(x), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2382 "' rather than 'matrix'.\n\n" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2383 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2384 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2385 cat_variable(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2386 return(FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2387 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2388 if (print_trace_messages) cat(sprintf("master_cex = %03f\n\n", master_cex)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2389 nrow_x <- nrow(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2390 ncol_x <- ncol(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2391 #if (nrow_x < 2) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2392 if (nrow_x < 1) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2393 cat("No plot because matrix has no rows.\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2394 return(FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2395 } else if (nrow_x < 2) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2396 cat("No plot because matrix has one row. Matrix looks like this:\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2397 cat("\n\\begin{verbatim}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2398 print(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2399 cat("\n\\end{verbatim}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2400 return(FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2401 } else if (ncol_x < 2) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2402 cat("No plot because matrix x has ", ncol_x, " columns.\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2403 cat_variable(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2404 return(FALSE) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2405 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2406 max_nchar_rowname <- max(nchar(rownames(x))) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2407 max_nchar_colname <- max(nchar(colnames(x))) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2408 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2409 my_row_cex_scale <- master_cex * 150 / nrow_x |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2410 # row cex shrink hack begin |
|
2
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
2411 my_row_cex_scale <- master_cex * 150 / max(nrow_x, ncol_x) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2412 # row cex shrink hack end |
|
2
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
2413 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2414 my_col_cex_scale <- 3.0 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2415 # col cex shrink hack begin |
|
2
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
2416 if (ncol_x > 40) |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
2417 my_col_cex_scale <- 3.0 * 40 / ncol_x |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2418 # col cex shrink hack end |
|
2
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
2419 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2420 my_asterisk_scale <- 0.4 * my_row_cex_scale |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2421 my_row_warp <- 1 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2422 my_note_warp <- 2 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2423 my_row_warp <- 1 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2424 my_row_cex_asterisk <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2425 master_cex * my_row_warp * my_asterisk_scale |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2426 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2427 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2428 my_col_cex <- my_col_cex_scale * master_cex |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2429 my_row_cex <- min(3.5 * my_row_cex_asterisk, my_col_cex) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2430 my_key_cex <- 1.286 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2431 my_hm2_cex <- 1 * master_cex |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2432 my_offset <- (4.8 / (9 + nrow_x / 10)) - 0.4 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2433 if (print_trace_messages) cat(sprintf("nrow_x = %03f\n\n", nrow_x)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2434 if (print_trace_messages) cat(sprintf("my_offset = %03f\n\n", my_offset)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2435 my_offset <- 0.05 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2436 if (print_trace_messages) cat(sprintf("my_offset = %03f\n\n", my_offset)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2437 my_scale <- 3.0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2438 if (ncol_x < 10 && nrow_x < 10) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2439 my_scale <- my_scale * 10 / (10 - nrow_x) * 10 / (10 - ncol_x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2440 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2441 my_heights <- c( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2442 0.15, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2443 3.85 - my_offset, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2444 0.5 + my_offset |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2445 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2446 my_margins <- c(1, 1) + |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2447 c( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2448 margins[1] * 0.08 * max_nchar_colname * my_col_cex, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2449 margins[2] * 0.04 * max_nchar_rowname * my_row_cex |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2450 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2451 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2452 if (print_trace_messages) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2453 cat_variable(my_heights, suffix = "; ") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2454 cat_variable(my_margins, suffix = "\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2455 cat_variable(my_row_cex_scale, suffix = "; ") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2456 cat_variable(my_col_cex_scale, suffix = "\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2457 cat_variable(my_row_cex_asterisk, suffix = "\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2458 cat_variable(my_row_cex, suffix = "; ") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2459 cat_variable(my_col_cex, suffix = "\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2460 cat_variable(my_row_cex, suffix = "; ") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2461 cat_variable(my_col_cex, suffix = "\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2462 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2463 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2464 hm2plus( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2465 x = merged_scores, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2466 Colv = sample_cluster, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2467 cellnote = merged_asterisk, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2468 cex = my_hm2_cex, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2469 cexCol = my_col_cex, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2470 cexRow = my_row_cex, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2471 denhgt = 0.15, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2472 density_info = "none", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2473 denwid = 0.5, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2474 divergent = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2475 key_par = list(cex = my_key_cex), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2476 key_xlab = "Z-score", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2477 margins = my_margins, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2478 notecex = my_scale * min( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2479 1.5, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2480 my_row_cex_asterisk * my_note_warp, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2481 my_col_cex * my_note_warp |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2482 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2483 notecol = "white", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2484 scale = "none", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2485 srtcol = 90, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2486 srtrow = 0, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2487 trace = "none", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2488 mat = matrix( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2489 c( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2490 c(0, 3, 3), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2491 c(2, 1, 1), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2492 c(0, 4, 0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2493 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2494 nrow = 3, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2495 ncol = 3, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2496 byrow = TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2497 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2498 widths = c(0.5, 3.1, 0.9), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2499 heights = my_heights, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2500 ... |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2501 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2502 return(TRUE) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2503 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2504 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2505 # function drawing heatmap of contrast fold-change for each kinase, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2506 # adapted from KSEAapp::KSEA.Heatmap |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2507 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2508 # squash un-actionable cyclomatic_complexity warning |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2509 ksea_heatmap <- function( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2510 # nolint end |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2511 # the data frame outputs from the KSEA.Scores() function, in list format |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2512 score_list, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2513 # a character vector of all the sample names for heatmap annotation: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2514 # - the names must be in the same order as the data in score_list |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2515 # - please avoid long names, as they may get cropped in the final image |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2516 sample_labels, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2517 # character string of either "p.value" or "FDR" indicating the data column |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2518 # to use for marking statistically significant scores |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2519 stats, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2520 # a numeric value between 0 and infinity indicating the min. number of |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2521 # substrates a kinase must have to be included in the heatmap |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2522 m_cutoff, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2523 # a numeric value between 0 and 1 indicating the p-value/FDR cutoff |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2524 # for indicating significant kinases in the heatmap |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2525 p_cutoff = { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2526 cat("argument 'p_cutoff' is required for function 'ksea_heatmap'") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2527 param_df_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2528 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2529 }, |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2530 # a binary input of TRUE or FALSE, indicating whether or not to perform |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2531 # hierarchical clustering of the sample columns |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2532 sample_cluster, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2533 # a binary input of TRUE or FALSE, indicating whether or not to export |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2534 # the heatmap as a .png image into the working directory |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2535 export = FALSE, |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2536 # bottom and right margins; adjust as needed if contrast names are too long |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2537 margins = c(6, 6), |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2538 # print which kinases? |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2539 # - Mandatory argument, must be one of const_ksea_.*_kinases |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2540 which_kinases, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2541 # additional arguments to gplots::heatmap.2, such as: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2542 # - main: main title of plot |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2543 # - xlab: x-axis label |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2544 # - ylab: y-axis label |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2545 ... |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2546 ) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2547 filter_m <- function(dataset, m_cutoff) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2548 filtered <- dataset[(dataset$m >= m_cutoff), ] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2549 return(filtered) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2550 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2551 score_list_m <- lapply(score_list, function(...) filter_m(..., m_cutoff)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2552 for (i in seq_len(length(score_list_m))) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2553 names <- colnames(score_list_m[[i]])[c(2:7)] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2554 colnames(score_list_m[[i]])[c(2:7)] <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2555 paste(names, i, sep = ".") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2556 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2557 master <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2558 Reduce( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2559 f = function(...) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2560 base::merge(..., by = "Kinase.Gene", all = TRUE) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2561 }, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2562 x = score_list_m |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2563 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2564 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2565 row.names(master) <- master$Kinase.Gene |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2566 columns <- as.character(colnames(master)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2567 merged_scores <- as.matrix(master[, grep("z.score", columns), drop = FALSE]) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2568 colnames(merged_scores) <- sample_labels |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2569 merged_stats <- as.matrix(master[, grep(stats, columns)]) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2570 asterisk <- function(mtrx, p_cutoff) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2571 new <- data.frame() |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2572 for (i in seq_len(nrow(mtrx))) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2573 for (j in seq_len(ncol(mtrx))) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2574 my_value <- mtrx[i, j] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2575 if (!is.na(my_value) && my_value < p_cutoff) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2576 new[i, j] <- "*" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2577 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2578 new[i, j] <- "" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2579 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2580 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2581 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2582 return(new) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2583 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2584 merged_asterisk <- as.matrix(asterisk(merged_stats, p_cutoff)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2585 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2586 asterisk_rows <- rowSums(merged_asterisk == "*") > 0 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2587 all_rows <- rownames(merged_stats) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2588 names(asterisk_rows) <- all_rows |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2589 non_asterisk_rows <- names(asterisk_rows[asterisk_rows == FALSE]) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2590 asterisk_rows <- names(asterisk_rows[asterisk_rows == TRUE]) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2591 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2592 row_list <- list() |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2593 row_list[[const_ksea_astrsk_kinases]] <- asterisk_rows |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2594 row_list[[const_ksea_all_kinases]] <- all_rows |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2595 row_list[[const_ksea_nonastrsk_kinases]] <- non_asterisk_rows |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2596 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2597 i <- which_kinases |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2598 my_row_names <- row_list[[i]] |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2599 scrs <- merged_scores[my_row_names, , drop = FALSE] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2600 stts <- merged_stats[my_row_names, , drop = FALSE] |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2601 merged_asterisk <- as.matrix(asterisk(stts, p_cutoff)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2602 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2603 color_breaks <- create_breaks(scrs) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2604 if (is.null(color_breaks)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2605 cat("No plot because matrix has too few rows.\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2606 return(NULL) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2607 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2608 plot_height <- nrow(scrs) ^ 0.55 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2609 plot_width <- ncol(scrs) ^ 0.7 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2610 if (export == "TRUE") { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2611 png( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2612 "KSEA.Merged.Heatmap.png", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2613 width = plot_width * 300, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2614 height = 2 * plot_height * 300, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2615 res = 300, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2616 pointsize = 14 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2617 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2618 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2619 did_draw <- draw_kseaapp_summary_heatmap( |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2620 x = scrs, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2621 sample_cluster = sample_cluster, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2622 merged_asterisk = merged_asterisk, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2623 color_breaks = color_breaks, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2624 margins = margins |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2625 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2626 if (export == "TRUE") { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2627 dev.off() |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2628 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2629 if (!did_draw) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2630 return(NULL) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2631 return(my_row_names) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2632 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2633 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2634 # helpers for heatmaps of phosphopeptide intensities |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2635 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2636 # factory producing function to truncate string after n characters |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2637 trunc_n <- function(n) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2638 function(x) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2639 sapply( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2640 X = x, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2641 FUN = function(s) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2642 if (is.na(s)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2643 return("NA") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2644 cond <- try_catch_w_e(nchar(s) > n) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2645 if (!is.logical(cond$value)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2646 return(cond$value$message) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2647 } else if (cond$value) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2648 paste0( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2649 strtrim(s, n), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2650 "..." |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2651 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2652 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2653 s |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2654 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2655 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2656 USE.NAMES = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2657 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2658 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2659 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2660 trunc_long_ppep <- function(x) trunc_n(40)(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2661 trunc_ppep <- function(x) trunc_n(g_ppep_trunc_n)(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2662 trunc_subgene <- function(x) trunc_n(g_subgene_trunc_n)(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2663 trunc_enriched_substrate <- function(x) trunc_n(g_sbstr_trunc_n)(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2664 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2665 # factory producing a function that returns a covariance |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2666 # matrix's rows (and columns) having variance > v_min |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2667 keep_cov_w_var_gtr_min <- function(v_min) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2668 function(x) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2669 if (!is.matrix(x)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2670 return(NULL) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2671 keepers <- sapply( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2672 X = seq_len(nrow(x)), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2673 FUN = function(i) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2674 if (x[i, i] < v_min) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2675 NA |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2676 else |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2677 x[i, i] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2678 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2679 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2680 names(keepers) <- rownames(x) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2681 keepers <- keepers[!is.na(keepers)] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2682 keepers <- names(keepers) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2683 if (length(keepers) == 0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2684 return(NULL) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2685 x[keepers, keepers] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2686 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2687 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2688 # function that returns a matrix's rows having variance > 1 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2689 keep_cov_w_var_gtr_1 <- keep_cov_w_var_gtr_min(1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2690 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2691 # factory producing a function that returns |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2692 # - either a matrix's rows (rows = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2693 # - or a matrix's columns (rows = FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2694 # having variance > v_min |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2695 keep_var_gtr_min <- function(v_min) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2696 function(x, rows = TRUE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2697 nrowcol <- if (rows) nrow else ncol |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2698 if (!is.matrix(x)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2699 return(NULL) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2700 keepers <- sapply( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2701 X = seq_len(nrowcol(x)), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2702 FUN = function(i) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2703 row_var <- var( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2704 if (rows) x[i, ] else x[, i], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2705 na.rm = TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2706 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2707 if (is.na(row_var) || row_var <= v_min) NA else i |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2708 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2709 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2710 keepers <- keepers[!is.na(keepers)] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2711 if (rows) x[keepers, ] else x[, keepers] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2712 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2713 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2714 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2715 keep_var_gtr_0 <- keep_var_gtr_min(0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2716 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2717 # function drawing heatmap of phosphopeptide intensities |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2718 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2719 # squash un-actionable cyclomatic_complexity warning |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2720 ppep_heatmap <- |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2721 # nolint end |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2722 function( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2723 m, # matrix with rownames already formatted |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2724 cutoff, # cutoff used by hm_heading_function |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2725 hm_heading_function, # construct $ cat heading from m and cutoff |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2726 hm_main_title, # main title for plot (drawn below heading) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2727 suppress_row_dendrogram = TRUE, # set to false to show dendrogram |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2728 max_peptide_count = # experimental: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2729 g_intensity_hm_rows, # values of 50 and 75 worked well |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2730 master_cex = 1.0, # basis for text sizes |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2731 margins = NULL, # optional margins (bottom, right) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2732 cellnote = NULL, # optional matrix of character; dim = dim(m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2733 adj = 0.5, # adjust text: 0 left, 0.5 middle, 1 right |
|
2
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
2734 row_scaling = # should row-scaling be applied if possible? |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
2735 g_default_heatmap_row_scaling, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2736 ... # passthru to hm2plus or heatmap.2 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2737 ) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2738 peptide_count <- 0 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2739 # emit the heading for the heatmap |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2740 if (hm_heading_function(m, cutoff)) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2741 nrow_m <- nrow(m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2742 peptide_count <- min(max_peptide_count, nrow_m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2743 if (nrow_m > 1) { |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2744 m_margin <- m[peptide_count:1, ] |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2745 # Margin was heuristically derived to accommodate the widest label |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2746 row_mchar_max <- max(nchar(rownames(m_margin))) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2747 col_mchar_max <- max(nchar(colnames(m_margin))) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2748 row_margin <- master_cex * row_mchar_max * 2.6 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2749 col_margin <- master_cex * col_mchar_max * 2.6 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2750 if (print_trace_messages) cat( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2751 sprintf("row_margin = %0.3f; ", row_margin)) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2752 if (print_trace_messages) cat( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2753 sprintf("col_margin = %0.3f; ", col_margin)) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2754 hm_call <- NULL |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2755 tryCatch( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2756 { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2757 # set non-argument parameters for hm_call inner function |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2758 my_row_cex <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2759 master_cex * 200000 / ( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2760 (max(nchar(rownames(m_margin)))^2) * g_intensity_hm_rows |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2761 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2762 m_hm <- m[peptide_count:1, , drop = FALSE] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2763 if (is.null(cellnote)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2764 cellnote <- matrix("", nrow = nrow(m_hm), ncol = ncol(m_hm)) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2765 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2766 # squash un-actionable "no visible global for ..." |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2767 cellnote[is.na(m_hm)] <- params$heatMapNAcellNote |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2768 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2769 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2770 cellnote <- cellnote[peptide_count:1, , drop = FALSE] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2771 } |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2772 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2773 # squash un-actionable "no visible global for ..." |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2774 if (params$heatMapNAsubstitute) m_hm[is.na(m_hm)] <- 0 |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2775 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2776 nrow_m_hm <- nrow(m_hm) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2777 ncol_m_hm <- ncol(m_hm) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2778 if (nrow_m_hm < 1 || ncol_m_hm < 1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2779 return(peptide_count) # return zero as initialized above |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2780 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2781 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2782 my_row_cex <- master_cex * (100 / (2 + row_mchar_max)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2783 my_col_cex <- master_cex * 6 * row_margin / col_margin |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2784 my_col_adj <- min(my_col_cex, my_row_cex) / my_col_cex |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2785 my_col_cex <- min(my_col_cex, my_row_cex) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2786 col_margin <- sqrt(my_col_adj) * col_margin |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2787 if (print_trace_messages) cat( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2788 sprintf("my_row_cex = %0.3f; ", my_row_cex)) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2789 if (print_trace_messages) cat( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2790 sprintf("my_col_cex = %0.3f; ", my_col_cex)) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2791 if (is.null(margins)) my_margins <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2792 c( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2793 (my_col_cex + col_margin), # col |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2794 (my_row_cex + row_margin) / my_row_cex # row |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2795 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2796 else |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2797 my_margins <- margins |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2798 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2799 if (print_trace_messages) cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2800 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2801 "my_margins = c(%s)\n\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2802 paste(my_margins, collapse = ", ") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2803 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2804 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2805 my_hm2_cex <- 2 * master_cex |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2806 my_key_cex <- |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2807 0.9 - |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2808 0.1 * (g_intensity_hm_rows + nrow_m_hm) / g_intensity_hm_rows |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2809 my_key_warp <- 1.5 * 22.75 / row_margin |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2810 my_key_cex <- min(1.10, my_key_warp * my_key_cex) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2811 my_hgt_scale <- 3.70 - 0.4 * (max(1, 0.9 * my_row_cex) - 1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2812 my_hgt_scale <- 3.75 # 3.615 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2813 my_hgt_scale <- 3.60 # 3.615 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2814 if (print_trace_messages) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2815 cat_variable(my_hgt_scale, "\n\n", 3) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2816 my_warp <- max(0.1, 1.4 * (7.5 + nrow_m) / g_intensity_hm_rows) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2817 if (print_trace_messages) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2818 cat_variable(my_warp, "\n\n", 3) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2819 # added 0.9 heuristically... |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2820 my_plot_height <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2821 (0.566 + 0.354 * (nrow_m / g_intensity_hm_rows)) * |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2822 min(my_hgt_scale, my_hgt_scale * my_warp) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2823 my_plot_height <- |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2824 min(3.65, my_plot_height * g_intensity_hm_rows / 50) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2825 my_heights <- c( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2826 0.3, # title and top dendrogram |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2827 my_plot_height, # plot and bottom margin |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2828 4.15 - my_hgt_scale, # legend |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2829 0.05 + my_hgt_scale - my_plot_height # whitespace below legend |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2830 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2831 my_note_cex <- min(0.8, my_row_cex, my_col_cex) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2832 if (print_trace_messages) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2833 cat_variable(my_plot_height, "\n\n", 3) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2834 cat_variable(4.19 - my_hgt_scale, "\n\n", 3) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2835 cat_variable(nrow_m_hm, "; ", 0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2836 cat_variable(ncol_m_hm, "; ", 0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2837 cat_variable(my_row_cex, "; ", 3) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2838 cat_variable(my_col_cex, "; ", 3) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2839 cat_variable(my_note_cex, "; ", 3) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2840 cat_variable(my_key_cex, "\n\n", 3) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2841 cat_variable(my_hgt_scale, "; ", 3) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2842 cat_variable(my_plot_height, "; ", 3) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2843 cat_variable(my_warp, "\n\n", 3) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2844 cat_variable(my_heights, "; ", 2) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2845 cat_variable(sum(my_heights), "\n\n", 3) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2846 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2847 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2848 # define hm_call inner function |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2849 hm_call <- function(x, scaling, title) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2850 my_cex_main <- min(5.0, 220 / nchar(title)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2851 op <- par( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2852 cex.main = my_cex_main * master_cex, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2853 adj = adj |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2854 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2855 if ( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2856 !is.null( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2857 hm2plus( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2858 x, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2859 Colv = NA, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2860 Rowv = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2861 cexRow = my_row_cex, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2862 cexCol = my_col_cex, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2863 dendrogram = "row", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2864 las = 1, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2865 main = title, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2866 key_xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2867 cex = my_hm2_cex, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2868 key_par = list(cex = my_key_cex), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2869 margins = my_margins, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2870 widths = c(0.4, 2.6, 1.5), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2871 heights = my_heights, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2872 mat = matrix( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2873 c( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2874 c(0, 3, 3), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2875 c(2, 1, 1), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2876 c(0, 4, 0), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2877 c(0, 0, 0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2878 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2879 nrow = 4, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2880 ncol = 3, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2881 byrow = TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2882 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2883 na.rm = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2884 scale = scaling, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2885 srtcol = 90, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2886 srtrow = 0, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2887 xlab = "", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2888 cellnote = cellnote, |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2889 # ref for na.color: |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2890 # https://cran.r-project.org/web/packages/gplots/gplots.pdf |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2891 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2892 # squash un-actionable "no visible global for ..." |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2893 na.color = params$heatMapNAcellColor, |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2894 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2895 notecex = my_note_cex, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2896 ... |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2897 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2898 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2899 ) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2900 if (print_trace_messages) cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2901 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2902 "my_heights = c(%s); sum = %0.3f\n\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2903 paste( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2904 sprintf("%0.3f", my_heights), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2905 collapse = ", " |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2906 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2907 sum(my_heights) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2908 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2909 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2910 if (print_trace_messages) cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2911 sprintf("my_key_cex = %0.3f\n\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2912 my_key_cex) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2913 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2914 if (print_trace_messages) cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2915 sprintf("my_key_cex/my_heights[3] = %0.3f\n\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2916 my_key_cex / my_heights[3]) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2917 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2918 if (print_trace_messages) cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2919 sprintf("my_heights[2]/my_heights[3] = %0.3f\n\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2920 my_heights[2] / my_heights[3]) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2921 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2922 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2923 par(op) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2924 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2925 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2926 # invoke hm_call inner function |
|
2
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
2927 if (row_scaling != "row" || sum(rowSums(!is.na(m_hm)) < 2)) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2928 hm_call( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2929 m_hm, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2930 "none", |
|
2
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
2931 "log(intensities), unimputed, and unnormalized" |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2932 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2933 else |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2934 hm_call( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2935 m_hm, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2936 "row", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2937 "log(intensities), row-scaled, unimputed, and unnormalized" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2938 ) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2939 }, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2940 error = function(e) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2941 if (!is.null(hm_call)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2942 m_hm[is.na(m_hm)] <- 0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2943 tryCatch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2944 { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2945 if (nrow(m_hm) > 1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2946 hm_call( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2947 m_hm, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2948 "none", |
|
2
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
2949 "log(intensities), zero-imputed, unnormalized" |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2950 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2951 else |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2952 cat("\nThere are too few peptides to produce a heatmap.\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2953 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2954 error = function(r) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2955 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2956 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2957 "\n%s %s Internal message: %s\n\\newline\n\n", |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2958 "Failure drawing heatmap, possibly because of ", |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2959 "too many missing values.\n\\newline\n\n", |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2960 r$message |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2961 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2962 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2963 cat_margins() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2964 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2965 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2966 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2967 cat( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2968 "\nFailure drawing heatmap, ", |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2969 "possibly because of too many missing values.\n" |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2970 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2971 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2972 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2973 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2974 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2975 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2976 # return value: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2977 peptide_count |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2978 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2979 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2980 # function drawing heatmap of correlations if they exist, else covariances |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2981 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2982 # squash un-actionable cyclomatic_complexity warning |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2983 # squash un-actionable "no visible global for ..." |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2984 cov_heatmap <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2985 function( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2986 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2987 m, # matrix with rownames already formatted |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2988 kinase_name, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2989 top_substrates = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2990 ... # passthru to hm2plus or heatmap.2 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2991 ) { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2992 if (print_nb_messages) nbe( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
2993 see_variable(m), " [", nrow(m), "x", ncol(m), "\n") |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2994 colnames_m <- colnames(m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2995 is_na_m <- is.na(m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2996 tmp <- m |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2997 tmp[is_na_m] <- 0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2998 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2999 tmp <- m[, 0 < colSums(x = tmp)] # by default, na.rm is FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3000 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3001 colnames_tmp <- colnames(tmp) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3002 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3003 my_low_p_seq <- seq( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3004 from = min(g_intensity_hm_rows, nrow(m)), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3005 to = 1, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3006 by = -1 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3007 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3008 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3009 if (g_correlate_substrates) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3010 # zap samples having zero or near-zero variance |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3011 tmp[is.na(tmp)] <- 0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3012 nzv <- caret::nearZeroVar( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3013 tmp, # matrix of values, samples x variables |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3014 freqCut = 1.01, # min(freq most prevalent value / |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3015 # freq second most prevalent) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3016 uniqueCut = 99 # max(number of unique values / |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3017 # total number of samples) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3018 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3019 tmp <- if (length(nzv) > 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3020 m[, -nzv, drop = FALSE] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3021 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3022 m |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3023 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3024 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3025 tmp <- m[my_low_p_seq, , drop = FALSE] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3026 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3027 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3028 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3029 t_m <- t(tmp) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3030 t_m[is.na(t_m)] <- 0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3031 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3032 my_corcov <- cov(t_m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3033 did_filter_rows <- did_filter_cols <- FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3034 if (g_correlate_substrates && !is_positive_definite(my_corcov)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3035 my_correlate_substrates <- FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3036 t_m <- t(m[my_low_p_seq, , drop = FALSE]) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3037 t_m[is.na(t_m)] <- 0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3038 unfiltered_row_count <- ncol(t_m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3039 unfiltered_col_count <- nrow(t_m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3040 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3041 # zap empty samples |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3042 t_m <- t_m[0 < rowSums(x = t_m), ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3043 # zap substrates present in fewer than two samples |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3044 foo <- t_m > 0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3045 foo <- colSums(x = foo) > 1 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3046 t_m <- t_m[, foo] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3047 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3048 did_filter_rows <- unfiltered_row_count > ncol(t_m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3049 did_filter_cols <- unfiltered_col_count > nrow(t_m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3050 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3051 colnames_tmp <- rownames(t_m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3052 my_corcov <- cov(t_m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3053 if (g_filter_cov_var_gt_1) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3054 my_corcov <- keep_cov_w_var_gtr_1(my_corcov) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3055 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3056 } else if (g_correlate_substrates) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3057 my_corcov <- cov2cor(my_corcov) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3058 my_correlate_substrates <- TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3059 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3060 my_correlate_substrates <- FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3061 if (g_filter_cov_var_gt_1) my_corcov <- keep_cov_w_var_gtr_1(my_corcov) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3062 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3063 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3064 omitted_samples <- colnames_m[colnames_m %notin% colnames_tmp] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3065 suffix <- if (length(omitted_samples) > 1) "s" else "" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3066 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3067 f_omissions <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3068 function(is_corr) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3069 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3070 sprintf( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3071 "Below is the %s plot for %s sites", |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3072 if (is_corr) "correlation" else "covariance", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3073 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3074 if (top_substrates) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3075 "%0.0f \"highest-quality\"" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3076 else |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3077 "%0.0f", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3078 ncol(t_m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3079 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3080 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3081 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3082 if (did_filter_cols) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3083 cat(sprintf(", omitting sample%s ", suffix)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3084 latex_collapsed_vector(", ", omitted_samples) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3085 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3086 cat(".\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3087 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3088 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3089 if (is.null(my_corcov) || sum(!is.na(t_m)) < 2) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3090 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3091 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3092 "\\newline\n%s %s plot.\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3093 "Insufficient covariance to produce", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3094 if (my_correlate_substrates) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3095 "correlation" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3096 else |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3097 "covariance" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3098 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3099 "\\newpage\n" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3100 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3101 return(NULL) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3102 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3103 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3104 cat("\\leavevmode\n", "\\newpage\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3105 f_omissions(my_correlate_substrates) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3106 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3107 master_cex <- 0.4 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3108 max_nchar <- max(nchar(rownames(t_m))) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3109 my_limit <- g_intensity_hm_rows |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3110 diminution <- sqrt(my_limit / (my_limit + ncol(t_m))) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3111 my_row_cex <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3112 my_col_cex <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3113 min(1.75, master_cex * 9 * diminution ^ 1.5) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3114 my_margin <- 3 + my_row_cex * 64 / (8 + max_nchar) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3115 my_key_cex <- 1.4 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3116 my_hm2_cex <- 1.0 * master_cex |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3117 my_hgt_scale <- 3.50 - 0.26 * (max(0.4, my_key_cex) - 0.4) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3118 my_hgt_scale <- 2.7 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3119 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3120 my_legend_height <- 4.0 - my_hgt_scale |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3121 my_legend_height <- 0.5 * my_key_cex |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3122 my_warp <- 0.65 * (my_limit + ncol(t_m)) / my_limit |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3123 my_warp <- 0.8 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3124 my_legend_height <- 0.77 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3125 my_legend_height <- 0.67 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3126 my_plot_height <- my_hgt_scale + (1 - my_warp) * my_legend_height |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3127 my_legend_height <- my_warp * my_legend_height |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3128 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3129 parjust <- par(adj = 0.5) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3130 on.exit(par(parjust)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3131 my_corcov <- my_corcov[order(rownames(my_corcov)), ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3132 my_main <- |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3133 sprintf("%s among %s sites %s", |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3134 if (my_correlate_substrates) "Correlation" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3135 else "Covariance", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3136 kinase_name, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3137 if (!my_correlate_substrates && |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3138 g_filter_cov_var_gt_1 && |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3139 did_filter_rows |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3140 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3141 "having variance > 1" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3142 else "" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3143 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3144 my_main_nchar <- nchar(my_main) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3145 my_heights <- c( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3146 0.3, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3147 my_plot_height, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3148 my_legend_height # was 4.0 - my_hgt_scale # was 4.19 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3149 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3150 if (print_trace_messages) cat(sprintf("max_nchar = %0.3f; ", max_nchar)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3151 if (print_trace_messages) cat(sprintf("my_margin = %0.3f; ", my_margin)) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3152 if (print_trace_messages) cat( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3153 sprintf("my_plot_height = %0.3f\n\n", my_plot_height)) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3154 if (print_trace_messages) cat(sprintf("master_cex = %0.3f; ", master_cex)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3155 if (print_trace_messages) cat(sprintf("my_row_cex = %0.3f; ", my_row_cex)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3156 if (print_trace_messages) cat(sprintf("my_col_cex = %0.3f; ", my_col_cex)) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3157 if (print_trace_messages) cat( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3158 sprintf("my_key_cex = %0.3f\n\n", my_key_cex)) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3159 if (print_trace_messages) cat( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3160 sprintf("my_hgt_scale = %0.3f\n\n", my_hgt_scale)) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3161 if (print_trace_messages) cat( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3162 sprintf("legend height = %0.3f\n\n", my_legend_height)) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3163 if (print_trace_messages) cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3164 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3165 "my_heights = c(%s); sum = %0.3f\n\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3166 paste( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3167 sprintf("%0.3f", my_heights), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3168 collapse = ", " |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3169 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3170 sum(my_heights) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3171 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3172 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3173 op <- par(cex.main = (30 + my_main_nchar) / my_main_nchar) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3174 on.exit(par(op)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3175 hm2plus( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3176 x = my_corcov, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3177 cex = my_hm2_cex, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3178 cexCol = my_col_cex, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3179 cexRow = my_row_cex, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3180 density_info = "none", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3181 denhgt = 0.15, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3182 denwid = 0.5, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3183 divergent = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3184 key_par = list(cex = my_key_cex), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3185 key_xlab = if (my_correlate_substrates) "Correlation" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3186 else "Covariance", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3187 main = my_main, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3188 mat = matrix( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3189 c( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3190 c(0, 3, 3), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3191 c(2, 1, 1), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3192 c(0, 4, 0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3193 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3194 nrow = 3, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3195 ncol = 3, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3196 byrow = TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3197 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3198 heights = my_heights, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3199 margins = c(my_margin, my_margin), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3200 widths = c(0.5, 3.1, 0.9), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3201 scale = "none", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3202 symkey = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3203 symbreaks = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3204 symm = FALSE #TODO evaluate TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3205 # ... |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3206 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3207 } # end cov_heatmap |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3208 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3209 ### FILE IMPORT |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3210 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3211 # function reading bzipped file to data.frame |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3212 bzip2df <- function(d, f, ctor = bzfile) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3213 # read.delim file (by default, compressed by bzip2) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3214 if (file.exists(f)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3215 conn <- NULL |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3216 pf <- parent.frame() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3217 tryCatch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3218 assign( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3219 as.character(substitute(d)), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3220 read.delim(conn <- bzfile(f, open = "r")), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3221 pf |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3222 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3223 finally = if (!is.null(conn)) close(conn) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3224 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3225 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3226 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3227 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3228 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3229 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3230 # Purpose |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3231 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3232 The purpose of this analysis is to perform for phosphopeptides: |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3233 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3234 - imputation of missing values, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3235 - quantile normalization, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3236 - ANOVA (using the R stats::`r params$oneWayManyCategories` function), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3237 - assignment of an FDR-adjusted $p$-value and a "quality score" to each phosphopeptide, and |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3238 - KSEA (Kinase-Substrate Enrichment Analysis) using code adapted from the CRAN `KSEAapp` package to search for kinase substrates from the following databases: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3239 - PhosphoSitesPlus [https://www.phosphosite.org](https://www.phosphosite.org) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3240 - The Human Proteome Database [http://hprd.org](http://hprd.org) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3241 - NetworKIN [http://networkin.science/](http://networkin.science/) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3242 - Phosida [http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx](http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3243 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3244 ```{r include = FALSE} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3245 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3246 if (params$kseaUseAbsoluteLog2FC) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3247 sfc <- "|s|" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3248 pfc <- "|p|" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3249 pfc_txt <- "$\\text{absolute value}({\\log_2 (\\text{fold-change})})$" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3250 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3251 sfc <- "s" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3252 pfc <- "p" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3253 pfc_txt <- "${\\log_2 (\\text{fold-change}})$" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3254 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3255 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3256 ksea_heatmap_titles <- list() |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3257 ksea_heatmap_titles[[const_ksea_astrsk_kinases]] <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3258 sprintf( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3259 "Summary for all kinases enriched in one or more contrasts at %s < %s", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3260 ksea_cutoff_statistic, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3261 ksea_cutoff_threshold |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3262 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3263 ksea_heatmap_titles[[const_ksea_all_kinases]] <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3264 "Summary figure for all contrasts and all kinases" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3265 ksea_heatmap_titles[[const_ksea_nonastrsk_kinases]] <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3266 sprintf( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3267 "Summary for all kinases not enriched at %s < %s in any contrast", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3268 ksea_cutoff_statistic, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3269 ksea_cutoff_threshold |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3270 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3271 # hash to hold names of significantly enriched kinases |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3272 ksea_asterisk_hash <- new_env() |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3273 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3274 # PROCESS (mostly read) PARAMETERS |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3275 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3276 # False discovery rate adjustment for ANOVA |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3277 # Since pY abundance is low, set to 0.10 and 0.20 in addition to 0.05 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3278 val_fdr <- read.table(file = alpha_file, sep = "\t", header = FALSE, quote = "") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3279 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3280 if ( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3281 ncol(val_fdr) != 1 || |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3282 sum(!is.numeric(val_fdr[, 1])) || |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3283 sum(val_fdr[, 1] < 0) || |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3284 sum(val_fdr[, 1] > 1) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3285 ) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3286 cat("alphaFile should be one column of numbers within the range [0.0,1.0]") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3287 param_df_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3288 knitr::knit_exit() |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3289 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3290 val_fdr <- val_fdr[, 1] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3291 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3292 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3293 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3294 ```{r echo = FALSE, results = 'asis'} |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3295 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3296 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3297 result <- file.copy( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3298 from = preproc_db, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3299 to = ksea_app_prep_db, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3300 overwrite = TRUE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3301 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3302 if (!result) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3303 write( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3304 sprintf( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3305 "fatal error copying initial database '%s' to output '%s'", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3306 preproc_db, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3307 ksea_app_prep_db, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3308 ), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3309 stderr() |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3310 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3311 if (sys.nframe() > 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3312 cat("Cannot continue and quit() failed. Goodbye.") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3313 param_df_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3314 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3315 # in case knit_exit doesn't exit |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3316 quit(save = "no", status = 1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3317 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3318 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3319 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3320 if (FALSE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3321 write.table(x = param_df, file = "test-data/params.txt") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3322 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3323 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3324 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3325 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3326 ```{r echo = FALSE} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3327 ### READ DATA |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3328 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3329 # read.table reads a file in table format and creates a data frame from it. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3330 # - note that `quote = ""` means that quotation marks are treated literally. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3331 full_data <- read.table( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3332 file = input_file, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3333 sep = "\t", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3334 header = TRUE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3335 quote = "", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3336 check.names = FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3337 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3338 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3339 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3340 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3341 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3342 # Extraction of Sample Classes and Names from Input Data |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3343 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3344 ```{r echo = FALSE, results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3345 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3346 data_column_indices <- grep(first_data_column, names(full_data), perl = TRUE) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3347 my_column_names <- names(full_data) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3348 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3349 if (!fdc_is_integer) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3350 if (length(data_column_indices) > 0) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3351 first_data_column <- data_column_indices[1] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3352 } else { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3353 cat(paste("failed to convert firstDataColumn:", first_data_column)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3354 param_df_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3355 knitr::knit_exit() |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3356 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3357 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3358 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3359 cat( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3360 sprintf( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3361 paste( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3362 "\n\nThe input data file has peptide-intensity data", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3363 "in columns %d (\"%s\") through %d (\"%s\")." |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3364 ), |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3365 tmp <- min(data_column_indices), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3366 my_column_names[tmp], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3367 tmp <- max(data_column_indices), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3368 my_column_names[tmp] |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3369 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3370 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3371 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3372 if (TRUE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3373 cat0( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3374 table_offset(i = 1, new = TRUE), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3375 "Sample classes and names are shown in ", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3376 table_href(), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3377 ".\n\n" |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3378 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3379 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3380 cat0( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3381 "\\newcounter{offset}\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3382 "\\setcounter{offset}{\\value{table}}\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3383 "\\stepcounter{offset}\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3384 "Sample classes and names are shown in ", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3385 table_href(), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3386 ".\n\n" |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3387 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3388 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3389 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3390 #TODO remove this unused variable and assignment |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3391 if (FALSE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3392 # Write column names as a LaTeX enumerated list. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3393 column_name_df <- data.frame( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3394 column = seq_len(length(colnames(full_data))), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3395 name = paste0("\\verb@", colnames(full_data), "@") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3396 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3397 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3398 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3399 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3400 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3401 ```{r echo = FALSE, results = 'asis'} |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3402 # extract intensity columns from full_data to quant_data |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3403 quant_data <- full_data[first_data_column:length(full_data)] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3404 quant_data[quant_data == 0] <- NA |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3405 rownames(quant_data) <- rownames(full_data) <- full_data$Phosphopeptide |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3406 full_data_names <- colnames(quant_data) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3407 # Extract factors and trt-replicates using regular expressions. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3408 # Typically: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3409 # regex_sample_names is "\\.\\d+[A-Z]$" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3410 # regex_sample_grouping is "\\d+" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3411 # This would distinguish trt-replicates by terminal letter [A-Z] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3412 # in sample names and group them into trts by the preceding digits. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3413 # e.g.: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3414 # group .1A .1B .1C into group 1; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3415 # group .2A .2B .2C, into group 2; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3416 # etc. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3417 m <- regexpr(regex_sample_names, colnames(quant_data), perl = TRUE) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3418 sample_name_matches <- regmatches(names(quant_data), m) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3419 colnames(quant_data) <- sample_name_matches |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3420 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3421 write_debug_file(quant_data) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3422 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3423 rx_match <- regexpr(regex_sample_grouping, sample_name_matches, perl = TRUE) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3424 smpl_trt <- as.factor(regmatches(sample_name_matches, rx_match)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3425 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3426 if (print_nb_messages) nbe(see_variable(smpl_trt, "\n\n")) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3427 if (print_nb_messages) nbe(see_variable(sample_name_matches, "\n\n")) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3428 if (print_nb_messages) nbe(see_variable(full_data_names, "\n\n")) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3429 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3430 sample_treatment_df <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3431 save_sample_treatment_df <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3432 data.frame( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3433 class = smpl_trt, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3434 sample = sample_name_matches, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3435 full_sample_names = full_data_names |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3436 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3437 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3438 if (print_nb_messages) nbe(see_variable(sample_treatment_df, "\n\n")) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3439 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3440 # reorder data |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3441 my_order <- with(sample_treatment_df, order(class, sample)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3442 quant_data <- quant_data[, my_order] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3443 sample_name_matches <- sample_name_matches[my_order] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3444 smpl_trt <- smpl_trt[my_order] |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3445 sample_treatment_df <- data.frame( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3446 class = smpl_trt, |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3447 sample = sample_name_matches |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3448 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3449 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3450 # filter smpl_trt as appropriate |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3451 if (sample_group_filter %in% c("include", "exclude")) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3452 include_sample <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3453 mgrepl( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3454 v = sample_group_filter_patterns, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3455 s = as.character(smpl_trt), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3456 fixed = sample_group_filter_fixed, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3457 perl = sample_group_filter_perl, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3458 ignore.case = sample_group_filter_nocase |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3459 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3460 if (sum(include_sample) < 2) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3461 errmsg <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3462 paste( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3463 "ERROR:", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3464 sum(include_sample), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3465 "samples are too few for analysis;", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3466 "check input parameters for sample-name parsing" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3467 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3468 cat0( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3469 errmsg, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3470 "\\stepcounter{offset}\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3471 " in ", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3472 table_href(), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3473 ".\n\n" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3474 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3475 data_frame_tabbing_latex( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3476 x = save_sample_treatment_df, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3477 tabstops = c(1.25, 1.25), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3478 caption = "Sample classes", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3479 use_subsubsection_header = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3480 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3481 data_frame_tabbing_latex( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3482 x = |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3483 param_df[ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3484 c("regexSampleNames", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3485 "regexSampleGrouping", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3486 "groupFilterPatterns", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3487 "groupFilter", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3488 "groupFilterMode" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3489 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3490 ], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3491 tabstops = c(1.75), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3492 underscore_whack = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3493 caption = "Input parameters for sample-name parsing", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3494 verbatim = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3495 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3496 param_df_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3497 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3498 return(invisible(-1)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3499 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3500 sample_treatment_df <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3501 if (sample_group_filter == "include") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3502 sample_treatment_df[include_sample, ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3503 else |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3504 sample_treatment_df[!include_sample, ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3505 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3506 include_sample <- rep.int(TRUE, length(smpl_trt)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3507 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3508 sample_name_matches <- sample_treatment_df$sample |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3509 rx_match <- regexpr(regex_sample_grouping, sample_name_matches, perl = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3510 smpl_trt <- as.factor(regmatches(sample_name_matches, rx_match)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3511 sample_treatment_df$class <- smpl_trt |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3512 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3513 # filter quant_data as appropriate |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3514 number_of_samples <- length(sample_name_matches) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3515 quant_data <- quant_data[, sample_name_matches] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3516 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3517 sample_level_integers <- as.integer(smpl_trt) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3518 sample_treatment_levels <- levels(smpl_trt) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3519 count_of_treatment_levels <- length(sample_treatment_levels) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3520 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3521 # for each phosphopeptide, across treatment levels, compute minimum |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3522 # count of observed (i.e., non-missing) values |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3523 my_env <- new_env() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3524 for (l in sample_treatment_levels) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3525 my_env[[as.character(l)]] <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3526 as.vector(rowSums(!is.na(quant_data[l == smpl_trt]))) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3527 min_group_obs_count <- row_apply( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3528 x = Reduce( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3529 f = function(l, r) cbind(l, my_env[[r]]), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3530 x = sample_treatment_levels, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3531 init = c() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3532 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3533 fun = min |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3534 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3535 names(min_group_obs_count) <- rownames(quant_data) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3536 rm(my_env) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3537 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3538 # display (possibly-filtered) results |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3539 cat("\\newpage\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3540 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3541 if (sum(include_sample) > 1) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3542 data_frame_tabbing_latex( |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3543 x = sample_treatment_df, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3544 tabstops = c(1.25), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3545 caption = "Sample classes", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3546 use_subsubsection_header = FALSE |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3547 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3548 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3549 sample_name_grow <- 10 / (10 + max(nchar(sample_name_matches) + 6)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3550 sample_colsep <- transition_positions(as.integer(sample_treatment_df$class)) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3551 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3552 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3553 ```{r echo = FALSE, results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3554 cat("\\newpage\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3555 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3556 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3557 ## Are the log-transformed sample distributions similar? |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3558 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3559 ```{r echo = FALSE, fig.dim = c(9, 6.5), results = 'asis'} |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3560 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3561 quant_data[quant_data == 0] <- NA #replace 0 with NA |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3562 quant_data_log <- log10(quant_data) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3563 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3564 rownames(quant_data_log) <- rownames(quant_data) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3565 colnames(quant_data_log) <- sample_name_matches |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3566 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3567 write_debug_file(quant_data_log) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3568 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3569 g_ppep_distrib_ctl <- new_env() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3570 g_ppep_distrib_ctl$xlab_line <- 3.5 + 11.86 * (0.67 - sample_name_grow) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3571 g_ppep_distrib_ctl$mai_bottom <- (0.5 + 3.95 * (0.67 - sample_name_grow)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3572 g_ppep_distrib_ctl$axis <- (0.6 + 0.925 * (0.67 - sample_name_grow)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3573 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3574 my_ppep_distrib_bxp <- function( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3575 x |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3576 , sample_name_grow = sample_name_grow |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3577 , main |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3578 , varwidth = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3579 , sub = NULL |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3580 , xlab |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3581 , ylab |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3582 , col = const_boxplot_fill |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3583 , notch = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3584 , ppep_distrib_ctl = g_ppep_distrib_ctl |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3585 , ... |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3586 ) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3587 my_xlab_line <- g_ppep_distrib_ctl$xlab_line |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3588 my_mai_bottom <- g_ppep_distrib_ctl$mai_bottom |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3589 my_axis <- g_ppep_distrib_ctl$axis |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3590 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3591 if (print_trace_messages) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3592 cat_variable(my_xlab_line, suffix = "; ") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3593 cat_variable(my_mai_bottom, suffix = "; ") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3594 cat_variable(my_axis, suffix = "\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3595 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3596 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3597 old_par <- par( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3598 mai = par("mai") + c(my_mai_bottom, 0, 0, 0), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3599 cex.axis = my_axis, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3600 cex.lab = 1.2 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3601 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3602 tryCatch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3603 { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3604 # Vertical plot |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3605 boxplot( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3606 x |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3607 , las = 2 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3608 , col = col |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3609 , main = main |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3610 , sub = NULL |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3611 , ylab = ylab |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3612 , xlab = NULL |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3613 , notch = notch |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3614 , varwidth = varwidth |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3615 , ... |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3616 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3617 title( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3618 sub = sub |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3619 , cex.sub = 1.0 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3620 , line = my_xlab_line + 1 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3621 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3622 title( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3623 xlab = xlab |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3624 , line = my_xlab_line |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3625 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3626 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3627 finally = par(old_par) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3628 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3629 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3630 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3631 my_ppep_distrib_bxp( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3632 x = quant_data_log |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3633 , sample_name_grow = sample_name_grow |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3634 , main = "Peptide intensities for each sample" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3635 , varwidth = boxplot_varwidth |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3636 , sub = "Box widths reflect number of peptides for sample" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3637 , xlab = "Sample" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3638 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3639 , col = const_boxplot_fill |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3640 , notch = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3641 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3642 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3643 cat("\n\n\n\n") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3644 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3645 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3646 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3647 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4), results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3648 if (nrow(quant_data_log) > 1) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3649 quant_data_log_stack <- stack(quant_data_log) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3650 ggplot2::ggplot(quant_data_log_stack, ggplot2::aes(x = values)) + |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3651 ggplot2::xlab(latex2exp::TeX("$log_{10}$(peptide intensity)")) + |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3652 ggplot2::ylab("Probability density") + |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3653 ggplot2::geom_density(ggplot2::aes(group = ind, colour = ind), na.rm = TRUE) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3654 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3655 cat("No density plot because there are too few peptides.\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3656 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3657 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3658 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3659 ## Globally, are peptide intensities are approximately unimodal? |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3660 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3661 <!-- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3662 # bquote could be used as an alternative to latex2exp::TeX below particularly |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3663 # and when plotting math expressions generally, at the expense of mastering |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3664 # another syntax, which hardly seems worthwhile when I need to use TeX |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3665 # elsewhere; here's an introduction to bquote: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3666 # https://www.r-bloggers.com/2018/03/math-notation-for-r-plot-titles-expression-and-bquote/ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3667 --> |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3668 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5), results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3669 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3670 # identify the location of missing values |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3671 fin <- is.finite(as.numeric(as.matrix(quant_data_log))) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3672 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3673 logvalues <- as.numeric(as.matrix(quant_data_log))[fin] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3674 logvalues_density <- density(logvalues) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3675 plot( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3676 x = logvalues_density, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3677 main = latex2exp::TeX( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3678 "Smoothed estimated probability density vs. $log_{10}$(peptide intensity)" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3679 ), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3680 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3681 ylab = "Probability density" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3682 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3683 hist( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3684 x = as.numeric(as.matrix(quant_data_log)), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3685 xlim = c(min(logvalues_density$x), max(logvalues_density$x)), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3686 breaks = 100, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3687 main = latex2exp::TeX("Frequency vs. $log_{10}$(peptide intensity)"), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3688 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3689 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3690 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3691 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3692 # Characterization of Input Data |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3693 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3694 ## Distribution of standard deviations of $log_{10}(\text{intensity})$, ignoring missing values |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3695 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3696 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5), results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3697 # determine quantile |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3698 q1 <- quantile(logvalues, probs = mean_percentile)[1] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3699 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3700 # 1 = row of matrix (ie, phosphopeptide) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3701 sds <- row_apply(quant_data_log, sd_finite) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3702 if (sum(!is.na(sds)) > 2) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3703 plot( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3704 density(sds, na.rm = TRUE) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3705 , main = "Smoothed estimated probability density vs. std. deviation" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3706 , sub = "(probability estimation made with Gaussian smoothing)" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3707 , ylab = "Probability density" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3708 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3709 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3710 cat( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3711 "At least two non-missing values are required to plot", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3712 "probability density.\n\n" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3713 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3714 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3715 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3716 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3717 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3718 ```{r echo = FALSE} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3719 # Determine number of cells to impute |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3720 temp <- quant_data[is.na(quant_data)] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3721 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3722 # Determine number of values to impute |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3723 number_to_impute <- length(temp) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3724 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3725 # Determine percent of missing values |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3726 pct_missing_values <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3727 round(length(temp) / (length(logvalues) + length(temp)) * 100) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3728 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3729 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3730 ```{r echo = FALSE} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3731 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3732 # prep for trt-median based imputation |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3733 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3734 ``` |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3735 # Imputation of Missing Values |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3736 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3737 ```{r echo = FALSE} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3738 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3739 imp_smry_pot_peptides_before <- nrow(quant_data_log) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3740 imp_smry_missing_values_before <- number_to_impute |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3741 imp_smry_pct_missing <- pct_missing_values |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3742 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3743 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3744 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3745 ```{r echo = FALSE} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3746 #Determine number of cells to impute |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3747 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3748 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3749 ```{r echo = FALSE} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3750 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3751 # Identify which values are missing and need to be imputed |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3752 ind <- which(is.na(quant_data), arr.ind = TRUE) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3753 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3754 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3755 ```{r echo = FALSE, results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3756 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3757 # Apply imputation |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3758 switch( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3759 imputation_method |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3760 , "group-median" = { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3761 quant_data_imp <- quant_data |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3762 imputation_method_description <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3763 paste("Substitute missing value with", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3764 "median peptide-intensity for sample group.\n" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3765 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3766 # Take the accurate ln(x+1) because the data are log-normally distributed |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3767 # and because median can involve an average of two measurements. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3768 quant_data_imp <- log1p(quant_data_imp) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3769 for (i in seq_len(count_of_treatment_levels)) { |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3770 # Determine the columns for this factor-level |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3771 level_cols <- i == sample_level_integers |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3772 # Extract those columns |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3773 lvlsbst <- quant_data_imp[, level_cols, drop = FALSE] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3774 # assign to ind the row-column pairs corresponding to each NA |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3775 ind <- which(is.na(lvlsbst), arr.ind = TRUE) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3776 # No group-median exists if there is only one sample |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3777 # a given ppep has no measurement; otherwise, proceed. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3778 if (ncol(lvlsbst) > 1) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3779 the_centers <- |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3780 row_apply(lvlsbst, median, na.rm = TRUE) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3781 for (j in seq_len(nrow(lvlsbst))) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3782 for (k in seq_len(ncol(lvlsbst))) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3783 if (is.na(lvlsbst[j, k])) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3784 lvlsbst[j, k] <- the_centers[j] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3785 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3786 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3787 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3788 quant_data_imp[, level_cols] <- lvlsbst |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3789 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3790 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3791 # Take the accurate e^x - 1 to match scaling of original input. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3792 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3793 good_rows <- !is.na(rowMeans(quant_data_imp)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3794 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3795 , "median" = { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3796 quant_data_imp <- quant_data |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3797 imputation_method_description <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3798 paste("Substitute missing value with", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3799 "median peptide-intensity across all sample classes.\n" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3800 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3801 # Take the accurate ln(x+1) because the data are log-normally distributed |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3802 # and because median can involve an average of two measurements. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3803 quant_data_imp <- log1p(quant_data_imp) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3804 quant_data_imp[ind] <- |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3805 row_apply(quant_data_imp, median, na.rm = TRUE)[ind[, 1]] |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3806 # Take the accurate e^x - 1 to match scaling of original input. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3807 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3808 good_rows <- !is.nan(rowMeans(quant_data_imp)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3809 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3810 , "mean" = { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3811 quant_data_imp <- quant_data |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3812 imputation_method_description <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3813 paste("Substitute missing value with", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3814 "geometric-mean peptide intensity across all sample classes.\n" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3815 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3816 # Take the accurate ln(x+1) because the data are log-normally distributed, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3817 # so arguments to mean should be previously transformed. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3818 # this will have to be |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3819 quant_data_imp <- log1p(quant_data_imp) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3820 # Assign to NA cells the mean for the row |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3821 quant_data_imp[ind] <- |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3822 row_apply(quant_data_imp, mean, na.rm = TRUE)[ind[, 1]] |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3823 # Take the accurate e^x - 1 to match scaling of original input. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3824 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3825 good_rows <- !is.nan(rowMeans(quant_data_imp)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3826 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3827 , "random" = { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3828 quant_data_imp <- quant_data |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3829 # sd to be used is the median sd |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3830 m1 <- median(sds, na.rm = TRUE) * sd_percentile |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3831 # If you want results to be reproducible, you will want to call |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3832 # base::set.seed before calling stats::rnorm |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3833 imputation_method_description <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3834 paste("Substitute each missing value with random intensity", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3835 sprintf( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3836 "random intensity $N \\sim (%0.2f, %0.2f)$.\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3837 q1, m1 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3838 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3839 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3840 cat(sprintf("mean_percentile (from input parameter) is %2.0f\n\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3841 100 * mean_percentile)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3842 cat(sprintf("sd_percentile (from input parameter) is %0.2f\n\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3843 sd_percentile)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3844 quant_data_imp[ind] <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3845 10 ^ rnorm(number_to_impute, mean = q1, sd = m1) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3846 quant_data_imp_ln <- log1p(quant_data_imp) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3847 good_rows <- !is.nan(rowMeans(quant_data_imp)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3848 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3849 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3850 quant_data_imp_log10 <- quant_data_imp_ln * const_log10_e |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3851 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3852 if (length(good_rows) < 1) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3853 print("ERROR: Cannot impute data; there are no good rows!") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3854 return(-1) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3855 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3856 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3857 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3858 ```{r echo = FALSE, results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3859 cat("\\quad\n\nImputation method:\n\n\n", imputation_method_description) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3860 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3861 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3862 ```{r echo = FALSE} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3863 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3864 imp_smry_pot_peptides_after <- sum(good_rows) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3865 imp_smry_rejected_after <- sum(!good_rows) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3866 imp_smry_missing_values_after <- sum(is.na(quant_data_imp[good_rows, ])) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3867 |
|
2
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
3868 # From ?`%in%`: |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3869 # %in% is currently defined |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3870 # as function(x, table) match(x, table, nomatch = 0) > 0 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3871 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3872 stock_in <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3873 names(good_rows) %in% |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3874 names(min_group_obs_count[g_intensity_min_per_class <= min_group_obs_count]) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3875 if (print_nb_messages) nbe(see_variable(stock_in), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3876 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3877 explicit_in <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3878 0 < match( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3879 names(good_rows), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3880 names(min_group_obs_count[g_intensity_min_per_class <= min_group_obs_count]) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3881 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3882 if (print_nb_messages) nbe(see_variable(explicit_in), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3883 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3884 great_enough_row_names <- good_rows[ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3885 names(good_rows) %in% |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3886 names(min_group_obs_count[g_intensity_min_per_class <= min_group_obs_count]) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3887 ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3888 if (print_nb_messages) nbe(see_variable(great_enough_row_names), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3889 great_enough_row_names <- great_enough_row_names[great_enough_row_names] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3890 if (print_nb_messages) nbe(see_variable(great_enough_row_names), "\n") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3891 ``` |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3892 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3893 ```{r echo = FALSE, results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3894 # ref: http://www1.maths.leeds.ac.uk/latex/TableHelp1.pdf |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3895 tabular_lines_fmt <- paste( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3896 "\\begin{table}[hb]", # h(inline); b(bottom); t (top) or p (separate page) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3897 " \\leavevmode", |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3898 " \\caption{Imputation Results}", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3899 " \\centering", # \centering centers the table on the page |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3900 " \\begin{tabular}{l c c c}", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3901 " \\hline\\hline", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3902 " \\ & potential peptides & missing values & rejected", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3903 " peptides \\\\ [0.5ex]", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3904 " \\hline", |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3905 " before imputation & %d & %d (%d\\%s) & \\\\", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3906 " after imputation & %d & %d & %d \\\\", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3907 " after keep comparable & %d & & %d \\\\ [1ex]", |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3908 " \\hline", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3909 " \\end{tabular}", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3910 #" \\label{table:nonlin}", # may be used to refer this table in the text |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3911 "\\end{table}", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3912 sep = "\n" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3913 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3914 tabular_lines <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3915 sprintf( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3916 tabular_lines_fmt, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3917 imp_smry_pot_peptides_before, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3918 imp_smry_missing_values_before, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3919 imp_smry_pct_missing, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3920 "%", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3921 imp_smry_pot_peptides_after, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3922 imp_smry_missing_values_after, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3923 imp_smry_rejected_after, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3924 length(great_enough_row_names), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3925 imp_smry_pot_peptides_before - |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3926 length(great_enough_row_names) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3927 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3928 cat(tabular_lines) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3929 ``` |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3930 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3931 ```{r filter_good_rows, echo = FALSE} |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3932 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3933 if (print_nb_messages) nbe( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3934 "before name extraction, ", see_variable(length(good_rows)), " ", |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3935 see_variable(good_rows), "\n") |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3936 good_rows <- names(good_rows[names(great_enough_row_names)]) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3937 if (print_nb_messages) nbe( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3938 "after name extraction, ", see_variable(length(good_rows)), |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3939 see_variable(good_rows), "\n") |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3940 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3941 min_group_obs_count <- min_group_obs_count[good_rows] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3942 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3943 # Zap rows where imputation was insufficiently effective |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3944 full_data <- full_data [good_rows, ] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3945 quant_data <- quant_data [good_rows, ] |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3946 quant_data_log <- quant_data_log [good_rows, ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3947 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3948 if (print_nb_messages) nbe( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3949 "before row filter, ", see_variable(nrow(quant_data_imp)), "\n") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3950 quant_data_imp <- quant_data_imp[good_rows, ] |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3951 if (print_nb_messages) nbe( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
3952 "after row filter, ", see_variable(nrow(quant_data_imp)), "\n") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3953 write_debug_file(quant_data_imp) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3954 quant_data_imp_good_rows <- quant_data_imp |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3955 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3956 write_debug_file(quant_data_imp_good_rows) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3957 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3958 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3959 ```{r echo = FALSE, results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3960 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3961 can_plot_before_after_imp <- TRUE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3962 d_combined <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3963 as.numeric( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3964 as.matrix( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3965 log10(quant_data_imp) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3966 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3967 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3968 d_original <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3969 as.numeric( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3970 as.matrix( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3971 log10(quant_data_imp[!is.na(quant_data)]) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3972 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3973 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3974 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3975 if (sum(!is.na(d_original)) > 2) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3976 d_original <- density(d_original) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3977 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3978 can_plot_before_after_imp <- FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3979 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3980 if (can_plot_before_after_imp && sum(is.na(d_combined)) < 1) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3981 d_combined <- density(d_combined) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3982 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3983 can_plot_before_after_imp <- FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3984 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3985 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3986 if (sum(is.na(quant_data)) > 0) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3987 # There ARE missing values |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3988 d_imputed <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3989 as.numeric( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3990 as.matrix( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3991 log10(quant_data_imp[is.na(quant_data)]) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3992 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3993 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3994 if (can_plot_before_after_imp && sum(is.na(d_imputed)) < 1) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3995 d_imputed <- (density(d_imputed)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3996 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3997 can_plot_before_after_imp <- FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3998 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3999 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4000 # There are NO missing values |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4001 d_imputed <- d_combined |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4002 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4003 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4004 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4005 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4006 ```{r echo = FALSE, fig.dim = c(9, 6.5), results = 'asis'} |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4007 zero_sd_rownames <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4008 rownames(quant_data_imp)[ |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4009 is.na((row_apply(quant_data_imp, sd, na.rm = TRUE)) == 0) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4010 ] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4011 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4012 if (length(zero_sd_rownames) >= nrow(quant_data_imp)) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4013 cat("All peptides have zero standard deviation. Cannot continue.") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4014 param_df_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4015 knitr::knit_exit() |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4016 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4017 if (length(zero_sd_rownames) > 0) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4018 cat( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4019 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4020 "%d %s %s", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4021 length(zero_sd_rownames), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4022 "peptides with zero variance", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4023 "were removed from statistical consideration" |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4024 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4025 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4026 zap_named_rows <- function(df, nms) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4027 return(df[!(row.names(df) %in% nms), ]) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4028 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4029 quant_data_imp <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4030 zap_named_rows(quant_data_imp, zero_sd_rownames) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4031 quant_data <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4032 zap_named_rows(quant_data, zero_sd_rownames) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4033 full_data <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4034 zap_named_rows(full_data, zero_sd_rownames) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4035 min_group_obs_count <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4036 min_group_obs_count[names(min_group_obs_count) %notin% zero_sd_rownames] |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4037 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4038 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4039 if (sum(is.na(quant_data)) > 0) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4040 cat("\\leavevmode\\newpage\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4041 # Copy quant data to x |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4042 x <- quant_data |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4043 # x gets to have values of: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4044 # - NA for observed values |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4045 # - 1 for missing values |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4046 x[is.na(x)] <- 0 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4047 x[x > 1] <- NA |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4048 x[x == 0] <- 1 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4049 # Log-transform imputed data |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4050 # update variable because rows may have been eliminated from quant_data_imp |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4051 quant_data_imp_log10 <- log10(quant_data_imp) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4052 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4053 write_debug_file(quant_data_imp_log10) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4054 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4055 # Set blue_dots to log of quant data or NA for NA quant data |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4056 blue_dots <- log10(quant_data) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4057 # Set red_dots to log of imputed data or NA for observed quant data |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4058 red_dots <- quant_data_imp_log10 * x |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4059 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4060 count_red <- sum(!is.na(red_dots)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4061 count_blue <- sum(!is.na(blue_dots)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4062 ylim_save <- ylim <- c( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4063 min(red_dots, blue_dots, na.rm = TRUE), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4064 max(red_dots, blue_dots, na.rm = TRUE) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4065 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4066 show_stripchart <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4067 50 > (count_red + count_blue) / length(sample_name_matches) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4068 if (show_stripchart) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4069 boxplot_sub <- "Light blue = data before imputation; Red = imputed data;" |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4070 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4071 boxplot_sub <- "" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4072 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4073 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4074 # Vertical plot |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4075 colnames(blue_dots) <- sample_name_matches |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4076 my_ppep_distrib_bxp( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4077 x = blue_dots |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4078 , sample_name_grow = sample_name_grow |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4079 , main = "Peptide intensities after eliminating unusable peptides" |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4080 , varwidth = boxplot_varwidth |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4081 , sub = paste(boxplot_sub, |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4082 "Box widths reflect number of peptides for sample") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4083 , xlab = "Sample" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4084 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4085 , col = const_boxplot_fill |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4086 , notch = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4087 , ylim = ylim |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4088 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4089 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4090 if (show_stripchart) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4091 # Points |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4092 # ref: https://r-charts.com/distribution/add-points-boxplot/ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4093 # NA values are not plotted |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4094 stripchart( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4095 blue_dots, # Data |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4096 method = "jitter", # Random noise |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4097 jitter = const_stripchart_jitter, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4098 pch = 19, # Pch symbols |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4099 cex = const_stripchart_cex, # Size of symbols reduced |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4100 col = "lightblue", # Color of the symbol |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4101 vertical = TRUE, # Vertical mode |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4102 add = TRUE # Add it over |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4103 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4104 stripchart( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4105 red_dots, # Data |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4106 method = "jitter", # Random noise |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4107 jitter = const_stripchart_jitter, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4108 pch = 19, # Pch symbols |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4109 cex = const_stripchart_cex, # Size of symbols reduced |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4110 col = "red", # Color of the symbol |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4111 vertical = TRUE, # Vertical mode |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4112 add = TRUE # Add it over |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4113 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4114 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4115 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4116 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4117 ``` |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4118 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4119 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'} |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4120 if (sum(is.na(quant_data)) > 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4121 # show measured values in blue on left half-violin plot |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4122 cat("\\leavevmode\n\\quad\n\n\\quad\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4123 old_par <- par( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4124 mai = par("mai") + c(g_ppep_distrib_ctl$mai_bottom, 0, 0, 0), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4125 cex.axis = g_ppep_distrib_ctl$axis, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4126 cex.lab = 1.2 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4127 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4128 tryCatch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4129 { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4130 vioplot::vioplot( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4131 x = lapply(blue_dots, function(x) x[!is.na(x)]), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4132 col = "lightblue1", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4133 side = "left", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4134 plotCentre = "line", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4135 ylim = ylim_save, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4136 main = "Distributions of observed and imputed data", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4137 sub = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4138 las = 2, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4139 xlab = NULL, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4140 ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4141 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4142 title( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4143 sub = "Light blue = observed data; Pink = imputed data", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4144 cex.sub = 1.0, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4145 line = g_ppep_distrib_ctl$xlab_line + 1 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4146 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4147 title( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4148 xlab = "Sample", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4149 line = g_ppep_distrib_ctl$xlab_line |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4150 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4151 red_violins <- lapply(red_dots, function(x) x[!is.na(x)]) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4152 cols_to_delete <- c() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4153 for (ix in seq_len(length(red_violins))) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4154 if (length(red_violins[[ix]]) < 1) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4155 cols_to_delete <- c(cols_to_delete, ix) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4156 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4157 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4158 # destroy any unimputable columns |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4159 if (!is.null(cols_to_delete)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4160 red_violins <- red_violins[-cols_to_delete] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4161 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4162 # plot imputed values in red on right half-violin plot |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4163 vioplot::vioplot( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4164 x = red_violins, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4165 col = "lightpink1", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4166 side = "right", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4167 plotCentre = "line", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4168 add = TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4169 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4170 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4171 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4172 finally = par(old_par) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4173 ) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4174 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4175 # density plot |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4176 cat("\\leavevmode\n\n\n\n\n\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4177 if (can_plot_before_after_imp) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4178 ylim <- c( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4179 0, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4180 max( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4181 if (is.list(d_combined)) d_combined$y else d_combined, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4182 if (is.list(d_original)) d_original$y else d_original, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4183 if (is.list(d_imputed)) d_imputed$y else d_imputed, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4184 na.rm = TRUE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4185 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4186 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4187 plot( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4188 d_combined, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4189 ylim = ylim, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4190 sub = |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4191 paste( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4192 "Blue = data before imputation; Red = imputed data;", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4193 "Black = combined" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4194 ), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4195 main = "Density of peptide intensity before and after imputation", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4196 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4197 ylab = "Probability density" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4198 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4199 lines(d_original, col = "blue") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4200 lines(d_imputed, col = "red") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4201 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4202 cat( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4203 "There are too few points to plot the density of peptide intensity", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4204 "before and after imputation." |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4205 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4206 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4207 cat("\\leavevmode\\newpage\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4208 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4209 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4210 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4211 # Quantile Normalization |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4212 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4213 The excellent `normalize.quantiles` function from |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4214 *[the `preprocessCore` Bioconductor package](http://bioconductor.org/packages/release/bioc/html/preprocessCore.html)* |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4215 performs "quantile normalization" as described Bolstad *et al.* (2003), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4216 DOI *[10.1093/bioinformatics/19.2.185](https://doi.org/10.1093%2Fbioinformatics%2F19.2.185)* |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4217 and its supplementary material [http://bmbolstad.com/misc/normalize/normalize.html](http://bmbolstad.com/misc/normalize/normalize.html), |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4218 i.e., it assumes that the goal is to detect |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4219 subtle differences among grossly similar samples (having similar distributions) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4220 by equalizing intra-quantile quantitations^[Unfortunately, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4221 one software library upon which `preprocessCore` depends |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4222 *[suffers from a concurrency defect](https://support.bioconductor.org/p/122925/#9135989)* |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4223 that requires that a specific, non-concurrent version of the library (`openblas` version $0.3.3$) be |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4224 installed. The installation command equivalent to what was used to install the library to produce the results presented here is: |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4225 \linebreak |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4226 ` conda install bioconductor-preprocesscore openblas=0.3.3`]. |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4227 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4228 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4229 <!-- |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4230 # Apply quantile normalization using preprocessCore::normalize.quantiles |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4231 # --- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4232 # tool repository: http://bioconductor.org/packages/release/bioc/html/preprocessCore.html |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4233 # except this: https://support.bioconductor.org/p/122925/#9135989 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4234 # says to install it like this: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4235 # ``` |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4236 # BiocManager::install("preprocessCore", configure.args="--disable-threading", force = TRUE, lib=.libPaths()[1]) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4237 # ``` |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4238 # conda installation (necessary because of a bug in recent openblas): |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4239 # conda install bioconductor-preprocesscore openblas=0.3.3 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4240 # ... |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4241 # --- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4242 # normalize.quantiles {preprocessCore} -- Quantile Normalization |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4243 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4244 # Description: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4245 # Using a normalization based upon quantiles, this function normalizes a |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4246 # matrix of probe level intensities. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4247 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4248 # THIS FUNCTIONS WILL HANDLE MISSING DATA (ie NA values), based on the |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4249 # assumption that the data is missing at random. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4250 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4251 # Usage: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4252 # normalize.quantiles(x, copy = TRUE, keep.names = FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4253 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4254 # Arguments: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4255 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4256 # - x: A matrix of intensities where each column corresponds to a chip and each row is a probe. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4257 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4258 # - copy: Make a copy of matrix before normalizing. Usually safer to work with a copy, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4259 # but in certain situations not making a copy of the matrix, but instead normalizing |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4260 # it in place will be more memory friendly. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4261 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4262 # - keep.names: Boolean option to preserve matrix row and column names in output. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4263 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4264 # Details: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4265 # This method is based upon the concept of a quantile-quantile plot extended to n dimensions. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4266 # No special allowances are made for outliers. If you make use of quantile normalization |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4267 # please cite Bolstad et al, Bioinformatics (2003). |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4268 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4269 # This functions will handle missing data (ie NA values), based on |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4270 # the assumption that the data is missing at random. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4271 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4272 # Note that the current implementation optimizes for better memory usage |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4273 # at the cost of some additional run-time. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4274 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4275 # Value: A normalized matrix. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4276 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4277 # Author: Ben Bolstad, bmbolstad.com |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4278 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4279 # References |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4280 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4281 # - Bolstad, B (2001) Probe Level Quantile Normalization of High Density Oligonucleotide |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4282 # Array Data. Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4283 # |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4284 # - Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003) A Comparison of |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4285 # Normalization Methods for High Density Oligonucleotide Array Data Based on Bias |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4286 # and Variance. Bioinformatics 19(2), pp 185-193. DOI 10.1093/bioinformatics/19.2.185 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4287 # http://bmbolstad.com/misc/normalize/normalize.html |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4288 # ... |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4289 --> |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4290 ```{r echo = FALSE, results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4291 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4292 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp)), "\n") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4293 if (nrow(quant_data_imp) > 0) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4294 quant_data_imp_qn <- preprocessCore::normalize.quantiles( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4295 as.matrix(quant_data_imp), keep.names = TRUE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4296 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4297 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4298 quant_data_imp_qn <- as.matrix(quant_data_imp) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4299 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4300 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4301 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp_qn)), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4302 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4303 quant_data_imp_qn <- as.data.frame(quant_data_imp_qn) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4304 write_debug_file(quant_data_imp_qn) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4305 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4306 quant_data_imp_qn_log <- log10(quant_data_imp_qn) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4307 write_debug_file(quant_data_imp_qn_log) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4308 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4309 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp_qn_log)), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4310 if (print_nb_messages) nbe(see_variable(ncol(quant_data_imp_qn_log)), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4311 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4312 quant_data_imp_qn_ls <- t(scale(t(log10(quant_data_imp_qn)))) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4313 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4314 sel <- row_apply(quant_data_imp_qn_ls, any_nan) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4315 quant_data_imp_qn_ls2 <- quant_data_imp_qn_ls |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4316 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4317 quant_data_imp_qn_ls2 <- quant_data_imp_qn_ls2[which(sel), ] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4318 quant_data_imp_qn_ls2 <- as.data.frame(quant_data_imp_qn_ls2) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4319 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4320 quant_data_imp_qn_ls <- as.data.frame(quant_data_imp_qn_ls) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4321 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4322 write_debug_file(quant_data_imp_qn_ls) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4323 write_debug_file(quant_data_imp_qn_ls2) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4324 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4325 # Create data.frame used by ANOVA analysis |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4326 data_table_imp_qn_lt <- cbind(full_data[1:9], quant_data_imp_qn_log) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4327 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4328 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4329 ## Are normalized, imputed, log-transformed sample distributions similar? |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4330 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4331 ```{r echo = FALSE, fig.dim = c(9, 6.5), results = 'asis'} |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4332 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4333 # Save unimputed quant_data_log for plotting below |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4334 unimputed_quant_data_log <- quant_data_log |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4335 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4336 # log10 transform (after preparing for zero values, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4337 # which should never happen...) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4338 quant_data_imp_qn[quant_data_imp_qn == 0] <- .000000001 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4339 quant_data_log <- log10(quant_data_imp_qn) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4340 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4341 how_many_peptides <- nrow(quant_data_log) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4342 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4343 if ((how_many_peptides) > 0) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4344 cat( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4345 sprintf( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4346 "Intensities for %d peptides:\n\n\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4347 how_many_peptides |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4348 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4349 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4350 cat("\n\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4351 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4352 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4353 # data visualization |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4354 if (TRUE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4355 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4356 my_ppep_distrib_bxp( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4357 x = quant_data_log |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4358 , sample_name_grow = sample_name_grow |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4359 , main = "Peptide intensities for each sample" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4360 , varwidth = boxplot_varwidth |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4361 , sub = NULL |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4362 , xlab = "Sample" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4363 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4364 , col = const_boxplot_fill |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4365 , notch = boxplot_notch |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4366 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4367 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4368 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4369 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4370 old_par <- par( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4371 mai = par("mai") + c(0.5, 0, 0, 0) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4372 , oma = par("oma") + c(0.5, 0, 0, 0) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4373 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4374 # ref: https://r-charts.com/distribution/add-points-boxplot/ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4375 # Vertical plot |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4376 colnames(quant_data_log) <- sample_name_matches |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4377 boxplot( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4378 quant_data_log |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4379 , las = 2 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4380 , cex.axis = 0.9 * sample_name_grow |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4381 , col = const_boxplot_fill |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4382 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4383 , xlab = "Sample" |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4384 , notch = boxplot_notch |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4385 , varwidth = boxplot_varwidth |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4386 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4387 par(old_par) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4388 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4389 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4390 cat("There are no peptides to plot\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4391 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4392 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4393 cat("\n\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4394 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4395 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4396 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4397 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4), results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4398 if (nrow(quant_data_log) > 1) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4399 quant_data_log_stack <- stack(quant_data_log) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4400 ggplot2::ggplot(quant_data_log_stack, ggplot2::aes(x = values)) + |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4401 ggplot2::xlab(latex2exp::TeX("$log_{10}$(peptide intensity)")) + |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4402 ggplot2::ylab("Probability density") + |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4403 ggplot2::geom_density(ggplot2::aes(group = ind, colour = ind), na.rm = TRUE) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4404 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4405 cat("No density plot because there are fewer than two peptides to plot.\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4406 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4407 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4408 ```{r echo = FALSE, results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4409 cat("\\leavevmode\\newpage\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4410 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4411 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4412 # ANOVA Analysis |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4413 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4414 ## Assignment of $p$-value and quality score |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4415 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4416 For each phosphopeptide, ANOVA analysis was performed to compute a $p$-value representing the evidence against the "null hypothesis" ($H_0$) that the intensity does not vary significantly among sample groups. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4417 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4418 However, because as more and more phosphopeptides are tested, there is increasd probability that, by random chance, a given peptide will have a $p$-value that appears to indicate significance. For this reason, the $p$-values were adjusted by applying the False Discovery Rate (FDR) correction from Benjamini and Hochberg (1995) [doi:10.1111/j.2517-6161.1995.tb02031.x](https://doi.org/10.1111/j.2517-6161.1995.tb02031.x). |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4419 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4420 Furthermore, to give more weight to phosphopeptides having fewer missing values, an (arbitrarily defined) quality score was assigned to each, defined as: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4421 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4422 $$ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4423 \textit{quality}_j |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4424 = \frac{1 + o_{j}}{v_{j}(1 + o_{j}) + 0.005} |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4425 $$ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4426 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4427 where: |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4428 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4429 - $o_j$ is the minimum number of non-missing observations per sample group for substrate $j$ for all sample groups, and |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4430 - $v_j$ is the FDR-adjusted ANOVA $p$-value for substrate $j$. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4431 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4432 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4433 ```{r, echo = FALSE, results = 'asis'} |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4434 cat("\\newpage\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4435 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4436 # Make new data frame containing only Phosphopeptides |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4437 # to connect preANOVA to ANOVA (connect_df) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4438 connect_df <- data.frame( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4439 data_table_imp_qn_lt$Phosphopeptide |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4440 , data_table_imp_qn_lt[, first_data_column] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4441 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4442 colnames(connect_df) <- c("Phosphopeptide", "Intensity") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4443 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4444 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4445 ```{r anova, echo = FALSE, fig.dim = c(10, 12), results = 'asis'} |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4446 g_can_run_ksea <- FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4447 old_oma <- par("oma") |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4448 |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4449 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4450 # squash un-actionable cyclomatic_complexity warning |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4451 if (count_of_treatment_levels < 2) { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4452 # nolint end |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4453 cat( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4454 "ERROR!!!! Cannot perform ANOVA analysis", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4455 "(see next page)\\newpage\n" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4456 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4457 cat( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4458 "ERROR: ANOVA analysis", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4459 "requires two or more factor levels!\n\n\n" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4460 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4461 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4462 cat("\n\n\n\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4463 cat("Unparsed sample names are:\n\n\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4464 "\\begin{quote}\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4465 paste(names(quant_data_imp_qn_log), collapse = "\n\n\n"), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4466 "\n\\end{quote}\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4467 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4468 regex_sample_names <- latex_printable_control_seqs(regex_sample_names) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4469 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4470 cat("\\leavevmode\n\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4471 cat("Parsing rule for SampleNames is", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4472 "\n\n\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4473 "\\text{'", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4474 regex_sample_names, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4475 "'}\n\n\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4476 sep = "" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4477 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4478 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4479 cat("\nParsed sample names are:\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4480 "\\begin{quote}\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4481 paste(sample_name_matches, collapse = "\n\n\n"), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4482 "\n\\end{quote}\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4483 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4484 regex_sample_grouping <- latex_printable_control_seqs(regex_sample_grouping) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4485 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4486 cat("\\leavevmode\n\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4487 cat("Parsing rule for SampleGrouping is", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4488 "\n\n\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4489 "\\text{'", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4490 regex_sample_grouping, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4491 "'}\n\n\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4492 sep = "" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4493 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4494 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4495 cat("\n\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4496 cat("Sample group assignments are:\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4497 "\\begin{quote}\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4498 paste(regmatches(sample_name_matches, rx_match), collapse = "\n\n\n"), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4499 "\n\\end{quote}\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4500 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4501 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4502 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4503 if (print_nb_messages) nbe("computing p_value_data_anova_ps\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4504 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp_qn_log)), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4505 if (print_nb_messages) nbe(see_variable(ncol(quant_data_imp_qn_log)), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4506 if (print_nb_messages) nbe(see_variable(quant_data_imp_qn_log), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4507 if (print_nb_messages) nbe(see_variable(anova_func), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4508 if (print_nb_messages) nbe(see_variable(smpl_trt), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4509 if (print_nb_messages) nbe(see_variable(one_way_all_categories), "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4510 tryCatch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4511 { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4512 p_value_data_anova_ps <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4513 row_apply( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4514 quant_data_imp_qn_log, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4515 anova_func, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4516 grouping_factor = smpl_trt, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4517 one_way_f = one_way_all_categories |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4518 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4519 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4520 error = function(e) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4521 mesg <- paste("Could not compute ANOVA because", e$message) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4522 cat("\n\n", mesg, "\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4523 param_df_noexit(e) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4524 sink(stderr()) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4525 cat("\n\n", mesg, "\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4526 values <- paste(param_df$parameter, "=", param_df$value, collapse = "\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4527 cat(values) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4528 sink() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4529 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4530 exit(code = 1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4531 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4532 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4533 if (print_nb_messages) nbe(see_variable(p_value_data_anova_ps), "\n") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4534 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4535 p_value_data_anova_ps_fdr <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4536 p.adjust(p_value_data_anova_ps, method = "fdr") |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4537 my_ppep_v <- full_data[, 1] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4538 p_value_data <- list( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4539 phosphopeptide = my_ppep_v, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4540 raw_anova_p = p_value_data_anova_ps, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4541 fdr_adjusted_anova_p = p_value_data_anova_ps_fdr, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4542 missing_values = rowSums(is.na(quant_data)), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4543 min_group_obs_count = min_group_obs_count |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4544 ) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4545 p_value_data <- data.frame( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4546 phosphopeptide = my_ppep_v, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4547 raw_anova_p = p_value_data_anova_ps, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4548 fdr_adjusted_anova_p = p_value_data_anova_ps_fdr, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4549 missing_values = rowSums(is.na(quant_data)), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4550 min_group_obs_count = min_group_obs_count |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4551 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4552 p_value_data$quality <- 1.0 / with( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4553 p_value_data, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4554 fdr_adjusted_anova_p + 0.005 / (1 + min_group_obs_count) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4555 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4556 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4557 p_value_data$ranking <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4558 with( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4559 p_value_data, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4560 switch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4561 g_intensity_hm_criteria, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4562 "quality" = order(-quality), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4563 "na_count" = order(missing_values, fdr_adjusted_anova_p), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4564 # the default is "p_value" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4565 order(fdr_adjusted_anova_p) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4566 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4567 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4568 p_value_data <- p_value_data[p_value_data$ranking, , drop = FALSE] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4569 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4570 write.table( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4571 p_value_data, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4572 file = "p_value_data.txt", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4573 sep = "\t", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4574 col.names = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4575 row.names = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4576 quote = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4577 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4578 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4579 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4580 # output ANOVA file to constructed filename, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4581 # e.g. "Outputfile_pST_ANOVA_STEP5.txt" |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4582 # becomes "Outputfile_pST_ANOVA_STEP5_FDR0.05.txt" |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4583 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4584 # Re-output datasets to include p-values |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4585 metadata_plus_p <- cbind(full_data[1:9], p_value_data[, 2:ncol(p_value_data)]) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4586 write.table( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4587 cbind(metadata_plus_p, quant_data_imp), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4588 file = imputed_data_filename, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4589 sep = "\t", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4590 col.names = TRUE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4591 row.names = FALSE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4592 quote = FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4593 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4594 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4595 write.table( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4596 cbind(metadata_plus_p, quant_data_imp_qn_log), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4597 file = imp_qn_lt_data_filenm, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4598 sep = "\t", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4599 col.names = TRUE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4600 row.names = FALSE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4601 quote = FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4602 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4603 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4604 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4605 first_page_suppress <- 1 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4606 number_of_peptides_found <- 0 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4607 cutoff <- val_fdr[1] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4608 for (cutoff in val_fdr) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4609 #loop through FDR cutoffs |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4610 if (number_of_peptides_found > g_intensity_hm_rows - 1) { |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4611 cat("\\leavevmode\n\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4612 break |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4613 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4614 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4615 if (print_trace_messages) { |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4616 cat_variable(cutoff) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4617 cat("\n\n") |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4618 } |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4619 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4620 bool_1 <- (p_value_data$fdr_adjusted_anova_p < cutoff) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4621 bool_2 <- (p_value_data$min_group_obs_count >= g_intensity_min_per_class) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4622 g_can_run_ksea <- g_can_run_ksea || (sum(bool_2) > 0) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4623 bool_4 <- (p_value_data$quality >= params$minQuality) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4624 bool_3 <- as.logical( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4625 as.integer(bool_1) * |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4626 as.integer(bool_2) * |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4627 as.integer(bool_4) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4628 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4629 if (print_trace_messages) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4630 if (length(bool_1) > 30) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4631 cat_variable(bool_1, force_str = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4632 cat_variable(bool_2, force_str = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4633 cat_variable(bool_3, force_str = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4634 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4635 cat_variable(bool_1, suffix = "\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4636 cat_variable(bool_2, suffix = "\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4637 cat_variable(bool_3, suffix = "\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4638 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4639 cat_variable(length(bool_3), digits = 0, suffix = "; ") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4640 cat_variable(sum(bool_3), digits = 0, suffix = "\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4641 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4642 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4643 filtered_p <- |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4644 p_value_data[bool_3, , drop = FALSE] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4645 filtered_p <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4646 filtered_p[!is.na(filtered_p$phosphopeptide), , drop = FALSE] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4647 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4648 if (print_trace_messages) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4649 cat_variable(filtered_p, force_str = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4650 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4651 have_remaining_peptides <- sum(bool_3, na.rm = TRUE) > 0 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4652 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4653 filter_result_string <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4654 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4655 "%s, %s of %0.0f peptides remained having both %s and %s.\n\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4656 "After filtering for ANOVA results", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4657 if (have_remaining_peptides) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4658 as.character(sum(bool_3, na.rm = TRUE)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4659 else |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4660 "none", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4661 length(bool_3), |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4662 adj_p_string <- |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4663 sprintf("adjusted p-value < %s", as.character(signif(cutoff, 2))), |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4664 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4665 "more than %0.0f observations in some groups", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4666 max(0, g_intensity_min_per_class - 1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4667 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4668 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4669 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4670 filtered_data_filtered <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4671 quant_data_imp_qn_log[ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4672 rownames(filtered_p), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4673 , drop = FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4674 ] |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4675 # order by p-value |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4676 filtered_data_filtered <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4677 filtered_data_filtered[ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4678 order(filtered_p$fdr_adjusted_anova_p), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4679 , drop = FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4680 ] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4681 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4682 if (have_remaining_peptides |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4683 && nrow(filtered_p) > 0 |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4684 && nrow(filtered_data_filtered) > 0 |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4685 ) { |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4686 if (first_page_suppress == 1) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4687 first_page_suppress <- 0 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4688 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4689 cat("\\newpage\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4690 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4691 latex_samepage({ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4692 cat(filter_result_string) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4693 if (nrow(filtered_data_filtered) > 1) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4694 cat(subsection_header(sprintf( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4695 "Intensity distributions for %d phosphopeptides, %s\n", |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4696 nrow(filtered_data_filtered), |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4697 adj_p_string |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4698 ))) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4699 } else { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4700 cat( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4701 subsection_header( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4702 sprintf( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4703 "Intensity distribution for one phosphopeptide, %s\n", |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4704 adj_p_string |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4705 ) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4706 ), |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4707 rownames(filtered_data_filtered)[1], |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4708 "\n" |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4709 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4710 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4711 }) # end latex_samepage |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4712 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4713 old_par <- par( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4714 mai = (par("mai") + c(0.7, 0, 0, 0)) * c(1, 1, 0.3, 1), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4715 oma = old_oma * c(1, 1, 0.3, 1), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4716 cex.main = 0.9, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4717 cex.axis = 0.7, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4718 fin = c(9, 7.25) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4719 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4720 # Vertical plot |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4721 colnames(filtered_data_filtered) <- sample_name_matches |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4722 tryCatch( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4723 boxplot( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4724 filtered_data_filtered, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4725 main = "Imputed, normalized intensities", # no line plot |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4726 las = 2, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4727 cex.axis = 0.9 * sample_name_grow, |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4728 col = const_boxplot_fill, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4729 ylab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4730 notch = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4731 varwidth = boxplot_varwidth |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4732 ), |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4733 error = function(e) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4734 print(e) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4735 cat_margins() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4736 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4737 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4738 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4739 par(old_par) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4740 } else { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4741 cat(sprintf( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4742 "%s < %0.2f\n\n\n\n\n", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4743 "No peptides were found to have cutoff adjusted p-value", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4744 cutoff |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4745 )) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4746 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4747 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4748 if (have_remaining_peptides && nrow(filtered_data_filtered) > 0) { |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4749 # Add Phosphopeptide column to anova_filtered table |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4750 # The assumption here is that the first intensity is unique; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4751 # this is a hokey assumption but almost definitely will |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4752 # be true in the real world unless there is a computation |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4753 # error upstream. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4754 anova_filtered_merge <- base::merge( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4755 x = connect_df, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4756 y = filtered_data_filtered, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4757 by.x = "Intensity", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4758 by.y = 1 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4759 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4760 anova_filtered_merge_order <- rownames(filtered_p) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4761 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4762 anova_filtered <- data.frame( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4763 ppep = anova_filtered_merge$Phosphopeptide, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4764 intense = anova_filtered_merge$Intensity, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4765 data = anova_filtered_merge[, 2:number_of_samples + 1] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4766 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4767 colnames(anova_filtered) <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4768 c("Phosphopeptide", colnames(filtered_data_filtered)) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4769 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4770 # Merge qualitative columns into the ANOVA data |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4771 output_table <- data.frame(anova_filtered$Phosphopeptide) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4772 output_table <- base::merge( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4773 x = output_table, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4774 y = data_table_imp_qn_lt, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4775 by.x = "anova_filtered.Phosphopeptide", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4776 by.y = "Phosphopeptide" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4777 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4778 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4779 # Produce heatmap to visualize significance and the effect of imputation |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4780 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4781 cat_hm_heading <- function(m, cutoff) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4782 if (nrow(m) > g_intensity_hm_rows) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4783 cat("\\clearpage\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4784 cat(subsection_header( |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4785 paste( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4786 sprintf("Heatmap for the %d most-significant peptides", |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4787 g_intensity_hm_rows), |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4788 sprintf("whose adjusted p-value < %0.2f\n", cutoff) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4789 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4790 )) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4791 } else { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4792 if (nrow(m) < 2) { |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4793 return(FALSE) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4794 } else { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4795 cat(subsection_header( |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4796 paste( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4797 sprintf("Heatmap for %d usable peptide genes whose", nrow(m)), |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4798 sprintf("adjusted p-value < %0.2f\n", cutoff) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4799 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4800 )) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4801 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4802 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4803 cat("\n\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4804 cat("\n\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4805 return(TRUE) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4806 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4807 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4808 # construct matrix with appropriate rownames |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4809 m <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4810 as.matrix(unimputed_quant_data_log[anova_filtered_merge_order, ]) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4811 nrow_m <- nrow(m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4812 ncol_m <- ncol(m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4813 if (nrow_m > 0) { |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4814 rownames_m <- rownames(m) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4815 q <- data.frame(pepname = rownames_m) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4816 g <- sqldf::sqldf(" |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4817 SELECT q.pepname, substr(met.Gene_Name, 1, 30) AS gene_name |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4818 FROM q, metadata_plus_p AS met |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4819 WHERE q.pepname = met.Phosphopeptide |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4820 ORDER BY q.rowid |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4821 ") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4822 tmp <- sapply( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4823 X = seq_len(nrow(g)), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4824 FUN = function(i) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4825 pre <- strsplit(g$gene_name[i], "; ")[[1]] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4826 rslt <- paste(unique(pre), sep = "; ") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4827 return(rslt) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4828 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4829 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4830 tmp <- unlist(tmp) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4831 tmp <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4832 make.names(tmp, unique = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4833 tmp <- sub( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4834 "No_Gene_Name", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4835 "not_found", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4836 tmp, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4837 fixed = TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4838 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4839 ten_trunc_names <- trunc_ppep(rownames_m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4840 tmp <- sapply( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4841 X = seq_len(nrow_m), |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4842 FUN = function(i) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4843 sprintf( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4844 "(%s) %s", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4845 tmp[i], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4846 ten_trunc_names[i] |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4847 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4848 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4849 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4850 rownames(m) <- tmp |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4851 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4852 # draw the heading and heatmap |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4853 if (nrow_m > 0) { |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4854 number_of_peptides_found <- |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4855 ppep_heatmap( |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4856 m = m, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4857 cutoff = cutoff, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4858 hm_heading_function = cat_hm_heading, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4859 hm_main_title = |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4860 "log(intensities), row-scaled, unimputed, unnormalized", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4861 suppress_row_dendrogram = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4862 master_cex = 0.35, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4863 sepcolor = "black", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4864 colsep = sample_colsep |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4865 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4866 if (number_of_peptides_found > 1) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4867 cat("\\leavevmode\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4868 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4869 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4870 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4871 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4872 } |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4873 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4874 cat("\\leavevmode\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4875 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4876 if (!g_can_run_ksea) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4877 errmsg <- paste("Cannot proceed with KSEA analysis", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4878 "because too many values are missing.") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4879 if (FALSE) cat0( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4880 errmsg, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4881 "\\stepcounter{offset}\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4882 "\\stepcounter{offset}\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4883 "\\stepcounter{offset}\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4884 " in ", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4885 table_href(), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4886 ".\n\n" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4887 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4888 if (FALSE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4889 if (print_nb_messages) nbe(see_variable(p_value_data)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4890 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4891 if (print_nb_messages) nbe(see_variable(p_value_data)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4892 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4893 display_p_value_data <- p_value_data |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4894 display_p_value_data$raw_anova_p <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4895 sprintf("%0.3g", display_p_value_data$raw_anova_p) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4896 display_p_value_data$fdr_adjusted_anova_p <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4897 sprintf("%0.3g", display_p_value_data$fdr_adjusted_anova_p) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4898 display_p_value_data$quality <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4899 sprintf("%0.3g", display_p_value_data$quality) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4900 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4901 headers_1st_line <- |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4902 c("", "Raw ANOVA", "FDR-adj.", "Missing", "Min. #", |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4903 "", "") |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4904 headers_2nd_line <- |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4905 c("Phosphopeptide", "p-value", "p-value", "values", "group-obs", |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
4906 "Quality", "Ranking") |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4907 data_frame_tabbing_latex( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4908 x = display_p_value_data, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4909 tabstops = c(2.75, 0.80, 0.80, 0.5, 0.6, 0.60), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4910 use_subsubsection_header = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4911 headings = c(headers_1st_line, headers_2nd_line), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4912 caption = "ANOVA results" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4913 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4914 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4915 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4916 data_frame_tabbing_latex( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4917 x = save_sample_treatment_df, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4918 tabstops = c(1.25, 1.25), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4919 caption = "Sample classes", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4920 use_subsubsection_header = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4921 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4922 param_df_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4923 knitr::knit_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4924 return(invisible(-1)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4925 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4926 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4927 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4928 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4929 ```{r sqlite, echo = FALSE, fig.dim = c(9, 10), results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4930 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4931 if (g_can_run_ksea && count_of_treatment_levels > 1) { |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4932 # Prepare two-way contrasts with adjusted p-values |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4933 # Strategy: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4934 # - use imputed, log-transformed data: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4935 # - remember this when computing log2(fold-change) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4936 # - each contrast is between a combination of trt levels |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4937 # - for each contrast, compute samples that are members |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4938 # - compute one-way test: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4939 # - use `oneway.test` (Welch test) if numbers of samples |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4940 # are not equivalent between trt levels |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4941 # - otherwise, aov is fine but offers no advantage |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4942 # - adjust p-value, assuming that |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4943 # (# of pppeps)*(# of contrasts) tests were performed |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4944 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4945 # Each contrast is between a combination of trt levels |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4946 m2 <- combn( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4947 x = seq_len(length(levels(smpl_trt))), |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4948 m = 2, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4949 simplify = TRUE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4950 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4951 contrast_count <- ncol(m2) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4952 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4953 # For each contrast, compute samples that are members |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4954 # - local function to construct a data.frame for each contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4955 # - the contrast in the first "column" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4956 f_m2 <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4957 function(cntrst, lvl1, lvl2) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4958 return( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4959 data.frame( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4960 contrast = cntrst, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4961 level = smpl_trt[ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4962 smpl_trt %in% |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4963 levels(smpl_trt)[c(lvl1, lvl2)] |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4964 ], |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4965 label = sample_name_matches[ |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4966 smpl_trt %in% |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4967 levels(smpl_trt)[c(lvl1, lvl2)] |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4968 ] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4969 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4970 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4971 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4972 # - compute a df for each contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4973 sample_level_dfs <- lapply( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4974 X = 1:contrast_count, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4975 FUN = function(i) f_m2(i, m2[1, i], m2[2, i]) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4976 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4977 # - compute a single df for all contrasts |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4978 combined_contrast_df <- Reduce(f = rbind, x = sample_level_dfs) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4979 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4980 # - dispose objects to free resources |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4981 rm(sample_level_dfs) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4982 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4983 # - write the df to a DB for later join-per-contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4984 db <- RSQLite::dbConnect(RSQLite::SQLite(), ksea_app_prep_db) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4985 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4986 RSQLite::dbWriteTable( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4987 conn = db, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4988 name = "contrast", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4989 value = combined_contrast_df, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4990 overwrite = TRUE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4991 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4992 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4993 # Create UK for insert |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4994 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4995 CREATE UNIQUE INDEX IF NOT EXISTS contrast__uk__idx |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4996 ON contrast(contrast, label); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4997 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4998 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4999 # Create indexes for join |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5000 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5001 -- index for join in contrast_ppep_smpl_qnlt on a.label < b.label |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5002 CREATE INDEX IF NOT EXISTS contrast__label__idx |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5003 ON contrast(label); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5004 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5005 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5006 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5007 -- index for joining two contrast_lvl_ppep_avg_quant on contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5008 CREATE INDEX IF NOT EXISTS contrast__contrast__idx |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5009 ON contrast(contrast); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5010 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5011 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5012 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5013 -- index for joining two contrast_lvl_ppep_avg_quant on phophospep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5014 CREATE INDEX IF NOT EXISTS contrast__level__idx |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5015 ON contrast(level); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5016 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5017 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5018 # - dispose objects to free resources |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5019 rm(combined_contrast_df) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5020 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5021 # Use imputed, log-transformed data |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5022 # - remember that this was donoe when computing log2(fold-change) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5023 # - melt data matrix for use in later join-per-contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5024 casted <- cbind( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5025 data.frame(vrbl = rownames(quant_data_imp_qn_log)), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5026 quant_data_imp_qn_log |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5027 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5028 quant_data_imp_qn_log_melted <- reshape2::melt( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5029 casted, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5030 id.vars = "vrbl" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5031 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5032 colnames(quant_data_imp_qn_log_melted) <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5033 c("phosphopep", "sample", "quant") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5034 # - dispose objects to free resources |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5035 rm(casted) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5036 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5037 # - write the df to a DB for use in later join-per-contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5038 RSQLite::dbWriteTable( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5039 conn = db, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5040 name = "ppep_smpl_qnlt", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5041 value = quant_data_imp_qn_log_melted, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5042 overwrite = TRUE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5043 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5044 # Create UK for insert |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5045 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5046 CREATE UNIQUE INDEX IF NOT EXISTS ppep_smpl_qnlt__uk__idx |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5047 ON ppep_smpl_qnlt(phosphopep, sample); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5048 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5049 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5050 # Create index for join |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5051 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5052 -- index for join in contrast_ppep_smpl_qnlt |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5053 CREATE INDEX IF NOT EXISTS ppep_smpl_qnlt__sample__idx |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5054 ON ppep_smpl_qnlt(sample); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5055 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5056 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5057 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5058 -- index for joining two contrast_lvl_ppep_avg_quant on phopho.pep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5059 CREATE INDEX IF NOT EXISTS ppep_smpl_qnlt__phosphopep__idx |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5060 ON ppep_smpl_qnlt(phosphopep); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5061 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5062 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5063 # - dispose objects to free resources |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5064 rm(quant_data_imp_qn_log_melted) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5065 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5066 # - drop views if exist |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5067 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5068 -- drop view dependent on contrast_lvl_ppep_avg_quant |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5069 DROP VIEW IF EXISTS v_contrast_log2_fc; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5070 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5071 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5072 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5073 -- drop table dependent on contrast_ppep_smpl_qnlt |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5074 DROP TABLE IF EXISTS contrast_lvl_ppep_avg_quant; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5075 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5076 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5077 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5078 DROP TABLE IF EXISTS contrast_lvl_lvl_metadata; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5079 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5080 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5081 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5082 DROP VIEW IF EXISTS v_contrast_lvl_metadata; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5083 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5084 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5085 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5086 -- drop view dependent on contrast_ppep_smpl_qnlt |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5087 DROP VIEW IF EXISTS v_contrast_lvl_ppep_avg_quant; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5088 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5089 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5090 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5091 DROP VIEW IF EXISTS v_contrast_lvl_lvl; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5092 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5093 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5094 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5095 -- drop view upon which other views depend |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5096 DROP VIEW IF EXISTS contrast_ppep_smpl_qnlt; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5097 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5098 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5099 # - create view |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5100 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5101 -- view contrast_ppep_smpl_qnlt is used for each phopshopep to |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5102 -- compute p-value for test of trt effect for two trt levels |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5103 CREATE VIEW contrast_ppep_smpl_qnlt |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5104 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5105 SELECT contrast, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5106 level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5107 phosphopep, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5108 sample, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5109 quant |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5110 FROM contrast AS c, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5111 ppep_smpl_qnlt AS q |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5112 WHERE q.sample = c.label |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5113 ORDER BY contrast, level, phosphopep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5114 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5115 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5116 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5117 # - create simplification views |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5118 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5119 CREATE VIEW v_contrast_lvl_metadata |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5120 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5121 SELECT contrast, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5122 level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5123 group_concat(label, ';') AS samples |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5124 FROM contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5125 GROUP BY contrast, level |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5126 /* view v_contrast_lvl_metadata is used |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5127 to simplify creation of table contrast_lvl_lvl_metadata */ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5128 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5129 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5130 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5131 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5132 CREATE VIEW v_contrast_lvl_ppep_avg_quant |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5133 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5134 SELECT contrast, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5135 level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5136 phosphopep, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5137 avg(quant) AS avg_quant |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5138 FROM contrast_ppep_smpl_qnlt |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5139 GROUP BY contrast, level, phosphopep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5140 /* view v_contrast_lvl_ppep_avg_quant is used |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5141 to simplify view v_contrast_log2_fc */ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5142 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5143 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5144 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5145 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5146 # - create contrast-metadata table |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5147 if (print_nb_messages) nbe("CREATE TABLE contrast_lvl_lvl_metadata") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5148 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5149 CREATE TABLE contrast_lvl_lvl_metadata |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5150 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5151 SELECT DISTINCT |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5152 a.contrast AS ab_contrast, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5153 a.level AS a_level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5154 b.level AS b_level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5155 a.samples AS a_samples, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5156 b.samples AS b_samples, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5157 'log2(level_'||a.level||'/level_'||b.level||')' |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5158 AS fc_description |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5159 FROM v_contrast_lvl_metadata AS a, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5160 v_contrast_lvl_metadata AS b |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5161 WHERE a.contrast = b.contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5162 AND a.level > b.level |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5163 /* view v_contrast_lvl_lvl is used |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5164 to simplify view v_contrast_log2_fc */ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5165 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5166 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5167 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5168 # - create pseudo-materialized view table |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5169 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5170 CREATE VIEW v_contrast_lvl_lvl |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5171 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5172 SELECT DISTINCT |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5173 a.contrast AS ab_contrast, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5174 a.level AS a_level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5175 b.level AS b_level |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5176 FROM contrast AS a, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5177 contrast AS b |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5178 WHERE a.contrast = b.contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5179 AND a.level > b.level |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5180 /* view v_contrast_lvl_lvl is used |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5181 to simplify view v_contrast_log2_fc */ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5182 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5183 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5184 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5185 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5186 # - create view to compute log2(fold-change) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5187 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5188 CREATE VIEW v_contrast_log2_fc |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5189 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5190 SELECT ab.ab_contrast AS contrast, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5191 m.a_level AS a_level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5192 c.avg_quant AS a_quant, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5193 m.a_samples AS a_samples, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5194 ab.b_level AS b_level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5195 d.avg_quant AS b_quant, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5196 m.b_samples AS b_samples, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5197 m.fc_description AS fc_description, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5198 3.32193 * ( d.avg_quant - c.avg_quant) AS log2_fc, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5199 d.phosphopep AS phosphopep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5200 FROM contrast_lvl_lvl_metadata AS m, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5201 v_contrast_lvl_ppep_avg_quant AS d, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5202 v_contrast_lvl_lvl AS ab |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5203 INNER JOIN v_contrast_lvl_ppep_avg_quant AS c |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5204 ON c.contrast = ab.ab_contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5205 AND c.level = ab.a_level |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5206 WHERE d.contrast = ab.ab_contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5207 AND m.ab_contrast = ab.ab_contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5208 AND d.level = ab.b_level |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5209 AND d.phosphopep = c.phosphopep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5210 /* view to compute log2(fold-change) */ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5211 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5212 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5213 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5214 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5215 # For each contrast, compute samples that are members |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5216 # compute one-way test: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5217 # - use `oneway.test` (Welch test) if numbers of samples |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5218 # are not equivalent between trt levels |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5219 # - otherwise, aov is fine but offers no advantage |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5220 for (contrast in contrast_count:2) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5221 invisible(contrast) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5222 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5223 for (contrast in 1:contrast_count) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5224 contrast_df <- sqldf::sqldf( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5225 x = paste0(" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5226 SELECT level, phosphopep, sample, quant |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5227 FROM contrast_ppep_smpl_qnlt |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5228 WHERE contrast = ", contrast, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5229 ORDER BY phosphopep, level, sample |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5230 "), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5231 connection = db |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5232 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5233 contrast_cast <- reshape2::dcast( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5234 data = contrast_df, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5235 formula = phosphopep ~ sample, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5236 value.var = "quant" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5237 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5238 contrast_cast_ncol <- ncol(contrast_cast) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5239 contrast_cast_data <- contrast_cast[, 2:contrast_cast_ncol] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5240 contrast_cast_samples <- colnames(contrast_cast_data) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5241 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5242 # - order grouping_factor by order of sample columns of contrast_cast_data |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5243 grouping_factor <- sqldf::sqldf( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5244 x = paste0(" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5245 SELECT sample, level |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5246 FROM contrast_ppep_smpl_qnlt |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5247 WHERE contrast = ", contrast, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5248 ORDER BY phosphopep, level, sample |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5249 LIMIT ", contrast_cast_ncol - 1 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5250 ), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5251 connection = db |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5252 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5253 rownames(grouping_factor) <- grouping_factor$sample |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5254 grouping_factor <- grouping_factor[, "level", drop = FALSE] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5255 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5256 # - run the two-level (one-way) test |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5257 p_value_data_contrast_ps <- |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5258 row_apply( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5259 x = contrast_cast_data, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5260 fun = anova_func, |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5261 grouping_factor = |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5262 as.factor(grouping_factor$level), # anova_func arg2 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5263 one_way_f = one_way_two_categories, # anova_func arg3 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5264 simplify = TRUE # TRUE is the default for simplify |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5265 ) |
|
2
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5266 |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5267 if (!is.null(p_value_data_contrast_ps)) { |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5268 contrast_data_adj_p_values <- |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5269 p.adjust( |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5270 p = p_value_data_contrast_ps, |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5271 method = "fdr", |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5272 n = length(p_value_data_contrast_ps) # this is the default, length(p) |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5273 ) |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5274 |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5275 # - compute the fold-change |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5276 contrast_p_df <- |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5277 data.frame( |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5278 contrast = contrast, |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5279 phosphopep = contrast_cast$phosphopep, |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5280 p_value_raw = p_value_data_contrast_ps, |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5281 p_value_adj = contrast_data_adj_p_values |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5282 ) |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5283 db_write_table_overwrite <- (contrast < 2) |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5284 db_write_table_append <- !db_write_table_overwrite |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5285 RSQLite::dbWriteTable( |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5286 conn = db, |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5287 name = "contrast_ppep_p_val", |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5288 value = contrast_p_df, |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5289 append = db_write_table_append |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5290 ) |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5291 # Create UK for insert |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5292 ddl_exec(db, " |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5293 CREATE UNIQUE INDEX IF NOT EXISTS contrast_ppep_p_val__uk__idx |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5294 ON contrast_ppep_p_val(phosphopep, contrast); |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5295 " |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5296 ) |
|
2
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
5297 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5298 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5299 # Perhaps this could be done more elegantly using unique keys |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5300 # or creating the tables before saving data to them, but this |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5301 # is fast and, if the database exists on disk rather than in |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5302 # memory, it doesn't stress memory. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5303 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5304 CREATE TEMP table contrast_log2_fc |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5305 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5306 SELECT * |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5307 FROM v_contrast_log2_fc |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5308 ORDER BY contrast, phosphopep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5309 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5310 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5311 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5312 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5313 CREATE TEMP table ppep_p_val |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5314 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5315 SELECT p_value_raw, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5316 p_value_adj, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5317 contrast AS p_val_contrast, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5318 phosphopep AS p_val_ppep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5319 FROM contrast_ppep_p_val |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5320 ORDER BY contrast, phosphopep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5321 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5322 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5323 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5324 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5325 DROP TABLE IF EXISTS contrast_log2_fc_p_val |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5326 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5327 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5328 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5329 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5330 CREATE TABLE contrast_log2_fc_p_val |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5331 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5332 SELECT a.*, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5333 b.p_value_raw, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5334 b.p_value_adj, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5335 b.p_val_contrast, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5336 b.p_val_ppep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5337 FROM contrast_log2_fc a, ppep_p_val b |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5338 WHERE a.rowid = b.rowid |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5339 AND a.phosphopep = b.p_val_ppep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5340 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5341 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5342 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5343 # Create UK |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5344 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5345 CREATE UNIQUE INDEX IF NOT EXISTS contrast_log2_fc_p_val__uk__idx |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5346 ON contrast_log2_fc_p_val(phosphopep, contrast); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5347 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5348 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5349 # Create indices for future queries |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5350 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5351 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__contrast__idx |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5352 ON contrast_log2_fc_p_val(contrast); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5353 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5354 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5355 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5356 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__phosphopep__idx |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5357 ON contrast_log2_fc_p_val(phosphopep); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5358 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5359 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5360 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5361 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__p_value_raw__idx |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5362 ON contrast_log2_fc_p_val(p_value_raw); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5363 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5364 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5365 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5366 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__p_value_adj__idx |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5367 ON contrast_log2_fc_p_val(p_value_adj); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5368 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5369 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5370 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5371 DROP VIEW IF EXISTS v_contrast_log2_fc_p_val |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5372 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5373 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5374 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5375 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5376 CREATE VIEW v_contrast_log2_fc_p_val |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5377 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5378 SELECT contrast, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5379 a_level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5380 a_samples, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5381 b_level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5382 b_samples, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5383 a_quant, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5384 b_quant, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5385 fc_description, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5386 log2_fc, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5387 p_value_raw, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5388 p_value_adj, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5389 phosphopep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5390 FROM contrast_log2_fc_p_val |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5391 ORDER BY contrast, phosphopep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5392 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5393 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5394 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5395 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5396 DROP TABLE IF EXISTS kseaapp_metadata |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5397 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5398 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5399 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5400 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5401 CREATE TABLE kseaapp_metadata |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5402 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5403 WITH extended(deppep, ppep, gene_name, uniprot_id, phosphoresidue) AS ( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5404 SELECT DISTINCT |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5405 deppep.seq, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5406 ppep.seq, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5407 GeneName||';', |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5408 UniProtID||';', |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5409 PhosphoResidue||';' |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5410 FROM |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5411 ppep, deppep, mrgfltr_metadata |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5412 WHERE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5413 mrgfltr_metadata.ppep_id = ppep.id |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5414 AND |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5415 ppep.deppep_id = deppep.id |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5416 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5417 SELECT |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5418 ppep AS `ppep`, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5419 SUBSTR(uniprot_id, 1, INSTR(uniprot_id,';') - 1 ) AS `Protein`, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5420 SUBSTR(gene_name, 1, INSTR(gene_name,';') - 1 ) AS `Gene`, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5421 deppep AS `Peptide`, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5422 REPLACE( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5423 REPLACE( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5424 SUBSTR(phosphoresidue, 1, INSTR(phosphoresidue,';') - 1 ), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5425 'p', |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5426 '' |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5427 ), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5428 ', ', |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5429 ';' |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5430 ) AS `Residue.Both` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5431 FROM extended |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5432 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5433 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5434 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5435 # Create indexes for join |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5436 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5437 CREATE INDEX IF NOT EXISTS kseaapp_metadata__ppep__idx |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5438 ON kseaapp_metadata(ppep); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5439 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5440 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5441 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5442 DROP VIEW IF EXISTS v_kseaapp_contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5443 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5444 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5445 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5446 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5447 CREATE VIEW v_kseaapp_contrast |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5448 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5449 SELECT a.*, b.Protein, b.Gene, b.Peptide, b.`Residue.Both` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5450 FROM v_contrast_log2_fc_p_val a, kseaapp_metadata b |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5451 WHERE b.ppep = a.phosphopep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5452 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5453 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5454 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5455 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5456 DROP VIEW IF EXISTS v_kseaapp_input |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5457 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5458 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5459 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5460 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5461 CREATE VIEW v_kseaapp_input |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5462 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5463 SELECT v.contrast, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5464 v.phosphopep, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5465 m.`Protein`, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5466 m.`Gene`, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5467 m.`Peptide`, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5468 m.`Residue.Both`, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5469 v.p_value_raw AS `p`, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5470 v.log2_fc AS `FC` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5471 FROM kseaapp_metadata AS m, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5472 v_contrast_log2_fc_p_val AS v |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5473 WHERE m.ppep = v.phosphopep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5474 AND NOT m.`Gene` = 'No_Gene_Name' |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5475 AND NOT v.log2_fc = 0 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5476 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5477 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5478 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5479 # We are done with DDL and insertion |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5480 RSQLite::dbDisconnect(db) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5481 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5482 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5483 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5484 ```{r echo = FALSE, results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5485 cat("\\newpage\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5486 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5487 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5488 # KSEA Analysis Summaries |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5489 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5490 Results of Kinase-Substrate Enrichment Analysis are presented here, if the substrates for any kinases are relatively enriched. Enrichments are found by the CRAN `KSEAapp` package: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5491 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5492 - The package is available on CRAN, at https://cran.r-project.org/package=KSEAapp |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5493 - The method used is described in Casado et al. (2013) [doi:10.1126/scisignal.2003573](https://doi.org/10.1126/scisignal.2003573) and Wiredja et al (2017) [doi:10.1093/bioinformatics/btx415](https://doi.org/10.1093/bioinformatics/btx415). |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5494 - An online alternative (supporting only analysis of human data) is available at [https://casecpb.shinyapps.io/ksea/](https://casecpb.shinyapps.io/ksea/). |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5495 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5496 For each kinase, $i$, and each two-way contrast of treatments, $j$, an enrichment $z$-score is computed as: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5497 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5498 $$ |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5499 \text{kinase enrichment }z\text{-score}_{j,i} = \frac{(\overline{`r sfc`}_{j,i} - \overline{`r pfc`}_j)\sqrt{m_{j,i}}}{\delta_j} |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5500 $$ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5501 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5502 and fold-enrichment is computed as: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5503 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5504 $$ |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5505 \text{Enrichment}_{j,i} = \frac{\overline{`r sfc`}_{j,i}}{\overline{`r pfc`}_j} |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5506 $$ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5507 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5508 where: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5509 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5510 - $\overline{`r sfc`}_{j,i}$ is the mean `r pfc_txt` in intensities of known substrates of the kinase $i$ in contrast $j$, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5511 - $\overline{`r pfc`}_j$ is the mean `r pfc_txt` of all phosphosites identified in contrast $j$, and |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5512 - $m_{j,i}$ is the total number of phosphosite substrates of kinase $i$ identified in contrast $j$, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5513 - $\delta_j$ is the standard deviation of the $\log_2 (\text{fold-change})$ for contrast $j$ across all phosphosites in the dataset. |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5514 - Note that the absolute value of fold-change is used so that both increased and decreased substrates of a kinase will contribute to its enrichment score. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5515 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5516 $\text{FDR}_{j,i}$ is the False Discovery Rate corrected kinase enrichment score. |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5517 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5518 Color intensity in heatmaps reflects magnitude of $z$-score for enrichment of respective kinase in respective contrast; hue reflects the sign of the $z$-score (blue, negative; red, positive). |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5519 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5520 Asterisks in heatmaps reflect enrichments that are significant at `r ksea_cutoff_statistic` < `r ksea_cutoff_threshold`. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5521 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5522 - Kinase names are generally as presented at Phospho.ELM [http://phospho.elm.eu.org/kinases.html](http://phospho.elm.eu.org/kinases.html) (when available), although Phospho.ELM data are not yet incorporated into this analysis. |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5523 - Kinase names having the suffix '(HPRD)' are as presented at [http://hprd.org/serine_motifs](http://hprd.org/serine_motifs) and [http://hprd.org/tyrosine_motifs](http://hprd.org/tyrosine_motifs) and are as originally reported in the Amanchy et al., 2007 (doi: [10.1038/nbt0307-285](https://doi.org/10.1038/nbt0307-285)). |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5524 - Kinase-substrate data were also taken from [http://networkin.science/download.shtml](http://networkin.science/download.shtml) and from PhosphoSitePlus [https://www.phosphosite.org/staticDownloads](https://www.phosphosite.org/staticDownloads). |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5525 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5526 For each enriched kinase, a heatmap showing the intensities is presented for up to `r g_intensity_hm_rows` substrates, i.e., those substrates having the highest"quality". |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5527 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5528 Where possible, a heatmap of the correlations among these the selected substrates is also presented; if correlations cannot be computed (because of too many missing values), then the covariances are heatmapped for substrates having a variance greater than 1. |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5529 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5530 ```{r ksea, echo = FALSE, fig.dim = c(12, 14.5), results = 'asis'} |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5531 cat("\\clearpage\n") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5532 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5533 db <- RSQLite::dbConnect(RSQLite::SQLite(), ksea_app_prep_db) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5534 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5535 # -- eliminate the table that's about to be defined |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5536 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5537 DROP TABLE IF EXISTS site_metadata; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5538 ") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5539 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5540 # -- define the site_metadata table |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5541 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5542 CREATE TABLE site_metadata( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5543 id INTEGER PRIMARY KEY |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5544 , site_type_id INTEGER REFERENCES site_type(id) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5545 , full TEXT UNIQUE ON CONFLICT IGNORE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5546 , abbrev TEXT |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5547 , pattern TEXT |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5548 , motif TEXT |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5549 ); |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5550 ") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5551 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5552 # -- populate the table with initial values |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5553 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5554 INSERT INTO site_metadata(full, abbrev, site_type_id) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5555 SELECT DISTINCT kinase_map, kinase_map, site_type_id |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5556 FROM ppep_gene_site |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5557 ORDER BY kinase_map; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5558 ") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5559 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5560 # -- drop bogus KSData view if exists |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5561 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5562 DROP VIEW IF EXISTS ks_data_v; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5563 ") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5564 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5565 # -- create view to serve as an impostor for KSEAapp::KSData |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5566 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5567 CREATE VIEW IF NOT EXISTS ks_data_v |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5568 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5569 SELECT |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5570 'NA' AS KINASE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5571 'NA' AS KIN_ACC_ID, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5572 kinase_map AS GENE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5573 'NA' AS KIN_ORGANISM, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5574 'NA' AS SUBSTRATE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5575 0 AS SUB_GENE_ID, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5576 'NA' AS SUB_ACC_ID, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5577 gene_names AS SUB_GENE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5578 'NA' AS SUB_ORGANISM, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5579 phospho_peptide AS SUB_MOD_RSD, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5580 0 AS SITE_GROUP_ID, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5581 'NA' AS 'SITE_7AA', |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5582 2 AS networkin_score, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5583 type_name AS Source |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5584 FROM ppep_gene_site_view; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5585 ") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5586 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5587 contrast_metadata_df <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5588 sqldf::sqldf("select * from contrast_lvl_lvl_metadata", connection = db) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5589 rslt <- new_env() |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5590 rslt$score_list <- list() |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5591 rslt$name_list <- list() |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5592 rslt$longname_list <- list() |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5593 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5594 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5595 DROP TABLE IF EXISTS contrast_ksea_scores; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5596 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5597 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5598 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5599 next_index <- 0 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5600 err_na_subscr_df_const <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5601 "missing values are not allowed in subscripted assignments of data frames" |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5602 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5603 for (i_cntrst in seq_len(nrow(contrast_metadata_df))) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5604 cntrst_a_level <- contrast_metadata_df[i_cntrst, "a_level"] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5605 cntrst_b_level <- contrast_metadata_df[i_cntrst, "b_level"] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5606 cntrst_fold_change <- contrast_metadata_df[i_cntrst, 6] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5607 contrast_label <- sprintf("%s -> %s", cntrst_b_level, cntrst_a_level) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5608 contrast_longlabel <- ( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5609 sprintf( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5610 "Class %s -> Class %s", |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5611 contrast_metadata_df[i_cntrst, "b_level"], |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5612 contrast_metadata_df[i_cntrst, "a_level"] |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5613 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5614 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5615 kseaapp_input <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5616 sqldf::sqldf( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5617 x = sprintf(" |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5618 SELECT `Protein`,`Gene`,`Peptide`,phosphopep AS `Residue.Both`,`p`,`FC` |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5619 FROM v_kseaapp_input |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5620 WHERE contrast = %d |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5621 ", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5622 i_cntrst |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5623 ), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5624 connection = db |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5625 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5626 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5627 pseudo_ksdata <- dbReadTable(db, "ks_data_v") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5628 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5629 # This hack is because SQL table has the log2-transformed values |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5630 kseaapp_input[, "FC"] <- 2 ** kseaapp_input[, "FC", drop = TRUE] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5631 main_title <- ( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5632 sprintf( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5633 "Change from treatment %s to treatment %s", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5634 contrast_metadata_df[i_cntrst, "b_level"], |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5635 contrast_metadata_df[i_cntrst, "a_level"] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5636 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5637 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5638 sub_title <- contrast_longlabel |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5639 tryCatch( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5640 expr = { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5641 ksea_scores_rslt <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5642 ksea_scores( |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5643 ksdata = pseudo_ksdata, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5644 px = kseaapp_input, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5645 networkin = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5646 networkin_cutoff = 2, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5647 minimum_substrate_count = ksea_min_substrate_count |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5648 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5649 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5650 if (FALSE) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5651 ksea_scores_rslt <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5652 ksea_scores_rslt[ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5653 ksea_scores_rslt$m >= ksea_min_substrate_count, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5654 , |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5655 drop = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5656 ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5657 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5658 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5659 if (FALSE) { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5660 if (print_nb_messages) nbe( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5661 "Output contents of `ksea_scores_rslt` table\n") |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5662 cat_variable(ksea_scores_rslt) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5663 cat("\n\\clearpage\n") |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5664 data_frame_tabbing_latex( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5665 x = ksea_scores_rslt, |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5666 tabstops = c(1.8, 0.8, 0.8, 0.3, 0.8, 0.8), |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5667 caption = paste("KSEA scores for contrast ", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5668 cntrst_b_level, "to", cntrst_a_level), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5669 use_subsubsection_header = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5670 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5671 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5672 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5673 if (0 < sum(!is.nan(ksea_scores_rslt$FDR))) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5674 next_index <- 1 + next_index |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5675 rslt$score_list[[next_index]] <- ksea_scores_rslt |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5676 rslt$name_list[[next_index]] <- contrast_label |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5677 rslt$longname_list[[next_index]] <- contrast_longlabel |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5678 ksea_low_fdr_print( |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5679 rslt = rslt, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5680 i_cntrst = i_cntrst, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5681 i = next_index, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5682 a_level = cntrst_a_level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5683 b_level = cntrst_b_level, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5684 fold_change = cntrst_fold_change, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5685 caption = contrast_longlabel |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5686 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5687 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5688 }, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5689 error = function(e) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5690 str(e) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5691 cat_margins() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5692 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5693 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5694 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5695 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5696 plotted_kinases <- NULL |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5697 if (g_can_run_ksea && length(rslt$score_list) > 1) { |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5698 for (i in seq_len(length(ksea_heatmap_titles))) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5699 hdr <- ksea_heatmap_titles[[i]] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5700 which_kinases <- i |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5701 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5702 cat("\\clearpage\n\\begin{center}\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5703 if (i == const_ksea_astrsk_kinases) { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5704 cat(subsection_header(hdr)) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5705 } else { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5706 cat(subsection_header(hdr)) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5707 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5708 cat("\\end{center}\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5709 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5710 plotted_kinases <- ksea_heatmap( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5711 # the data frame outputs from the KSEA.Scores() function, in list format |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5712 score_list = rslt$score_list, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5713 # a character vector of all the sample names for heatmap annotation: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5714 # - the names must be in the same order as the data in score_list |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5715 # - please avoid long names, as they may get cropped in the final image |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5716 sample_labels = rslt$name_list, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5717 # character string of either "p.value" or "FDR" indicating the data column |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5718 # to use for marking statistically significant scores |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5719 stats = c("p.value", "FDR")[2], |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5720 # a numeric value between 0 and infinity indicating the min. number of |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5721 # substrates a kinase must have to be included in the heatmap |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5722 m_cutoff = 1, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5723 # a numeric value between 0 and 1 indicating the p-value/FDR cutoff |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5724 # for indicating significant kinases in the heatmap |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5725 p_cutoff = params$kseaCutoffThreshold, |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5726 # a binary input of TRUE or FALSE, indicating whether or not to perform |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5727 # hierarchical clustering of the sample columns |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5728 sample_cluster = TRUE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5729 # a binary input of TRUE or FALSE, indicating whether or not to export |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5730 # the heatmap as a .png image into the working directory |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5731 export = FALSE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5732 # additional arguments to gplots::heatmap.2, such as: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5733 # - main: main title of plot |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5734 # - xlab: x-axis label |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5735 # - ylab: y-axis label |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5736 xlab = "Contrast", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5737 ylab = "Kinase", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5738 # print which kinases: |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5739 # - 1 : all kinases |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5740 # - 2 : significant kinases |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5741 # - 3 : non-significant kinases |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5742 which_kinases = which_kinases, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5743 margins = c(7, 15) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5744 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5745 if (!is.null(plotted_kinases)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5746 cat("\\begin{center}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5747 if (which_kinases != const_ksea_nonastrsk_kinases) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5748 cat("Asterisks reflect significance.\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5749 cat("\\end{center}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5750 } |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5751 } # end for (i in ... |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5752 } # end if (length ... |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5753 ``` |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5754 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5755 ```{r kseabar_calc, echo = FALSE, fig.dim = c(9.5, 6), results = 'asis'} |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5756 ksea_prints <- list() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5757 ksea_barplots <- list() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5758 for (i_cntrst in seq_len(length(rslt$score_list))) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5759 next_index <- i_cntrst |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5760 cntrst_a_level <- contrast_metadata_df[i_cntrst, "a_level"] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5761 cntrst_b_level <- contrast_metadata_df[i_cntrst, "b_level"] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5762 cntrst_fold_change <- contrast_metadata_df[i_cntrst, 6] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5763 contrast_label <- sprintf("%s -> %s", cntrst_b_level, cntrst_a_level) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5764 contrast_longlabel <- ( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5765 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5766 "Class %s -> Class %s", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5767 contrast_metadata_df[i_cntrst, "b_level"], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5768 contrast_metadata_df[i_cntrst, "a_level"] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5769 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5770 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5771 main_title <- ( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5772 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5773 "Change from treatment %s to treatment %s", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5774 contrast_metadata_df[i_cntrst, "b_level"], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5775 contrast_metadata_df[i_cntrst, "a_level"] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5776 ) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5777 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5778 sub_title <- contrast_longlabel |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5779 tryCatch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5780 expr = { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5781 ksea_scores_rslt <- rslt$score_list[[next_index]] |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5782 if (print_nb_messages) nbe(see_variable(ksea_scores_rslt)) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5783 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5784 if (0 < sum(!is.nan(ksea_scores_rslt$FDR))) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5785 sink(deferred <- file()) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5786 ksea_low_fdr_print( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5787 rslt = rslt, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5788 i_cntrst = i_cntrst, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5789 i = next_index, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5790 a_level = cntrst_a_level, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5791 b_level = cntrst_b_level, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5792 fold_change = cntrst_fold_change, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5793 caption = contrast_longlabel, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5794 write_db = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5795 anchor = const_table_anchor_t |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5796 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5797 cat("\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5798 sink() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5799 lines <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5800 paste( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5801 readLines(deferred, warn = FALSE), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5802 collapse = "\n" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5803 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5804 close(deferred) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5805 sq_put(ksea_prints, lines) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5806 sink(stderr()) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5807 cat("\n---\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5808 cat_variable(ksea_prints) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5809 barplot_closure <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5810 ksea_low_fdr_barplot_factory( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5811 rslt = rslt, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5812 i_cntrst = i_cntrst, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5813 i = next_index, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5814 a_level = cntrst_a_level, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5815 b_level = cntrst_b_level, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5816 fold_change = cntrst_fold_change, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5817 caption = contrast_longlabel |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5818 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5819 if (rlang::is_closure(barplot_closure)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5820 sq_put(ksea_barplots, barplot_closure) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5821 else |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5822 sq_put(ksea_barplots, no_op) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5823 str(ksea_barplots) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5824 cat("\n...\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5825 sink() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5826 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5827 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5828 error = function(e) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5829 str(e) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5830 cat_margins() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5831 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5832 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5833 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5834 ``` |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5835 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5836 ```{r phosphoelm_kinase_upid_desc, echo = FALSE, fig.dim = c(12, 13.7), results = 'asis'} |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5837 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5838 have_kinase_descriptions <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5839 if (!is.null(bzip2df(kinase_uprt_desc_lut, kinase_uprt_desc_lut_bz2)) && |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5840 !is.null(bzip2df(kinase_name_uprt_lut, kinase_name_uprt_lut_bz2)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5841 ) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5842 rownames(kinase_uprt_desc_lut) <- kinase_uprt_desc_lut$UniProtID |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5843 kinase_name_to_desc_uprt <- function(s) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5844 rslt <- NULL |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5845 tryCatch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5846 { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5847 which_rows <- eval(s == kinase_name_uprt_lut$kinase) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5848 kinase_uprtid <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5849 kinase_name_uprt_lut[which_rows, 2] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5850 # filter for first _HUMAN match if any |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5851 grepl_human <- grepl("_HUMAN$", kinase_uprtid) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5852 if (0 < sum(grepl_human)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5853 kinase_uprtid <- kinase_uprtid[grepl_human] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5854 # filter for first match if any |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5855 if (0 < length(kinase_uprtid)) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5856 kinase_uprtid <- kinase_uprtid[1] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5857 kinase_desc <- kinase_uprt_desc_lut[kinase_uprtid, 2] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5858 if (!is.na(kinase_desc)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5859 rslt <- c(kinase_desc, kinase_uprtid) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5860 else |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5861 rslt <- c(kinase_desc, "") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5862 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5863 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5864 warning = str |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5865 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5866 rslt |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5867 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5868 TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5869 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5870 kinase_name_to_desc_uprt <- function(s) NULL |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5871 FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5872 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5873 ``` |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5874 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5875 ```{r write_params, echo = FALSE, results = 'asis'} |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5876 # perhaps this should be moved into the functions section, eventually ... |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5877 write_params <- function(db) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5878 # write parameters to report |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5879 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5880 # write parameters to SQLite output |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5881 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5882 mqppep_anova_script_param_df <- data.frame( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5883 script = "mqppep_anova_script.Rmd", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5884 parameter = names(param_unlist), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5885 value = param_unlist |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5886 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5887 ddl_exec(db, " |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5888 DROP TABLE IF EXISTS script_parameter; |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5889 " |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5890 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5891 ddl_exec(db, " |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5892 CREATE TABLE IF NOT EXISTS script_parameter( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5893 script TEXT, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5894 parameter TEXT, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5895 value ANY, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5896 UNIQUE (script, parameter) ON CONFLICT REPLACE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5897 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5898 ; |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5899 " |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5900 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5901 RSQLite::dbWriteTable( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5902 conn = db, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5903 name = "script_parameter", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5904 value = mqppep_anova_script_param_df, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5905 append = TRUE |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5906 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5907 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5908 loaded_packages_df <- sessioninfo::package_info("loaded") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5909 loaded_packages_df[, "library"] <- as.character(loaded_packages_df$library) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5910 loaded_packages_df <- data.frame( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5911 package = loaded_packages_df$package, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5912 version = loaded_packages_df$loadedversion, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5913 date = loaded_packages_df$date |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5914 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5915 cat("\\clearpage\n\\section{Input parameter settings}\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5916 data_frame_tabbing_latex( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5917 x = param_df, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5918 tabstops = c(1.75), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5919 underscore_whack = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5920 caption = "Input parameters", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5921 verbatim = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5922 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5923 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5924 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5925 if (!have_kinase_descriptions) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5926 write_params(db) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5927 # We are done with output |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5928 RSQLite::dbDisconnect(db) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5929 param_df_exit() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5930 knitr::knit_exit() |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5931 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5932 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5933 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5934 ```{r kseabar, echo = FALSE, fig.dim = c(9.5, 12.3), results = 'asis'} |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5935 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5936 # squash un-actionable cyclomatic_complexity warning |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5937 if (have_kinase_descriptions) { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5938 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5939 my_section_header <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5940 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5941 "inases whose KSEA %s < %s\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5942 ksea_cutoff_statistic, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5943 signif(ksea_cutoff_threshold, 2) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5944 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5945 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5946 # Use enriched kinases to find enriched kinase-substrate pairs |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5947 enriched_kinases <- data.frame(kinase = ls(ksea_asterisk_hash)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5948 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5949 enriched_kinase_descs <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5950 Reduce( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5951 f = function(l, r) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5952 lkup <- kinase_name_to_desc_uprt(r) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5953 if (is.null(lkup)) l |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5954 else r2 <- rbind( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5955 l, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5956 data.frame( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5957 kinase = r, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5958 uniprot_id = lkup[2], |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5959 description = lkup[1] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5960 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5961 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5962 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5963 x = enriched_kinases$kinase, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5964 init = NULL |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5965 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5966 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5967 if (length(enriched_kinase_descs) > 0 && nrow(enriched_kinase_descs) > 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5968 cat("\n\\clearpage\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5969 data_frame_tabbing_latex( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5970 x = enriched_kinase_descs, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5971 tabstops = c(0.9, 1.3), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5972 headings = c("Kinase", "UniProt ID", "Description"), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5973 caption = paste0("Descriptions of k", my_section_header) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5974 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5975 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5976 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5977 if (FALSE) { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5978 cat_variable(sqldf::sqldf("SELECT kinase FROM enriched_kinases")) |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5979 cat_variable(sqldf::sqldf(" |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5980 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5981 FROM pseudo_ksdata |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5982 WHERE gene IN (SELECT kinase FROM enriched_kinases) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5983 ")) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5984 data_frame_table_latex( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5985 x = sqldf::sqldf(" |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5986 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5987 FROM pseudo_ksdata |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5988 WHERE gene IN (SELECT kinase FROM enriched_kinases) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5989 "), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5990 justification = "l l l", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5991 centered = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5992 caption = "substrates of enriched kinases", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5993 anchor = c(const_table_anchor_p, const_table_anchor_t), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5994 underscore_whack = TRUE |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5995 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5996 data_frame_table_latex( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
5997 x = sqldf::sqldf(" |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5998 SELECT |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5999 gene AS kinase, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6000 ppep, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6001 sub_gene, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6002 '('||group_concat(gene||'-'||sub_gene)||') '||ppep AS label, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6003 fdr_adjusted_anova_p, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6004 quality, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6005 min_group_obs_count |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6006 FROM ( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6007 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6008 FROM pseudo_ksdata |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6009 WHERE gene IN (SELECT kinase FROM enriched_kinases) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6010 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6011 p_value_data |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6012 WHERE ppep = phosphopeptide |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6013 GROUP BY kinase, ppep |
|
4
2d9f216c1048
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 1c1dbc5a9838e5cd45724b6e53246eb80437e1f1
galaxyp
parents:
3
diff
changeset
|
6014 ORDER BY kinase, p_value_data.quality DESC |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6015 "), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6016 justification = "l l l l l l l", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6017 centered = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6018 caption = "labeled substrates of enriched kinases", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6019 anchor = c(const_table_anchor_p, const_table_anchor_t), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6020 underscore_whack = TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6021 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6022 } |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6023 all_enriched_substrates <- sqldf::sqldf(" |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6024 SELECT |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6025 gene AS kinase, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6026 ppep, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6027 sub_gene, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6028 '('||group_concat(gene||'-'||sub_gene)||') '||ppep AS label, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6029 fdr_adjusted_anova_p, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6030 quality, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6031 min_group_obs_count |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6032 FROM ( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6033 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6034 FROM pseudo_ksdata |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6035 WHERE gene IN (SELECT kinase FROM enriched_kinases) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6036 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6037 p_value_data |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6038 WHERE ppep = phosphopeptide |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6039 GROUP BY kinase, ppep |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6040 ORDER BY kinase, ppep, p_value_data.quality DESC |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6041 ") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6042 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6043 all_enriched_substrates <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6044 all_enriched_substrates[ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6045 all_enriched_substrates$quality >= params$minQuality, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6046 , |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6047 drop = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6048 ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6049 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6050 all_enriched_substrates$sub_gene <- |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6051 sub(" ///.*", "...", |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6052 all_enriched_substrates$sub_gene |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6053 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6054 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6055 all_enriched_substrates$label <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6056 with( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6057 all_enriched_substrates, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6058 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6059 "(%s-%s) %s", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6060 kinase, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6061 trunc_subgene(sub_gene), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6062 ppep |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6063 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6064 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6065 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6066 # this global is set to TRUE by cat_enriched_heading immediately below |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6067 g_neednewpage <- FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6068 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6069 # helper used to label per-kinase substrate enrichment figure |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6070 cat_enriched_heading <- function(m, cut_args) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6071 cutoff <- cut_args$cutoff |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6072 kinase <- cut_args$kinase |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6073 if (g_neednewpage) cat("\\newpage\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6074 g_neednewpage <- TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6075 if (nrow(m) > g_intensity_hm_rows) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6076 cat(subsection_header( |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6077 sprintf( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6078 "Highest-quality %d (of %d) enriched %s-sites", |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6079 g_intensity_hm_rows, |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6080 nrow(m), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6081 kinase |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6082 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6083 )) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6084 } else { |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6085 if (nrow(m) == 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6086 return(FALSE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6087 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6088 nrow_m <- nrow(m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6089 cat(subsection_header( |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6090 sprintf( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6091 "%d enriched %s-site%s", |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6092 nrow_m, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6093 kinase, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6094 if (nrow_m > 1) "s" else "" |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6095 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6096 )) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6097 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6098 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6099 cat("\n\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6100 cat("\n\n\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6101 return(TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6102 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6103 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6104 # -------------------------------- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6105 # hack begin - show all substrates |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6106 enriched_substrates <- all_enriched_substrates |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6107 # add "FALSE &&" to prevent listing of substrates |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6108 if (show_enriched_substrates && nrow(enriched_substrates) > 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6109 short_row_names <- sub( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6110 "$FAILED_MATCH_GENE_NAME", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6111 "not_found", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6112 enriched_substrates$sub_gene, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6113 fixed = TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6114 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6115 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6116 if (print_nb_messages) nbe(see_variable(enriched_substrates)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6117 substrates_df <- with( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6118 enriched_substrates, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6119 data.frame( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6120 kinase = kinase, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6121 substrate = sub(" ///*", "...", short_row_names), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6122 anova_p_value = signif(fdr_adjusted_anova_p, 2), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6123 min_group_obs_count = signif(min_group_obs_count, 0), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6124 quality = signif(quality, 3), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6125 sequence = trunc_n(30)(ppep) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6126 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6127 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6128 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6129 substrates_df <- substrates_df[ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6130 with(substrates_df, order(kinase, -quality)), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6131 , |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6132 drop = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6133 ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6134 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6135 if (print_nb_messages) nbe(see_variable(substrates_df)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6136 if (nrow(substrates_df) < 1) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6137 substrates_df$sequence <- c() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6138 if (print_nb_messages) nbe(see_variable(substrates_df)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6139 names(substrates_df) <- headers_2nd_line <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6140 c("Kinase", "Substrate", "p-value", "per group)", "quality", "Sequence") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6141 headers_1st_line <- c("", "", "ANOVA", "min(values", "", "") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6142 data_frame_tabbing_latex( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6143 x = substrates_df, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6144 tabstops = c(1.2, 0.8, 0.5, 0.65, 0.5), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6145 headings = c(headers_1st_line, headers_2nd_line), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6146 caption = "Details for all enriched substrates of enriched kinases" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6147 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6148 rm( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6149 enriched_substrates, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6150 substrates_df, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6151 short_row_names, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6152 headers_1st_line, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6153 headers_2nd_line |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6154 ) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6155 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6156 cat("\\clearpage\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6157 # hack end - show all substrates |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6158 # -------------------------------- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6159 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6160 # print deferred tables and graphs for kinases from contrasts |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6161 for (i_cntrst in seq_len(length(ksea_prints))) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6162 #latex_samepage({ |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6163 cat(ksea_prints[[i_cntrst]]) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6164 cat("\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6165 ksea_barplots[[i_cntrst]]() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6166 cat("\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6167 cat("\\clearpage\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6168 #}) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6169 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6170 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6171 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6172 ``` |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6173 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6174 ```{r enriched, echo = FALSE, fig.dim = c(12, 13.7), results = 'asis'} |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6175 # nolint start |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6176 # squash un-actionable cyclomatic_complexity warning |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6177 if (g_can_run_ksea) { |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6178 # nolint end |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6179 g_did_enriched_header <- FALSE |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6180 for (kinase_name in sort(enriched_kinases$kinase)) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6181 enriched_substrates <- |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6182 all_enriched_substrates[ |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6183 all_enriched_substrates$kinase == kinase_name, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6184 , |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6185 drop = FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6186 ] |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6187 ten_trunc_ppep <- trunc_enriched_substrate(enriched_substrates$ppep) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6188 enriched_substrates$label <- with( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6189 enriched_substrates, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6190 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6191 "(%s) %s", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6192 make.names( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6193 sub("$FAILED_MATCH_GENE_NAME", "not_found", sub_gene, fixed = TRUE), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6194 unique = TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6195 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6196 ten_trunc_ppep |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6197 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6198 ) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6199 # Get the intensity values for the heatmap |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6200 enriched_intensities <- |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6201 as.matrix(unimputed_quant_data_log[ |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6202 enriched_substrates$ppep, , drop = FALSE |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6203 ]) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6204 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6205 # Remove rows having too many NA values to be relevant |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6206 good_rows <- (rowSums(enriched_intensities, na.rm = TRUE) != 0) |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6207 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6208 enriched_substrates <- enriched_substrates[good_rows, , drop = FALSE] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6209 enriched_intensities <- enriched_intensities[good_rows, , drop = FALSE] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6210 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6211 # Rename the rows with the display-name for the heatmap |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6212 short_row_names <- sub( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6213 "$FAILED_MATCH_GENE_NAME", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6214 "not_found", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6215 enriched_substrates$sub_gene, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6216 fixed = TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6217 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6218 short_row_names <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6219 make.names(short_row_names, unique = TRUE) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6220 long_row_names <- |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6221 sapply( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6222 X = rownames(enriched_intensities), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6223 FUN = function(rn) { |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6224 enriched_substrates[enriched_substrates$ppep == rn, "label"] |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6225 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6226 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6227 rownames(enriched_intensities) <- long_row_names |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6228 # Format as matrix for heatmap |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6229 m <- as.matrix(enriched_intensities) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6230 rownames(m) <- trunc_enriched_substrate(rownames(m)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6231 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6232 # Draw the heading and heatmap |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6233 nrow_m <- nrow(m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6234 if (nrow_m > 0) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6235 if (!g_did_enriched_header) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6236 cat("\n\\clearpage\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6237 cat(section_header(paste0("K", my_section_header))) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6238 g_did_enriched_header <- TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6239 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6240 is_na_m <- is.na(m) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6241 cellnote_m <- is_na_m |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6242 cellnote_m[!is_na_m] <- "" |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6243 cellnote_m[is_na_m] <- params$heatMapNAcellNote |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6244 cut_args <- new_env() |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6245 cut_args$cutoff <- cutoff |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6246 cut_args$kinase <- kinase_name |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6247 cut_args$statistic <- ksea_cutoff_statistic |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6248 cut_args$threshold <- ksea_cutoff_threshold |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6249 number_of_peptides_found <- |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6250 ppep_heatmap( |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6251 m = m, |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6252 cellnote = cellnote_m, |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6253 cutoff = cut_args, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6254 hm_heading_function = cat_enriched_heading, |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6255 hm_main_title = paste( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6256 "Unnormalized (zero-imputed)", |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6257 "intensities of enriched kinase-substrates"), |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6258 suppress_row_dendrogram = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6259 master_cex = 0.35, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6260 sepcolor = "black", |
|
2
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
6261 colsep = sample_colsep, |
|
2336fbff8866
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 423304b26e63d23cd8e5fb4c2fb729c5beea1254
galaxyp
parents:
1
diff
changeset
|
6262 row_scaling = "none" |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6263 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6264 if (number_of_peptides_found > 1) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6265 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6266 tryCatch( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6267 { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6268 rownames(m) <- short_row_names |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6269 cov_heatmap( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6270 m = m, |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6271 kinase_name = kinase_name, |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6272 top_substrates = nrow_m > g_intensity_hm_rows |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6273 ) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6274 }, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6275 error = function(e) { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6276 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6277 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6278 "ERROR: %s\n\\newline\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6279 mget("e") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6280 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6281 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6282 cat( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6283 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6284 "message: %s\n\\newline\n", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6285 e$message |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6286 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6287 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6288 cat_margins() |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6289 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6290 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6291 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6292 substrates_df <- with( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6293 enriched_substrates, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6294 data.frame( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6295 substrate = sub(" ///*", "...", short_row_names), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6296 sequence = trunc_long_ppep(ppep), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6297 anova_p_value = signif(fdr_adjusted_anova_p, 2), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6298 min_group_obs_count = signif(min_group_obs_count, 0), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6299 quality = signif(quality, 3) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6300 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6301 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6302 excess_substrates <- nrow(substrates_df) > g_intensity_hm_rows |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6303 if (excess_substrates) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6304 substrates_df <- substrates_df[1:g_intensity_hm_rows, ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6305 names(substrates_df) <- headers_2nd_line <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6306 c("Substrate", "Sequence", "p-value", "per group)", "quality") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6307 headers_1st_line <- c("", "", "ANOVA", "min(values", "") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6308 if (1 < nrow(enriched_substrates)) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6309 cat("\n\\newpage\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6310 cat(subsubsection_header( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6311 sprintf( |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6312 "Details for %s%s-sites", |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6313 if (excess_substrates) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6314 sprintf( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6315 "%s \"highest quality\" ", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6316 g_intensity_hm_rows |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6317 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6318 else "", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6319 kinase_name |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6320 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6321 )) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6322 substrates_df <- substrates_df[order(-substrates_df$quality), ] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6323 data_frame_tabbing_latex( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6324 x = substrates_df, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6325 tabstops = c(0.8, 3.8, 0.6, 0.8), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6326 headings = c(headers_1st_line, headers_2nd_line) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6327 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6328 } else { |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6329 if (print_nb_messages) nbe(see_variable(nrow_m > 0), "\n") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6330 } |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6331 if (print_nb_messages) nb("end kinase ", kinase_name, "\n") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6332 } |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6333 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6334 # Write output tabular files |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6335 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6336 # get kinase, ppep, concat(kinase) tuples for enriched kinases |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6337 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6338 if (print_nb_messages) nb("kinase_ppep_label <- ...\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6339 if (print_nb_messages) nbe("kinase_ppep_label <- ...\n") |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6340 kinase_ppep_label <- sqldf::sqldf(" |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6341 WITH |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6342 t(ppep, label) AS |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6343 ( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6344 SELECT DISTINCT |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6345 SUB_MOD_RSD AS ppep, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6346 group_concat(gene, '; ') AS label |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6347 FROM pseudo_ksdata |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6348 WHERE GENE IN (SELECT kinase FROM enriched_kinases) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6349 GROUP BY ppep |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6350 ), |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6351 k(kinase, ppep_join) AS |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6352 ( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6353 SELECT DISTINCT gene AS kinase, SUB_MOD_RSD AS ppep_join |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6354 FROM pseudo_ksdata |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6355 WHERE GENE IN (SELECT kinase FROM enriched_kinases) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6356 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6357 SELECT k.kinase, t.ppep, t.label |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6358 FROM t, k |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6359 WHERE t.ppep = k.ppep_join |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6360 ORDER BY k.kinase, t.ppep |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6361 ") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6362 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6363 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6364 # extract what we need from full_data |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6365 impish <- cbind(rownames(quant_data_imp), quant_data_imp) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6366 colnames(impish)[1] <- "Phosphopeptide" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6367 data_table_imputed_sql <- " |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6368 SELECT |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6369 f.*, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6370 k.label AS KSEA_enrichments, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6371 q.* |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6372 FROM |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6373 metadata_plus_p f |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6374 LEFT JOIN kinase_ppep_label k |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6375 ON f.Phosphopeptide = k.ppep, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6376 impish q |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6377 WHERE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6378 f.Phosphopeptide = q.Phosphopeptide |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6379 " |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6380 data_table_imputed <- sqldf::sqldf(data_table_imputed_sql) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6381 # Zap the duplicated 'Phosphopeptide' column named 'ppep' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6382 data_table_imputed <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6383 data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6384 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6385 # Output imputed, un-normalized data |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6386 if (print_nb_messages) nb("Output imputed, un-normalized data tabular file\n") |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6387 if (print_nb_messages) nbe( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6388 "Output imputed, un-normalized data tabular file\n") |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6389 write.table( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6390 data_table_imputed |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6391 , file = imputed_data_filename |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6392 , sep = "\t" |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6393 , col.names = TRUE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6394 , row.names = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6395 , quote = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6396 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6397 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6398 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6399 #output quantile normalized data |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6400 impish <- cbind(rownames(quant_data_imp_qn_log), quant_data_imp_qn_log) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6401 colnames(impish)[1] <- "Phosphopeptide" |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6402 data_table_imputed <- sqldf::sqldf(data_table_imputed_sql) |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6403 # Zap the duplicated 'Phosphopeptide' column named 'ppep' |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6404 data_table_imputed <- |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6405 data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))] |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6406 if (print_nb_messages) nb("Output quantile normalized data tabular file\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6407 if (print_nb_messages) nbe("Output quantile normalized data tabular file\n") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6408 write.table( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6409 data_table_imputed, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6410 file = imp_qn_lt_data_filenm, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6411 sep = "\t", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6412 col.names = TRUE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6413 row.names = FALSE, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6414 quote = FALSE |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6415 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6416 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6417 ppep_kinase <- sqldf::sqldf(" |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6418 SELECT DISTINCT k.ppep, k.kinase |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6419 FROM ( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6420 SELECT DISTINCT gene AS kinase, SUB_MOD_RSD AS ppep |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6421 FROM pseudo_ksdata |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6422 WHERE GENE IN (SELECT kinase FROM enriched_kinases) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6423 ) k |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6424 ORDER BY k.ppep, k.kinase |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6425 ") |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6426 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6427 RSQLite::dbWriteTable( |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6428 conn = db, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6429 name = "ksea_enriched_ks", |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6430 value = ppep_kinase, |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6431 append = FALSE |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6432 ) |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6433 } |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6434 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6435 if (print_nb_messages) nb("RSQLite::dbWriteTable anova_signif\n") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6436 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6437 RSQLite::dbWriteTable( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6438 conn = db, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6439 name = "anova_signif", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6440 value = p_value_data, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6441 append = FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6442 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6443 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6444 ddl_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6445 DROP VIEW IF EXISTS stats_metadata_v; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6446 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6447 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6448 dml_no_rows_exec(db, " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6449 CREATE VIEW stats_metadata_v |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6450 AS |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6451 SELECT DISTINCT m.*, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6452 p.raw_anova_p, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6453 p.fdr_adjusted_anova_p, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6454 kek.kinase AS ksea_enrichments |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6455 FROM |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6456 mrgfltr_metadata_view m |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6457 LEFT JOIN anova_signif p |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6458 ON m.phospho_peptide = p.phosphopeptide |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6459 LEFT JOIN ksea_enriched_ks kek |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6460 ON m.phospho_peptide = kek.ppep |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6461 ; |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6462 " |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6463 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6464 |
|
3
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6465 if (print_nb_messages) nb( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6466 "Output contents of `stats_metadata_v` table to tabular file\n") |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6467 if (print_nb_messages) nbe( |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6468 "Output contents of `stats_metadata_v` table to tabular file\n") |
|
dda27b9273a8
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3dcf0d08f006b888061ff83eadc65e550d751869
galaxyp
parents:
2
diff
changeset
|
6469 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6470 write.table( |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6471 dbReadTable(db, "stats_metadata_v"), |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6472 file = anova_ksea_mtdt_file, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6473 sep = "\t", |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6474 col.names = TRUE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6475 row.names = FALSE, |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6476 quote = FALSE |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6477 ) |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6478 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6479 cat("\n\\clearpage\n") |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6480 |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6481 ``` |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6482 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6483 # Data-processing summary flowchart |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6484 |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6485  |
|
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6486 |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6487 ```{r parmlist, echo = FALSE, fig.dim = c(9, 10), results = 'asis'} |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6488 cat("\\leavevmode\n\n\n") |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6489 |
|
1
08678c931f5d
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6490 write_params(db) |
|
0
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6491 # We are done with output |
|
dbff53e6f75f
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
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6492 RSQLite::dbDisconnect(db) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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6493 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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6494 cat("\\clearpage\n\\section{R package versions}\n") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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6495 utils::toLatex(utils::sessionInfo()) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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6496 ``` |