Mercurial > repos > galaxyp > mqppep_preproc
annotate mqppep_anova_script.Rmd @ 1:b76c75521d91 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
| author | galaxyp |
|---|---|
| date | Fri, 28 Oct 2022 18:26:42 +0000 |
| parents | 8dfd5d2b5903 |
| children | a5e7469dfdfa |
| rev | line source |
|---|---|
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8dfd5d2b5903
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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8dfd5d2b5903
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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8dfd5d2b5903
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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8dfd5d2b5903
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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8dfd5d2b5903
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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8dfd5d2b5903
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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8dfd5d2b5903
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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8dfd5d2b5903
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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8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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9 - "; revised June 23, 2022" |
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1
b76c75521d91
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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8dfd5d2b5903
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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8dfd5d2b5903
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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8dfd5d2b5903
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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1
b76c75521d91
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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8dfd5d2b5903
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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1
b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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8dfd5d2b5903
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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8dfd5d2b5903
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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8dfd5d2b5903
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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8dfd5d2b5903
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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8dfd5d2b5903
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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8dfd5d2b5903
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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8dfd5d2b5903
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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b76c75521d91
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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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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30 groupFilter: !r c("none", "exclude", "include")[1] |
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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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parents:
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40 # - "i": case insensitive matching (like `grep -i`) |
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b76c75521d91
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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b76c75521d91
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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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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43 # (extended grep pattern, case sensitive) |
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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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51 imputedDataFilename: "test-data/limbo/imputedDataFilename.txt" |
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b76c75521d91
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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8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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53 imputedQNLTDataFile: "test-data/limbo/imputedQNLTDataFile.txt" |
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b76c75521d91
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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8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
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55 anovaKseaMetadata: "test-data/limbo/anovaKseaMetadata.txt" |
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b76c75521d91
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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8dfd5d2b5903
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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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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58 # how to test one variable with 2 categories (e.g., oneway.test) |
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8dfd5d2b5903
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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65 # "perhaps better" meaning that KSEA is an hypothesis-generator, not -test |
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b76c75521d91
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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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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67 # minimum number of substrates required for a kinase to be considered in KSEA |
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b76c75521d91
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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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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69 # Should KSEA be performed aggregating signed log2FC or absolute? |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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70 # FALSE use raw log2FC for KSEA as for KSEAapp::KSEA.Scores |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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71 # TRUE use abs(log2FC) for KSEA as Justin Drake requested; this is a |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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72 # justifiable deviation from the KSEAapp::KSEA.Scores algorithm. |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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84 filterCovVarGT1: TRUE |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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85 # maximum number of residues to display for ppeps in rownames or columnames |
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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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b76c75521d91
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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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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99 showEnrichedSubstrates: 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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100 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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101 # should debugging nb/nbe messages be printed? |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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102 printNBMsgs: FALSE |
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103 # should debugging trace messages be printed? |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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104 printTraceMsgs: 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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105 # when debugging files are needed, set debugFileBasePath to the path |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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106 # to the directory where they should be writtn |
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107 debugFileBasePath: !r if (TRUE) NULL else "test-data" |
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108 --- |
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1
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109 |
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110 ```{r setup, include = FALSE, results = 'asis'} |
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111 |
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112 # simple debug messaging |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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113 print_nb_messages <- params$printNBMsgs |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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114 |
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115 nb <- if (!print_nb_messages) { |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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116 function(...) invisible() |
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117 } else { |
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118 function(..., f = cat) f("\n$\\exists{}\\supset\\forall{}$", ...) |
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119 } |
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120 |
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121 nbe <- if (!print_nb_messages) { |
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122 function(...) invisible() |
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123 } else { |
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124 function(..., f = cat, file = stderr()) { |
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125 cat( |
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126 stringi::stri_unescape_unicode("\nNBE \\u2203\\u2283\\u2200"), |
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127 ..., |
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128 file = file |
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129 ) |
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130 } |
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131 } |
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132 |
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0
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133 #ref for debugging: https://yihui.org/tinytex/r/#debugging |
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134 options(tinytex.verbose = TRUE) |
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135 |
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136 # ref for parameterizing Rmd document: https://stackoverflow.com/a/37940285 |
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137 # ref for top and bottom struts: https://tex.stackexchange.com/a/50355 |
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1
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138 knitr::opts_chunk$set(echo = FALSE, fig.dim = c(9, 10), dpi = 300) |
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0
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139 |
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140 # freeze the random number generator so the same results will be produced |
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141 # from run to run |
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142 set.seed(28571) |
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143 |
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144 ### LIBRARIES |
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1
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145 |
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146 if (print_nb_messages) nbe("library(gplots)") |
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147 library(gplots) |
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1
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148 if (print_nb_messages) nbe("library(caret)") |
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149 # load caret for nearZeroVar |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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150 if (print_nb_messages) nbe("Please ignore the messages about systemd, if any.\n") |
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151 library(caret) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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152 if (print_nb_messages) nbe("library(DBI)") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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153 library(DBI) |
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1
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154 if (print_nb_messages) nbe("library(RSQLite)") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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155 library(RSQLite) |
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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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156 if (print_nb_messages) nbe("library(sqldf)\n") |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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157 # Suppress "Warning: no DISPLAY variable so Tk is not available" |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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158 suppressWarnings(suppressMessages(library(sqldf))) |
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159 |
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160 # required but not added to search list: |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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161 # - DBI |
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162 # - RSQLite |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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163 # - ggplot2 |
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164 # - knitr |
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165 # - latex2exp |
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166 # - preprocessCore |
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167 # - reshape2 |
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168 # - vioplot |
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169 |
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170 ### CONSTANTS |
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171 |
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172 const_boxplot_fill <- "grey94" |
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173 const_ksea_astrsk_kinases <- 1 |
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174 const_ksea_nonastrsk_kinases <- 2 |
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175 const_ksea_all_kinases <- 3 |
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176 const_log10_e <- log10(exp(1)) |
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177 const_stripchart_cex <- 0.5 |
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178 const_stripchart_jitter <- 0.3 |
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179 const_table_anchor_bp <- "bp" |
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180 const_table_anchor_ht <- "ht" |
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181 const_table_anchor_p <- "p" |
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182 const_table_anchor_t <- "t" |
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183 const_table_anchor_tbp <- "tbp" |
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184 |
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185 |
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186 ### GLOBAL VARIABLES (params) |
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187 |
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188 ## functions to process params |
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189 |
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190 is_string_null_or_empty <- function(x) { |
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191 # N. B. non-strings are intentionally treated as NULL |
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192 if (is.null(x)) |
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193 TRUE |
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194 else if (!is.character(x)) |
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195 TRUE |
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196 else x == "" |
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197 } |
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198 |
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199 ##' Catch *and* save both errors and warnings, and in the case of |
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200 ##' a warning, also keep the computed result. |
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201 ##' return result as list(value = ..., warning = ...) |
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202 ##' - value will be: |
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203 ##' - the result if no exception is thrown |
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204 ##' - the exception if an exception is caught |
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205 ##' - warning will be a string except perhaps when warning argument is not NULL |
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206 ##' |
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207 ##' adapted from `demo(error.catching)` |
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208 ##' |
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209 ##' @title tryCatch both warnings (with value) and errors |
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210 ##' @param expr an \R expression to evaluate |
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211 ##' @return a list with 'value' and 'warning', where |
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212 ##' 'value' may be an error caught. |
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213 ##' @author Martin Maechler; |
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214 ##' Copyright (C) 2010-2012 The R Core Team |
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215 try_catch_w_e <- |
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216 function(expr, error = function(e) e, warning = NULL) { |
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217 wrn <- NULL |
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218 # warning handler |
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219 w_handler <- |
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220 if (is.function(warning)) |
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221 warning |
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222 else |
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223 function(w) { |
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224 wrn <<- w |
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225 invokeRestart("muffleWarning") |
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226 } |
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227 e_handler <- |
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228 if (is.function(error)) |
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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 error |
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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 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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231 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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232 # return result as list(value = ..., 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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233 # - 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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234 # - 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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235 # - 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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236 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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237 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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238 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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239 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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240 error = 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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241 ), |
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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 warning = 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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243 ), |
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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 warning = wrn |
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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 ) |
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246 } |
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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 |
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248 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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249 function(format, key, value, 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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250 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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251 !all( |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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252 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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253 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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254 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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255 is.character(suffix) |
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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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258 cat("all arguments to see_kvp should be 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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259 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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260 } |
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261 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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262 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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263 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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264 "%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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265 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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266 paste(result, collapse = ", "), |
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267 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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268 ) |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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269 } else { |
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270 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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271 "%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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272 key, |
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273 result, |
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274 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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275 ) |
|
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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 } |
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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 } |
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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 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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280 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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281 result <- as.character(as.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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282 # 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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283 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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284 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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285 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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286 key = xprssn, |
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287 value = result, |
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288 suffix = suffix |
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289 ) |
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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 } |
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291 |
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292 see_numeric <- |
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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 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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294 if (is.numeric(digits) && is.numeric(x)) { |
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295 digits <- as.integer(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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296 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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297 format <- paste0("%0.", as.character(digits), "g") |
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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 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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299 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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300 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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301 key = xprssn, |
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302 value = result, |
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303 suffix = suffix |
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304 ) |
|
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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305 } |
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306 } |
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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 |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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308 see_character <- |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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309 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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310 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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311 see_kvp( |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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312 format = "%s", |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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313 key = xprssn, |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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314 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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315 suffix = suffix |
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b76c75521d91
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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b76c75521d91
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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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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318 } |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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319 |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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320 see_variable <- |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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321 function(x, suffix = "", digits = 3, xprssn = deparse1(substitute(x))) { |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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322 if (is.character(x)) { |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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323 see_character(x, suffix, xprssn) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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324 } 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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325 see_numeric(x, suffix, digits, xprssn) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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326 } else if (is.logical(x)) { |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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327 see_logical(x, suffix, xprssn) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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328 } 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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329 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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330 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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331 str(x) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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332 msg <- paste(readLines(f), collapse = "\n") |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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333 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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334 close(f) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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335 paste0( |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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336 "see_variable - str(", |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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337 xprssn, |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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338 "):\n", |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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339 msg, "\n" |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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340 ) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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341 } |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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342 } |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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343 |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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344 # ref: https://tug.org/texinfohtml/latex2e.html |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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345 # LaTeX sets aside the following characters for special purposes. |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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346 # For example, the percent sign % is for comments. |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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347 # They are called reserved characters or special characters. |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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348 # They are all discussed elsewhere in this manual. |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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349 # |
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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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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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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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352 # If you want a reserved character to be printed as itself, in the text body |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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353 # font, for all but the final three characters in that list simply put |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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354 # 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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355 # Thus, typing \$1.23 will produce $1.23 in your output. |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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356 # |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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357 # As to the last three characters, to get a tilde in the text body font, |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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358 # use \~{} (omitting the curly braces would result in the next character |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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359 # receiving a tilde accent). |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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360 # Similarly, to get a text body font circumflex use \^{}. |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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361 # To get a backslash in the font of the text body enter \textbackslash{}. |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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362 whack_math <- |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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363 function(v) { |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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364 v <- as.character(v) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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365 w <- gsub("\\", "\\textbackslash ", v, fixed = TRUE) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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366 w <- Reduce( |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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367 f = function(l, r) { |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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368 gsub(r, paste0("\\", r), l, fixed = TRUE) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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369 }, |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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370 x = c("#", "$", "%", "&", "{", "}", "_"), |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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371 init = w |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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372 ) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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373 w <- gsub("^", "\\^{}", w, fixed = TRUE) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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374 return(w) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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375 if (all(v == w)) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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376 v |
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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 else |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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378 paste0("\\texttt{", w, "}") |
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0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
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379 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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380 whack_underscores <- whack_math |
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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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381 |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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382 ## dump params to stderr (remove this eventually) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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383 |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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384 if (FALSE) nbe(see_variable(params)) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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changeset
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385 |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
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386 ## unlist params for eventual output |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
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387 |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
388 param_unlist <- unlist(as.list(params)) |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
389 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
390 # no need to whack underscores and dollars because this is verbatim |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
391 param_df <- data.frame( |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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diff
changeset
|
392 parameter = paste0("\\verb@", names(param_unlist), "@"), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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diff
changeset
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393 value = paste0( |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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diff
changeset
|
394 "\n\\begin{tiny}\n\\verb@", |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
395 param_unlist, |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
396 "@\n\\end{tiny}" |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
397 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
398 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
399 param_df <- data.frame( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
400 parameter = names(param_unlist), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
401 value = param_unlist |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
402 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
403 param_df <- param_df[order(param_df$parameter), ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
404 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
405 ## general output control |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
406 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
407 debug_file_base_path <- params$debugFileBasePath |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
408 print_trace_messages <- params$printTraceMsgs |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
409 show_enriched_substrates <- params$showEnrichedSubstrates |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
410 boxplot_varwidth <- params$boxPlotVarWidth |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
411 boxplot_notch <- params$boxPlotNotch |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
412 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
413 ## parameters for static data |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
414 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
415 kinase_name_uprt_lut_bz2 <- params$kinaseNameUprtLutBz2 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
416 kinase_uprt_desc_lut_bz2 <- params$kinaseUprtDescLutBz2 |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
417 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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diff
changeset
|
418 ## parameters for input file |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
419 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
420 preproc_db <- params$preprocDb |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
421 alpha_file <- params$alphaFile |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
422 input_file <- params$inputFile |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
423 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
424 # First data column - ideally, this could be detected via |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
425 # regexSampleNames, but for now leave it as is. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
426 first_data_column <- params$firstDataColumn |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
427 fdc_is_integer <- is.integer(first_data_column) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
428 if (fdc_is_integer) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
429 first_data_column <- as.integer(params$firstDataColumn) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
430 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
431 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
432 ## parameters for output files |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
433 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
434 ksea_app_prep_db <- params$kseaAppPrepDb |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
435 imputed_data_filename <- params$imputedDataFilename |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
436 imp_qn_lt_data_filenm <- params$imputedQNLTDataFile |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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diff
changeset
|
437 anova_ksea_mtdt_file <- params$anovaKseaMetadata |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
438 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
439 ## parameters for imputation |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
440 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
441 # Imputation method, should be one of |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
442 # "random", "group-median", "median", or "mean" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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diff
changeset
|
443 imputation_method <- params$imputationMethod |
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b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
444 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
445 # Selection of percentile of logvalue data to set the mean for random number |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
446 # generation when using random imputation |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
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diff
changeset
|
447 mean_percentile <- params$meanPercentile / 100.0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
448 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
449 # deviation adjustment-factor for random values; real number. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
450 sd_percentile <- params$sdPercentile |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
451 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
452 ## parameters for group parsing and filtering |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
453 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
454 # Regular expression of Sample Names, e.g., "\\.(\\d+)[A-Z]$" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
455 regex_sample_names <- params$regexSampleNames |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
456 # Regular expression to extract Sample Grouping from Sample Name; |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
457 # if error occurs, compare smpl_trt vs. sample_name_matches |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
458 # to see if groupings/pairs line up |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
459 # e.g., "(\\d+)" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
460 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
461 regex_sample_grouping <- params$regexSampleGrouping |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
462 # What are the patterns for filtering sample groups? |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
463 # How should sample groups be filtered? |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
464 # - none: do not filter |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
465 # - include: include sample groups matching filter |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
466 # - exclude: include sample groups not matching filter |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
467 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
468 sample_group_filter <- params$groupFilter |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
469 if (grepl("f", params$groupFilterMode, fixed = TRUE)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
470 sample_group_filter_perl <- FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
471 sample_group_filter_fixed <- TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
472 } else if (grepl("p", params$groupFilterMode, fixed = TRUE)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
473 sample_group_filter_perl <- TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
474 sample_group_filter_fixed <- FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
475 } else { # normal regex |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
476 sample_group_filter_perl <- FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
477 sample_group_filter_fixed <- FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
478 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
479 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
480 sample_group_filter_nocase <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
481 grepl("i", params$groupFilterMode, fixed = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
482 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
483 # What PCRE patterns should be included or excluded |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
484 group_filter_patterns_csv <- params$groupFilterPatterns |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
485 sample_group_filter_patterns <- strsplit( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
486 x = group_filter_patterns_csv, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
487 split = ",", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
488 fixed = TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
489 )[[1]] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
490 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
491 ## parameters for hypothesis testing |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
492 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
493 one_way_all_categories_fname <- params$oneWayManyCategories |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
494 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
495 one_way_all_categories <- try_catch_w_e( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
496 match.fun(one_way_all_categories_fname)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
497 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
498 if (!is.function(one_way_all_categories$value)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
499 write("fatal error for parameter oneWayManyCategories:", stderr()) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
500 write(one_way_all_categories$value$message, stderr()) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
501 if (sys.nframe() > 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
502 cat("Cannot continue and quit() failed. Goodbye.") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
503 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
504 quit(save = "no", status = 1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
505 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
506 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
507 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
508 one_way_all_categories <- one_way_all_categories$value |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
509 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
510 one_way_two_categories_fname <- params$oneWayManyCategories |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
511 one_way_two_categories <- try_catch_w_e( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
512 match.fun(one_way_two_categories_fname)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
513 if (!is.function(one_way_two_categories$value)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
514 cat("fatal error for parameter oneWayTwoCategories: \n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
515 cat(one_way_two_categories$value$message, fill = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
516 if (sys.nframe() > 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
517 cat("Cannot continue and quit() failed. Goodbye.") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
518 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
519 quit(save = "no", status = 1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
520 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
521 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
522 one_way_two_categories <- one_way_two_categories$value |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
523 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
524 ## parameters for KSEA |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
525 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
526 ksea_cutoff_statistic <- params$kseaCutoffStatistic |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
527 ksea_cutoff_threshold <- params$kseaCutoffThreshold |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
528 ksea_min_substrate_count <- params$kseaMinSubstrateCount |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
529 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
530 ## parameters for global variables consumed by functions |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
531 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
532 # intensityHeatmapCriteria: !r c("na_count", "p_value")[2] # TODO switch to 1 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
533 # TODO Validate within list |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
534 g_intensity_hm_criteria <- params$intensityHeatmapCriteria |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
535 if (is_string_null_or_empty(g_intensity_hm_criteria)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
536 cat("invalid intensityHeatmapCriteria parameter (must be string)") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
537 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
538 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
539 switch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
540 g_intensity_hm_criteria, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
541 "quality" = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
542 "na_count" = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
543 "p_value" = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
544 { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
545 with( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
546 params, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
547 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
548 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
549 "invalid %s (must be %s)", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
550 see_variable(intensityHeatmapCriteria), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
551 "one of quality or na_count or p_value" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
552 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
553 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
554 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
555 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
556 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
557 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
558 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
559 # intensityHeatmapRows: 50 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
560 # TODO Validate >> 0 < 75 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
561 g_intensity_hm_rows <- params$intensityHeatmapRows |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
562 if (!is.integer(g_intensity_hm_rows) || g_intensity_hm_rows < 1) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
563 cat("invalid intensityHeatmapRows (must be integer > 0)") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
564 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
565 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
566 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
567 g_intensity_min_per_class <- params$intensityMinValuesPerGroup |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
568 if (!is.integer(g_intensity_min_per_class) || g_intensity_min_per_class < 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
569 cat("invalid intensityMinValuesPerGroup (must be integer > -1") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
570 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
571 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
572 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
573 if (is.na(as.logical(g_correlate_substrates <- params$correlateSubstrates))) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
574 cat("invalid correlateSubstrates (must be TRUE or FALSE)") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
575 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
576 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
577 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
578 if (is.na(as.logical(g_filter_cov_var_gt_1 <- params$filterCovVarGT1))) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
579 cat("invalid filterCovVarGT1 parameter (must be TRUE or FALSE)") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
580 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
581 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
582 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
583 # TODO Validate >> 0 < 30 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
584 g_ppep_trunc_n <- params$ppepTruncN |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
585 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
586 # TODO Validate >> 0 < 30 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
587 g_subgene_trunc_n <- params$subgeneTruncN |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
588 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
589 # TODO Validate >> 0 < 30 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
590 g_sbstr_trunc_n <- params$substTruncN |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
591 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
592 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
593 ### OPERATORS |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
594 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
595 # Test for exclusion |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
596 # ref: https://www.reneshbedre.com/blog/in-operator-r.html |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
597 `%notin%` <- Negate(`%in%`) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
598 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
599 # Augmented assignment |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
600 # ref: https://www2.cs.arizona.edu/icon/refernce/infix2.htm#aug_assign |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
601 `%||:=%` <- function(lvalue, ...) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
602 pf <- parent.frame() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
603 rvalue <- Reduce(paste0, x = ..., init = lvalue) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
604 assign( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
605 x = as.character(substitute(lvalue)), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
606 value = rvalue, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
607 pos = pf |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
608 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
609 invisible(rvalue) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
610 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
611 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
612 ### FUNCTIONS |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
613 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
614 no_op <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
615 function() { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
616 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
617 # this function is not used in this file and should be removed while |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
618 # factoring out reusable code |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
619 all_apply <- function(f, v, na_rm = TRUE, ...) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
620 Reduce( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
621 f = function(l, r) if (na_rm && is.na(r)) TRUE else l && r, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
622 x = sapply(X = v, FUN = f, ...), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
623 init = TRUE |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
624 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
625 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
626 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
627 write_debug_file <- function(data_frame) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
628 if (!is.null(debug_file_base_path)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
629 s_path <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
630 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
631 "%s/%s.txt", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
632 debug_file_base_path, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
633 deparse(substitute(data_frame)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
634 ) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
635 write.table( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
636 data_frame, |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
637 file = s_path, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
638 sep = "\t", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
639 col.names = TRUE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
640 row.names = TRUE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
641 quote = FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
642 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
643 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
644 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
645 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
646 # ref: http://adv-r.had.co.nz/Environments.html |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
647 # "When creating your own environment, note that you should set its parent |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
648 # environment to be the empty environment. This ensures you don't |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
649 # accidentally inherit objects from somewhere else." |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
650 # Caution: this prevents `with(my_env, expr)` from working when `expr` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
651 # contains anything from the global environment, even operators! |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
652 # Hence, `x <- 1; get("x", new_env())` fails by design. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
653 new_env <- function() { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
654 new.env(parent = emptyenv()) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
655 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
656 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
657 # make apply readable for rows |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
658 row_apply <- function(x, fun, ..., simplify = TRUE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
659 apply(x, MARGIN = 1, fun, ..., simplify = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
660 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
661 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
662 # make apply readable for columns |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
663 column_apply <- function(x, fun, ..., simplify = TRUE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
664 apply(x, MARGIN = 2, fun, ..., simplify = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
665 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
666 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
667 ##' Produce a vector of boolean values whose i-th value is TRUE when any |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
668 ##' member of v matches the i-th membr of s, where i in 1:seq_len(length(s)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
669 ##' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
670 ##' @title Search multiple strings for matches of multiple substrings |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
671 ##' @param v a vector of substrings to match |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
672 ##' @param s a vector of strings to search for matches |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
673 ##' @param ... additional arguments to grepl |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
674 ##' @return a list with keys in s and valuse that are vectors of elements of v |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
675 ##' @author Art Eschenlauer |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
676 ##' Copyright (C) 2022 Art Eschenlauer; |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
677 ##' MIT License; https://en.wikipedia.org/wiki/MIT_License#License_terms |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
678 mgrepl <- function(v, s, ...) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
679 grpl_rslt <- rep_len(0, length(s)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
680 for (vi in v) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
681 grpl_rslt_v <- sapply( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
682 X = s, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
683 FUN = function(t) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
684 Reduce( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
685 f = function(l, r) if (is.null(l)) r else c(l, r), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
686 x = sapply( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
687 X = vi, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
688 FUN = function(f) grepl(f, t, ...) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
689 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
690 init = c() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
691 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
692 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
693 simplify = "array" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
694 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
695 grpl_rslt <- grpl_rslt + grpl_rslt_v |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
696 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
697 rslt <- unname(grpl_rslt > 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
698 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
699 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
700 ##' Produce positions in a vector where succeeding value != current valus |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
701 ##' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
702 ##' @title Search vector for neighboring positions having different values |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
703 ##' @param v a vector of comparable numeric values (e.g. integers) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
704 ##' @return a vector of positions i where v[i] != v[i + 1] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
705 ##' @author Art Eschenlauer |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
706 ##' Copyright (C) 2022 Art Eschenlauer; |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
707 ##' MIT License; https://en.wikipedia.org/wiki/MIT_License#License_terms |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
708 transition_positions <- function(v) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
709 Reduce( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
710 f = function(l, i) if ((i != 1) && (v[i - 1] != v[i])) c(l, i - 1) else l, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
711 x = seq_along(v)[-1:0], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
712 init = c() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
713 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
714 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
715 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
716 ### figure debug functions |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
717 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
718 cat_par_vector <- function(par_name, lbl = "", newlines = TRUE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
719 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
720 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
721 "%spar(%s) = c(%s)%s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
722 lbl, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
723 par_name, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
724 paste(par(par_name), collapse = ", "), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
725 if (newlines) "\n\n" else "" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
726 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
727 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
728 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
729 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
730 cat_margins <- function(lbl = NULL) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
731 for (p in c("fig", "fin", "mar", "mai", "omd", "omi", "oma")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
732 cat_par_vector(p, if (!is.null(lbl)) paste0(lbl, " ") else NULL) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
733 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
734 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
735 cat_variable <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
736 function(x, suffix = "", digits = 3, force_str = FALSE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
737 xprssn <- deparse1(substitute(x)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
738 if (force_str || is.matrix(x) || is.list(x) || is.data.frame(x)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
739 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
740 paste0( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
741 "\n\\texttt{\\textbf{", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
742 whack_underscores(xprssn), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
743 "}} [", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
744 typeof(x), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
745 ",", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
746 mode(x), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
747 "] =\n" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
748 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
749 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
750 cat("\n\\begin{verbatim}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
751 str(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
752 cat("\n\\end{verbatim}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
753 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
754 cat("\n", see_variable(x, suffix, digits, xprssn)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
755 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
756 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
757 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
758 ### structure helper functions |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
759 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
760 # ref: staque.R - Icon-oriented stack and queue operations |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
761 # - https://gist.github.com/eschen42/917690355e53918b9e7ba7138a02d1f8 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
762 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
763 # sq_get(v):x produces the leftmost element of v and removes it from v, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
764 # but produces NA if v is empty |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
765 sq_get <- function(v) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
766 if (length(v) == 0) return(NA) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
767 assign(as.character(substitute(v)), v[-1], parent.frame()) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
768 return(v[1]) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
769 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
770 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
771 # sq_put(v,x1,...,xn):v puts x1, x2, ..., xn onto the right end of v, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
772 # producing v. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
773 # Values are pushed in order from left to right, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
774 # so xn becomes the last (rightmost) value on v. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
775 # sq_put(v) with no second argument does nothing. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
776 sq_put <- function(v, x = NA, ...) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
777 pf <- parent.frame() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
778 if (is.null(x)) return(pf$v) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
779 if ( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
780 !(length(x) > 1) && |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
781 !rlang::is_closure(x) && |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
782 is.na(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
783 ) return(pf$v) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
784 assign(as.character(substitute(v)), c(v, x, ...), pf) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
785 pf[[as.character(substitute(v))]] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
786 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
787 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
788 ### numerical/statistical helper functions |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
789 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
790 any_nan <- function(x) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
791 !any(x == "NaN") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
792 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
793 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
794 # determine standard deviation of quantile to impute |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
795 sd_finite <- function(x) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
796 ok <- is.finite(x) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
797 sd(x[ok]) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
798 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
799 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
800 # compute anova raw p-value |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
801 anova_func <- function(x, grouping_factor, one_way_f) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
802 subject <- data.frame( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
803 intensity = x |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
804 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
805 x_aov <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
806 one_way_f( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
807 formula = intensity ~ grouping_factor, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
808 data = subject |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
809 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
810 pvalue <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
811 if (identical(one_way_f, aov)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
812 summary(x_aov)[[1]][["Pr(>F)"]][1] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
813 else |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
814 pvalue <- x_aov$p.value |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
815 pvalue |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
816 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
817 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
818 # This code adapted from matrixcalc::is.positive.definite |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
819 # Notably, this simply tests without calling stop() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
820 is_positive_definite <- function(x, tol = 1e-08) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
821 if (!is.matrix(x)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
822 return(FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
823 if (!is.numeric(x)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
824 return(FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
825 if (nrow(x) < 1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
826 return(FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
827 if (ncol(x) < 1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
828 return(FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
829 if (nrow(x) != ncol(x)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
830 return(FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
831 sum_symm <- sum(x == t(x), na.rm = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
832 value_count <- Reduce("*", dim(x)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
833 if (sum_symm != value_count) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
834 return(FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
835 eigenvalues <- eigen(x, only.values = TRUE)$values |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
836 n <- nrow(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
837 for (i in 1:n) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
838 if (abs(eigenvalues[i]) < tol) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
839 eigenvalues[i] <- 0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
840 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
841 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
842 if (any(eigenvalues <= 0)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
843 return(FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
844 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
845 return(TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
846 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
847 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
848 ### LaTeX functions |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
849 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
850 # Use this like print.data.frame, from which it is adapted: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
851 data_frame_table_latex <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
852 function( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
853 x, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
854 # digits to pass to format.data.frame |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
855 digits = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
856 # TRUE -> right-justify columns; FALSE -> left-justify |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
857 right = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
858 # maximumn number of rows to print |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
859 max = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
860 # string with justification of each column |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
861 justification = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
862 # TRUE to center on page |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
863 centered = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
864 # optional caption |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
865 caption = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
866 # h(inline); b(bottom); t (top) or p (separate page) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
867 anchor = "h", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
868 # set underscore_whack to TRUE to escape underscores |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
869 underscore_whack = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
870 # how to emit results |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
871 emit = cat |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
872 ) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
873 if (is.null(justification)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
874 justification <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
875 Reduce( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
876 f = paste, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
877 x = rep_len(if (right) "r" else "l", length(colnames(x))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
878 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
879 n <- length(rownames(x)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
880 if (length(x) == 0L) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
881 emit( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
882 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
883 # if n is one, use singular 'row', else use plural 'rows' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
884 ngettext( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
885 n, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
886 "data frame with 0 columns and %d row", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
887 "data frame with 0 columns and %d rows" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
888 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
889 n |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
890 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
891 "\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
892 sep = "" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
893 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
894 } else if (n == 0L) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
895 emit("0 rows for:\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
896 latex_itemized_list( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
897 v = names(x), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
898 underscore_whack = underscore_whack |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
899 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
900 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
901 if (is.null(max)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
902 max <- getOption("max.print", 99999L) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
903 if (!is.finite(max)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
904 cat("Abend because: invalid 'max' / getOption(\"max.print\"): ", max) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
905 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
906 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
907 omit <- (n0 <- max %/% length(x)) < n |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
908 m <- as.matrix( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
909 format.data.frame( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
910 if (omit) x[seq_len(n0), , drop = FALSE] else x, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
911 digits = digits, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
912 na.encode = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
913 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
914 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
915 emit( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
916 # h(inline); b(bottom); t (top) or p (separate page) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
917 paste0("\\begin{table}[", anchor, "]"), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
918 "\\leavevmode", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
919 sep = "\n" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
920 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
921 if (!is.null(caption)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
922 emit(paste0(" \\caption{", caption, "}")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
923 if (centered) emit("\\centering\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
924 emit( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
925 paste( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
926 " \\begin{tabular}{", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
927 justification, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
928 "}\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
929 sep = "" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
930 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
931 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
932 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
933 # ref for top and bottom struts (\T and \B): |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
934 # https://tex.stackexchange.com/a/50355 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
935 if (!is.null(caption)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
936 emit("\\B \\\\\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
937 latex_table_row( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
938 v = colnames(m), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
939 extra = " \\T \\B", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
940 underscore_whack = underscore_whack |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
941 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
942 emit("\\hline \\\\\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
943 for (i in seq_len(length(m[, 1]))) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
944 latex_table_row( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
945 v = m[i, ], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
946 underscore_whack = underscore_whack |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
947 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
948 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
949 emit( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
950 paste( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
951 " \\end{tabular}", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
952 "\\end{table}", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
953 sep = "\n" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
954 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
955 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
956 if (omit) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
957 emit(" [ reached 'max' / getOption(\"max.print\") -- omitted", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
958 n - n0, "rows ]\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
959 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
960 invisible(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
961 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
962 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
963 # Use this like print.data.frame, from which it is adapted: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
964 data_frame_tabbing_latex <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
965 function( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
966 x, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
967 # vector of tab stops, in inches |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
968 tabstops, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
969 # vector of headings, registered with tab-stops |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
970 headings = colnames(x), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
971 # digits to pass to format.data.frame |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
972 digits = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
973 # maximumn number of rows to print |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
974 max = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
975 # optional caption |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
976 caption = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
977 # set underscore_whack to TRUE to escape underscores |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
978 underscore_whack = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
979 # flag for landscape mode |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
980 landscape = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
981 # flag indicating that subsubsection should be used for caption |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
982 # rather than subsection |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
983 use_subsubsection_header = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
984 # character-size indicator; for possible values, see: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
985 # https://tug.org/texinfohtml/latex2e.html#Font-sizes |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
986 charactersize = "small", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
987 # set verbatim to TRUE to debug output |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
988 verbatim = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
989 ) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
990 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
991 hlinport <- if (landscape) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
992 function() cat("\\hlinlscp \\\\\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
993 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
994 function() cat("\\hlinport \\\\\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
995 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
996 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
997 tabstops_tex <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
998 Reduce( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
999 f = function(l, r) paste0(l, r), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1000 x = sprintf("\\hspace{%0.2fin}\\=", tabstops), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1001 init = "" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1002 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1003 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1004 n <- length(rownames(x)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1005 if (length(x) == 0L) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1006 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1007 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1008 # if n is one, use singular 'row', else use plural 'rows' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1009 ngettext( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1010 n, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1011 "data frame with 0 columns and %d row", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1012 "data frame with 0 columns and %d rows" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1013 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1014 n |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1015 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1016 "\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1017 sep = "" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1018 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1019 } else if (n == 0L) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1020 cat("0 rows for:\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1021 latex_itemized_list( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1022 v = names(x), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1023 underscore_whack = underscore_whack |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1024 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1025 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1026 if (is.null(max)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1027 max <- getOption("max.print", 99999L) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1028 if (!is.finite(max)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1029 cat("Abend because: invalid 'max' / getOption(\"max.print\"): ", max) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1030 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1031 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1032 omit <- (n0 <- max %/% length(x)) < n |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1033 m <- as.matrix( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1034 format.data.frame( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1035 if (omit) x[seq_len(n0), , drop = FALSE] else x, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1036 digits = digits, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1037 na.encode = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1038 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1039 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1040 if (landscape) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1041 cat("\n\\begin{landscape}") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1042 tex_caption <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1043 if (!is.null(caption)) sprintf("\\captionof{table}{%s}\n", caption) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1044 else "\n" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1045 # build the column names, which have multiple lines when |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1046 # length(headings) is a multiple of the number of columns |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1047 column_names <- "" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1048 while (length(headings) > 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1049 my_row <- c() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1050 for (i in 1:(1 + length(tabstops))) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1051 my_field <- sq_get(headings) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1052 sq_put(my_row, if (is.na(my_field)) "" else my_field) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1053 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1054 column_names %||:=% latex_tabbing_row( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1055 v = my_row, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1056 underscore_whack = underscore_whack, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1057 action = paste0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1058 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1059 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1060 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1061 # Begin tabbing environment after beginning charactersize environment |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1062 if (verbatim) cat("\n\\begin{verbatim}") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1063 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1064 paste0( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1065 "\n\\begin{", charactersize, "}", tex_caption, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1066 "\\begin{tabwrap}{", tabstops_tex, "}\n" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1067 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1068 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1069 # emit column names |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1070 cat(column_names) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1071 # emit hline |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1072 hlinport() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1073 for (i in seq_len(length(m[, 1]))) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1074 my_row <- latex_tabbing_row( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1075 v = m[i, ], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1076 underscore_whack = underscore_whack, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1077 action = paste0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1078 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1079 if (FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1080 cat(my_row) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1081 else |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1082 cat(my_row) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1083 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1084 hlinport() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1085 if (omit) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1086 cat(" [ reached 'max' / getOption(\"max.print\") -- omitted", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1087 n - n0, "rows ]\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1088 # End charactersize environment after ending tabbing environment |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1089 cat(paste0("\\end{tabwrap}\n\\end{", charactersize, "}\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1090 if (verbatim) cat("\\end{verbatim}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1091 if (landscape) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1092 cat("\\end{landscape}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1093 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1094 invisible(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1095 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1096 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1097 param_df_noexit <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1098 function(e = NULL) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1099 data_frame_tabbing_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1100 x = param_df, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1101 tabstops = c(1.75), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1102 underscore_whack = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1103 caption = "Input parameters", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1104 verbatim = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1105 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1106 if (!is.null(e)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1107 sink(stderr()) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1108 cat("Caught fatal error:\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1109 str(e) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1110 sink() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1111 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1112 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1113 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1114 param_df_exit <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1115 function(e = NULL) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1116 param_df_noexit(e) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1117 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1118 exit(-1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1119 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1120 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1121 # exit with exit code (default 0) and optional msg |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1122 exit <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1123 function(code = 0, msg = NULL, use_stderr = FALSE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1124 if (!is.null(msg)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1125 if (use_stderr) sink(stderr()) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1126 cat("\n\n", msg, "\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1127 if (use_stderr) sink() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1128 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1129 q(save = "no", status = code) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1130 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1131 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1132 # make control sequences into printable latex sequences |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1133 latex_printable_control_seqs <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1134 function(s) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1135 s <- gsub("[\\]", "xyzzy_plugh", s) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1136 s <- gsub("[$]", "\\\\$", s) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1137 s <- gsub("xyzzy_plugh", "$\\\\backslash$", s) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1138 return(s) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1139 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1140 nolatex_verbatim <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1141 function(expr) eval(expr) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1142 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1143 latex_verbatim <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1144 function(expr) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1145 arg_string <- deparse1(substitute(expr)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1146 cat("\n\\begin{verbatim}\n___\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1147 tryCatch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1148 expr = expr, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1149 error = param_df_exit, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1150 #ACE error = |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1151 #ACE function(e) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1152 #ACE cat("Caught error:\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1153 #ACE str(e) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1154 #ACE knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1155 #ACE stop(e) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1156 #ACE }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1157 finally = cat("...\n\\end{verbatim}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1158 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1159 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1160 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1161 latex_samepage <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1162 function(expr) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1163 arg_string <- deparse1(substitute(expr)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1164 cat("\n\\begin{samepage}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1165 tryCatch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1166 expr = expr, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1167 error = param_df_exit, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1168 #ACE error = |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1169 #ACE function(e) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1170 #ACE cat("Caught error:\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1171 #ACE str(e) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1172 #ACE knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1173 #ACE stop(e) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1174 #ACE }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1175 finally = cat("\n\\end{samepage}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1176 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1177 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1178 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1179 # return the result of invocation after showing parameters |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1180 # ref: https://www.r-bloggers.com/2013/08/a-new-r-trick-for-me-at-least/ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1181 latex_show_invocation <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1182 function(f, f_name = deparse1(substitute(f)), head_patch = FALSE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1183 function(...) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1184 my_env <- (as.list(environment())) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1185 va <- list(...) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1186 my_rslt <- new_env() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1187 my_rslt$rslt <- NULL |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1188 latex_verbatim( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1189 expr = { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1190 cat(sprintf("\n .. Local variables for '%s':\n\n", f_name)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1191 str(va) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1192 if (!head_patch) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1193 # return this result |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1194 # ref: https://www.r-bloggers.com/2013/08/a-new-r-trick-for-me-at-least/ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1195 cat(sprintf("\n .. Invoking '%s'\n", f_name)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1196 tryCatch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1197 { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1198 cat("\n\\end{verbatim}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1199 rslt <- do.call(f, va) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1200 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1201 error = param_df_exit, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1202 #ACE error = function(e) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1203 #ACE cat("\n\\begin{verbatim}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1204 #ACE str(e) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1205 #ACE cat("\n\\end{verbatim}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1206 #ACE knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1207 #ACE stop(e) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1208 #ACE }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1209 finally = cat("\n\\begin{verbatim}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1210 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1211 cat(sprintf("\n .. '%s' returned:\n", f_name)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1212 str(rslt) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1213 my_rslt$rslt <- rslt |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1214 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1215 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1216 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1217 # return the result of invocation with the shown parameters |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1218 # ref: https://www.r-bloggers.com/2013/08/a-new-r-trick-for-me-at-least/ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1219 if (head_patch) my_rslt$rslt <- do.call(f, va) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1220 (my_rslt$rslt) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1221 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1222 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1223 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1224 latex_collapsed_vector <- function( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1225 collapse_string, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1226 v, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1227 underscore_whack = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1228 action = cat0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1229 ) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1230 v_sub <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1231 if (underscore_whack) whack_underscores(v) else v |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1232 action( |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1233 paste0( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1234 v_sub, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1235 collapse = collapse_string |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1236 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1237 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1238 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1239 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1240 latex_itemized_collapsed <- function(collapse_string, v, underscore_whack = TRUE) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1241 cat("\\begin{itemize}\n\\item ") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1242 latex_collapsed_vector(collapse_string, v, underscore_whack) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1243 cat("\n\\end{itemize}\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1244 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1245 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1246 latex_itemized_list <- function(v, underscore_whack = TRUE) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1247 latex_itemized_collapsed("\n\\item ", v, underscore_whack) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1248 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1249 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1250 latex_enumerated_collapsed <- function(collapse_string, v, underscore_whack = TRUE) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1251 cat("\\begin{enumerate}\n\\item ") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1252 latex_collapsed_vector(collapse_string, v, underscore_whack) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1253 cat("\n\\end{enumerate}\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1254 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1255 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1256 latex_enumerated_list <- function(v) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1257 latex_enumerated_collapsed("\n\\item ", v) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1258 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1259 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1260 latex_table_row <- function(v, extra = "", underscore_whack = TRUE) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1261 latex_collapsed_vector(" & ", v, underscore_whack) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1262 cat(extra) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1263 cat(" \\\\\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1264 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1265 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1266 latex_tabbing_row <- function( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1267 v, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1268 extra = "", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1269 underscore_whack = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1270 action = cat0 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1271 ) { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1272 # latex_collapsed_vector applies action to result of paste0; |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1273 # by default, action = cat; |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1274 # hence, a scalar string is assigned to v_collapsed |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1275 v_collapsed <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1276 latex_collapsed_vector( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1277 "} \\> \\tabfill{", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1278 v, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1279 underscore_whack, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1280 action = paste0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1281 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1282 action( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1283 "\\tabfill{", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1284 v_collapsed, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1285 "}", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1286 extra, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1287 " \\\\\n" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1288 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1289 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1290 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1291 # N.B. use con = "" to emulate regular cat |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1292 fcat0 <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1293 function(..., sprtr = " ", cnnctn = file()) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1294 cat0(..., sep = sprtr, file = cnnctn) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1295 invisible(cnnctn) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1296 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1297 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1298 hypersub <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1299 function(s) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1300 hyper <- tolower(s) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1301 hyper <- gsub("[^a-z0-9]+", "-", hyper) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1302 hyper <- gsub("[-]+", "-", hyper) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1303 hyper <- gsub("[_]+", "-", hyper) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1304 hyper <- sub("^[-]", "", hyper) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1305 hyper <- sub("[-]$", "", hyper) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1306 return(hyper) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1307 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1308 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1309 table_href <- function(s = "offset", caption = "") { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1310 paste0("\\hyperlink{table.\\arabic{", s, "}}{Table \\arabic{", s, "}}") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1311 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1312 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1313 table_offset <- function(i = 0, s = "offset", new = FALSE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1314 paste0( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1315 if (new) paste0("\\newcounter{", s, "}\n") else "", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1316 "\\setcounter{", s, "}{\\value{table}}\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1317 paste0(if (i > 0) rep(paste0("\\stepcounter{", s, "}"), i), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1318 ) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1319 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1320 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1321 a_section_header <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1322 function(s, prefix = "") { |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1323 hyper <- hypersub(s) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1324 my_subsection_header <- sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1325 "\\hypertarget{%s}{\\%ssection{%s}\\label{%s}}\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1326 hyper, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1327 prefix, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1328 gsub("_", "\\_", s, fixed = TRUE), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1329 hyper |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1330 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1331 my_subsection_header |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1332 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1333 section_header <- function(s) a_section_header(s, "") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1334 subsection_header <- function(s) a_section_header(s, "sub") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1335 subsubsection_header <- function(s) a_section_header(s, "subsub") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1336 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1337 ### SQLite functions |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1338 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1339 ddl_exec <- function(db, sql) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1340 discard <- DBI::dbExecute(conn = db, statement = sql) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1341 if (FALSE && discard != 0) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1342 need_newpage <- TRUE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1343 if (need_newpage) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1344 need_newpage <<- FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1345 cat("\\newpage\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1346 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1347 o_file <- stdout() |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1348 cat("\n\\begin{verbatim}\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1349 cat(sql, file = o_file) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1350 cat(sprintf("\n%d rows affected by DDL\n", discard), file = o_file) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1351 cat("\n\\end{verbatim}\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1352 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1353 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1354 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1355 dml_no_rows_exec <- function(db, sql) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1356 discard <- DBI::dbExecute(conn = db, statement = sql) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1357 if (discard != 0) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1358 need_newpage <- TRUE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1359 if (need_newpage) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1360 need_newpage <<- FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1361 cat("\\newpage\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1362 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1363 cat("\n\\begin{verbatim}\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1364 o_file <- stdout() |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1365 cat(sql, file = o_file) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1366 cat(sprintf("\n%d rows affected by DML\n", discard), file = o_file) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1367 cat("\n\\end{verbatim}\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1368 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1369 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1370 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1371 ### KSEA functions and helpers |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1372 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1373 #' The KSEA App Analysis (KSEA Kinase Scores Only) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1374 #' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1375 #' Compute KSEA kinase scores and statistics from phoshoproteomics data input |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1376 #' Adapted from KSEAapp::KSEA.Scores to allow retrieval of maximum log2(FC) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1377 #' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1378 #' Result is an R data.frame with column names |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1379 #' "Kinase.Gene", "mS", "Enrichment", "m", "z.score", "p.value", "FDR" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1380 #' "Please refer to the original Casado et al. publication for detailed |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1381 #' description of these columns and what they represent: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1382 #' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1383 #' - Kinase.Gene indicates the gene name for each kinase. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1384 #' - mS represents the mean log2(fold change) of all the |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1385 #' kinase's substrates. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1386 #' - Enrichment is the background-adjusted value of the kinase's mS. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1387 #' - m is the total number of detected substrates |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1388 #' from the experimental dataset for each kinase. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1389 #' - z.score is the normalized score for each kinase, weighted by |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1390 #' the number of identified substrates. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1391 #' - p.value represents the statistical assessment for the z.score. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1392 #' - FDR is the p-value adjusted for multiple hypothesis testing |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1393 #' using the Benjamini & Hochberg method." |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1394 #' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1395 #' @param ksdata the Kinase-Substrate dataset uploaded from the file |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1396 #' prefaced with "PSP&NetworKIN_" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1397 #' available from github.com/casecpb/KSEA/ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1398 #' @param px the experimental data file formatted as described in |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1399 #' the KSEA.Complete() documentation |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1400 #' @param networkin a binary input of TRUE or FALSE, indicating whether |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1401 #' or not to include NetworKIN predictions, where |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1402 #' \code{NetworKIN = TRUE} |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1403 #' means include NetworKIN predictions |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1404 #' @param networkin_cutoff a numeric value between 1 and infinity setting |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1405 #' the minimum NetworKIN score |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1406 #' (this can be omitted if NetworKIN = FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1407 #' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1408 #' @return creates a new R data.frame with all the KSEA kinase |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1409 #' scores, along with each one's statistical |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1410 #' assessment, as described herein. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1411 #' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1412 #' @references |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1413 #' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1414 #' Casado et al. (2013) Sci Signal. 6(268):rs6 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1415 #' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1416 #' Hornbeck et al. (2015) Nucleic Acids Res. 43:D512-20 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1417 #' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1418 #' Horn et al. (2014) Nature Methods 11(6):603-4 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1419 #' |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1420 ksea_scores <- function( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1421 # For human data, typically, ksdata = KSEAapp::ksdata |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1422 ksdata, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1423 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1424 # Input data file having columns: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1425 # - Protein : abbreviated protein name |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1426 # - Gene : HUGO gene name |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1427 # - Peptide : peptide sequence without indications of phosphorylation |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1428 # - Reside.Both : position(s) of phosphorylation within Gene sequence |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1429 # - First letter designates AA that is modified |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1430 # - Numbers indicate position within Gene |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1431 # - Multiple values are separated by semicolons |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1432 # - p : p-value |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1433 # - FC : fold-change |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1434 px, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1435 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1436 # A binary input of TRUE or FALSE, indicating whether or not to include |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1437 # NetworKIN predictions |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1438 networkin, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1439 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1440 # A numeric value between 1 and infinity setting the minimum NetworKIN |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1441 # score (can be left out if networkin = FALSE) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1442 networkin_cutoff, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1443 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1444 # Minimum substrate count, necessary to adjust the p-value appropriately. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1445 minimum_substrate_count |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1446 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1447 ) { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1448 # no px$FC should be <= 0, but abs(px$FC) is used below as a precaution. |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1449 if (length(grep(";", px$Residue.Both)) == 0) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1450 # There are no Residue.Both entries having semicolons, so new is |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1451 # simply px except two columns are renamed and a column is added |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1452 # for log2(abs(fold-change)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1453 new <- px |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1454 colnames(new)[c(2, 4)] <- c("SUB_GENE", "SUB_MOD_RSD") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1455 new$log2_fc <- log2(abs(as.numeric(as.character(new$FC)))) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1456 new <- new[complete.cases(new$log2_fc), ] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1457 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1458 # Split each row having semicolons in Residue.Both into rows that are |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1459 # duplicated in all respects except that each row has a single |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1460 # member of the set "split-on-semicolon-Residue.Both" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1461 px_double <- px[grep(";", px$Residue.Both), ] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1462 residues <- as.character(px_double$Residue.Both) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1463 residues <- as.matrix(residues, ncol = 1) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1464 split <- strsplit(residues, split = ";") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1465 # x gets count of residues in each row, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1466 # i.e., 1 + count of semicolons |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1467 x <- sapply(split, length) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1468 # Here is the set of split rows |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1469 px_single <- data.frame( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1470 Protein = rep(px_double$Protein, x), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1471 Gene = rep(px_double$Gene, x), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1472 Peptide = rep(px_double$Peptide, x), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1473 Residue.Both = unlist(split), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1474 p = rep(px_double$p, x), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1475 FC = rep(px_double$FC, x) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1476 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1477 # new first gets the split rows |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1478 new <- px[-grep(";", px$Residue.Both), ] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1479 # to new, append the rows that didn't need splitting in the first place |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1480 new <- rbind(new, px_single) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1481 # map Gene to SUB_GENE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1482 # map Residue.Both to SUB_MOD_RSD |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1483 colnames(new)[c(2, 4)] <- c("SUB_GENE", "SUB_MOD_RSD") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1484 # Eliminate any non-positive values to prevent introduction of |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1485 # infinite or NaN values |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1486 new[(0 <= new$log2_fc), "log2_fc"] <- NA |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1487 # Because of preceding step, there is no need for abs in the next line |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1488 new$log2_fc <- log2(as.numeric(as.character(new$FC))) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1489 # Convert any illegal values from NaN to NA |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1490 new[is.nan(new$log2_fc), "log2_fc"] <- NA |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1491 # Eliminate rows having missing values (e.g., non-imputed data) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1492 new <- new[complete.cases(new$log2_fc), ] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1493 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1494 # At this point, new$log2_fc is signed according to which contrast has |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1495 # the greater intensity |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1496 # To take the magnitude into account without taking the direction into |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1497 # account, set params$kseaUseAbsoluteLog2FC to TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1498 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1499 # Should KSEA be performed aggregating signed log2FC or absolute? |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1500 # FALSE use raw log2FC for KSEA as for KSEAapp::KSEA.Scores |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1501 if (params$kseaUseAbsoluteLog2FC) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1502 # TRUE use abs(log2FC) for KSEA as Justin requested; this is a |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1503 # justifiable deviation from the KSEAapp::KSEA.Scores algorithm. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1504 new$log2_fc <- abs(new$log2_fc) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1505 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1506 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1507 monitor_filtration_on_stderr <- TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1508 if (monitor_filtration_on_stderr) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1509 # set to TRUE to monitor filtration on stderr |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1510 sink(stderr()) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1511 cat(see_variable(networkin, "\n")) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1512 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1513 ksdata_filtered <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1514 sqldf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1515 sprintf("%s %s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1516 "select * from ksdata where not Source = 'NetworKIN'", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1517 if (networkin) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1518 sprintf("or networkin_score >= %d", networkin_cutoff) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1519 else |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1520 "" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1521 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1522 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1523 if (monitor_filtration_on_stderr) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1524 cat(see_variable(sqldf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1525 "select count(*), Source from ksdata group by Source"), "\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1526 cat(see_variable(sqldf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1527 "select count(*), Source from ksdata_filtered group by Source"), "\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1528 sink() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1529 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1530 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1531 ############################################################################ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1532 # Line numbers below refer to lines of: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1533 # https://github.com/casecpb/KSEAapp/blob/master/R/KSEA.Scores.R |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1534 # I would put the original line in a comment but then lint would complain... |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1535 # - Indeed, I had to rename all the variables because lint didn't like names |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1536 # containing periods or capital letters. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1537 # ACE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1538 ############################################################################ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1539 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1540 # (1) Join the two data.frames on common columns SUB_GENE and SUB_MOD_RSD |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1541 # colnames of ksdata_filtered: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1542 # "KINASE" "KIN_ACC_ID" "GENE" "KIN_ORGANISM" "SUBSTRATE" "SUB_GENE_ID" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1543 # "SUB_ACC_ID" "SUB_GENE" "SUB_ORGANISM" "SUB_MOD_RSD" "SITE_GRP_ID" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1544 # "SITE_...7_AA" "networkin_score" "Source" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1545 # colnames of new: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1546 # "Protein" "SUB_GENE" "Peptide" "SUB_MOD_RSD" "p" "FC" "log2_fc" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1547 # Equivalent to: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1548 # SELECT a.*. b.Protein, b.Peptide, b.p, b.FC, b.log2_fc |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1549 # FROM ksdata_filtered a |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1550 # INNER JOIN new b |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1551 # ON a.SUB_GENE = b.SUB_GENE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1552 # AND a.SUB_MOD_RSD = b.SUB_MOD_RSD |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1553 # (KSEA.Scores.R line # 105) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1554 # "Extract KSData.filtered annotations that are only found in new" |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1555 ksdata_dataset <- base::merge(ksdata_filtered, new) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1556 # colnames of ksdata_dataset: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1557 # "KINASE" "KIN_ACC_ID" "GENE" "KIN_ORGANISM" "SUBSTRATE" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1558 # "SUB_GENE_ID" "SUB_ACC_ID" "SUB_GENE" "SUB_ORGANISM" "SUB_MOD_RSD" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1559 # "SITE_GRP_ID" "SITE_...7_AA" "networkin_score" "Source" "Protein" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1560 # "Peptide" "p" "FC" "log2_fc" (uniprot_no_isoform) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1561 # Re-order dataset; prior to accounting for isoforms |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1562 # (KSEA.Scores.R line # 106) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1563 ksdata_dataset <- ksdata_dataset[order(ksdata_dataset$GENE), ] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1564 # Extract non-isoform accession in UniProtKB |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1565 # (KSEA.Scores.R line # 107) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1566 ksdata_dataset$uniprot_no_isoform <- sapply( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1567 ksdata_dataset$KIN_ACC_ID, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1568 function(x) unlist(strsplit(as.character(x), split = "-"))[1] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1569 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1570 # "last expression collapses isoforms ... for easy processing" |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1571 # Discard previous results while selecting interesting columns ... |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1572 # (KSEA.Scores.R line # 110) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1573 ksdata_dataset_abbrev <- ksdata_dataset[, c(5, 1, 2, 16:19, 14)] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1574 # Column names are now: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1575 # "GENE" "SUB_GENE" "SUB_MOD_RSD" "Peptide" "p" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1576 # "FC" "log2_fc" "Source" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1577 # Make column names human-readable |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1578 # (KSEA.Scores.R line # 111) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1579 colnames(ksdata_dataset_abbrev) <- c( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1580 "Kinase.Gene", "Substrate.Gene", "Substrate.Mod", "Peptide", "p", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1581 "FC", "log2FC", "Source" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1582 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1583 # SELECT * FROM ksdata_dataset_abbrev |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1584 # ORDER BY Kinase.Gene, Substrate.Gene, Substrate.Mod, p |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1585 # (KSEA.Scores.R line # 112) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1586 # "Extract KSData.filtered annotations that are only found in new" |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1587 ksdata_dataset_abbrev <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1588 ksdata_dataset_abbrev[ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1589 order( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1590 ksdata_dataset_abbrev$Kinase.Gene, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1591 ksdata_dataset_abbrev$Substrate.Gene, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1592 ksdata_dataset_abbrev$Substrate.Mod, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1593 ksdata_dataset_abbrev$p), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1594 ] |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1595 if (print_nb_messages) nbe(see_variable(ksdata_dataset_abbrev)) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1596 # First aggregation step to account for multiply phosphorylated peptides |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1597 # and differing peptide sequences; the goal here is to combine results |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1598 # for all measurements of the same substrate. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1599 # SELECT `Kinase.Gene`, `Substrate.Gene`, `Substrate.Mod`, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1600 # `Source`, avg(log2FC) AS log2FC |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1601 # FROM ksdata_dataset_abbrev |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1602 # GROUP BY `Kinase.Gene`, `Substrate.Gene`, `Substrate.Mod`, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1603 # `Source` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1604 # ORDER BY `Kinase.Gene`; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1605 # in two steps: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1606 # (1) compute average log_2(fold-change) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1607 # "take the mean of the log2FC amongst phosphosite duplicates" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1608 # (KSEA.Scores.R line # 115) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1609 ksdata_dataset_abbrev <- aggregate( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1610 log2FC ~ Kinase.Gene + Substrate.Gene + Substrate.Mod + Source, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1611 data = ksdata_dataset_abbrev, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1612 FUN = mean |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1613 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1614 if (print_nb_messages) nbe(see_variable(ksdata_dataset_abbrev)) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1615 # (2) order by Kinase.Gene |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1616 # (KSEA.Scores.R line # 117) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1617 ksdata_dataset_abbrev <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1618 ksdata_dataset_abbrev[order(ksdata_dataset_abbrev$Kinase.Gene), ] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1619 # SELECT `Kinase.Gene`, count(*) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1620 # FROM ksdata_dataset_abbrev |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1621 # GROUP BY `Kinase.Gene`; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1622 # in two steps: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1623 # (1) Extract the list of Kinase.Gene names |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1624 # "@@@@@@@@@@@@@@@@@@@@" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1625 # "Do analysis for KSEA" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1626 # "@@@@@@@@@@@@@@@@@@@@" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1627 # (KSEA.Scores.R line # 124) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1628 kinase_list <- as.vector(ksdata_dataset_abbrev$Kinase.Gene) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1629 # (2) Convert to a named list of counts of kinases in ksdata_dataset_abrev, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1630 # named by Kinase.Gene |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1631 # (KSEA.Scores.R line # 125) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1632 kinase_list <- as.matrix(table(kinase_list)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1633 # Second aggregation step to account for all substrates per kinase |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1634 # CREATE TABLE mean_fc |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1635 # AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1636 # SELECT `Kinase.Gene`, avg(log2FC) AS log2FC |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1637 # FROM ksdata_dataset_abbrev |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1638 # GROUP BY `Kinase.Gene` |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1639 # (KSEA.Scores.R line # 127) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1640 if (print_nb_messages) nb(see_variable(ksdata_dataset_abbrev), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1641 mean_fc <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1642 aggregate( |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1643 log2FC ~ Kinase.Gene, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1644 data = ksdata_dataset_abbrev, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1645 FUN = mean |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1646 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1647 if (print_nb_messages) nbe(see_variable(mean_fc), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1648 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1649 # for contrast j |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1650 # for each kinase i |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1651 # extract log2 of fold-change (from `new` above) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1652 # (used in KSEA.Scores.R lines # 130 & 132) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1653 log2_fc_j_each_i <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1654 new$log2_fc |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1655 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1656 # for contrast j |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1657 # for all kinases i |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1658 # compute mean of abs(log2 of fold-change) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1659 # (used in KSEA.Scores.R lines # 130) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1660 mean_abs_log2_fc_j_all_i <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1661 mean(abs(log2_fc_j_each_i), na.rm = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1662 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1663 # for contrast j |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1664 # for all kinases i |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1665 # compute mean of log2 of fold-change |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1666 # (used in KSEA.Scores.R lines # 132) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1667 mean_log2_fc_j_all_i <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1668 mean(log2_fc_j_each_i, na.rm = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1669 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1670 # Reorder mean_fc, although I don't see why |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1671 # (KSEA.Scores.R line 128 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1672 mean_fc <- mean_fc[order(mean_fc[, 1]), ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1673 # mean_fc columns so far: "Kinase.Gene", "log2FC" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1674 # - Kinase.Gene |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1675 # indicates the gene name for each kinase. |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1676 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1677 # Create column 3: mS |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1678 # - mS |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1679 # represents the mean log2(fold change) of all the |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1680 # kinase's substrates. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1681 # (KSEA.Scores.R line # 129) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1682 mean_fc$m_s <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1683 mean_fc_m_s <- mean_fc[, 2] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1684 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1685 # Create column 4: Enrichment |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1686 # - Enrichment |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1687 # is the background-adjusted value of the kinase's mS. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1688 # (KSEA.Scores.R line # 130) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1689 mean_fc$enrichment <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1690 mean_fc_m_s / mean_abs_log2_fc_j_all_i |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1691 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1692 # Create column 5: m, count of substrates of kinase (count of j for i) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1693 # - m |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1694 # is the total number of detected substrates |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1695 # from the experimental dataset for each kinase. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1696 # (KSEA.Scores.R line # 131) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1697 mean_fc$m <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1698 mean_fc_m <- kinase_list |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1699 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1700 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1701 # Create column 6: z-score |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1702 # - z.score |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1703 # is the normalized score for each kinase, weighted by |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1704 # the number of identified substrates. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1705 # (KSEA.Scores.R line # 132) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1706 mean_fc$z_score <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1707 (mean_fc_m_s - mean_log2_fc_j_all_i) * sqrt(mean_fc_m) / |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1708 sd(log2_fc_j_each_i, na.rm = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1709 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1710 # Create column 7: p-value, deduced from z-score |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1711 # - p.value |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1712 # represents the statistical assessment for the z.score. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1713 # (KSEA.Scores.R line # 133) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1714 # "one-tailed p-value" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1715 mean_fc$p_value <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1716 pnorm(-abs(mean_fc$z_score)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1717 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1718 # zap excluded kinases; this must be done before adjusting p-value |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1719 if (TRUE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1720 mean_fc <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1721 mean_fc[ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1722 mean_fc$m >= minimum_substrate_count, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1723 , |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1724 drop = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1725 ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1726 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1727 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1728 #ACE nb(see_variable(nrow(mean_fc)), "\n") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1729 # Create column 8: FDR, deduced by Benjamini-Hochberg adustment from p-value |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1730 # - FDR |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1731 # is the p-value adjusted for multiple hypothesis testing |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1732 # using the Benjamini & Hochberg method." |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1733 # (KSEA.Scores.R line # 134) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1734 mean_fc$fdr <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1735 p.adjust(mean_fc$p_value, method = "fdr") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1736 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1737 # It makes no sense to leave Z-scores negative when using |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1738 # absolute value of fold-change |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1739 if (params$kseaUseAbsoluteLog2FC) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1740 mean_fc$z_score <- abs(mean_fc$z_score) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1741 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1742 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1743 # Remove second column (log2FC), which is duplicated as mS |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1744 # (KSEA.Scores.R line # 136) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1745 mean_fc <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1746 mean_fc[order(mean_fc$Kinase.Gene), -2] |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1747 # Correct the column names which we had to hack because of the linter... |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1748 colnames(mean_fc) <- c( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1749 "Kinase.Gene", "mS", "Enrichment", "m", "z.score", "p.value", "FDR" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1750 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1751 # (KSEA.Scores.R line # 138) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1752 return(mean_fc) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1753 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1754 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1755 ksea_low_fdr_barplot_factory <- function( |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1756 rslt, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1757 i_cntrst, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1758 i, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1759 a_level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1760 b_level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1761 fold_change, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1762 caption |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1763 ) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1764 rslt_score_list_i <- rslt$score_list[[i]] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1765 if (!is.null(rslt_score_list_i)) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1766 rslt_score_list_i_nrow <- nrow(rslt_score_list_i) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1767 k <- data.frame( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1768 contrast = as.integer(i_cntrst), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1769 a_level = rep.int(a_level, rslt_score_list_i_nrow), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1770 b_level = rep.int(b_level, rslt_score_list_i_nrow), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1771 kinase_gene = rslt_score_list_i$Kinase.Gene, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1772 mean_log2_fc = rslt_score_list_i$mS, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1773 enrichment = rslt_score_list_i$Enrichment, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1774 substrate_count = rslt_score_list_i$m, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1775 z_score = rslt_score_list_i$z.score, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1776 p_value = rslt_score_list_i$p.value, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1777 fdr = rslt_score_list_i$FDR |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1778 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1779 selector <- switch( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1780 ksea_cutoff_statistic, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1781 "FDR" = { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1782 k$fdr |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1783 }, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1784 "p.value" = { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1785 k$p_value |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1786 }, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1787 { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1788 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1789 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1790 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1791 ksea_cutoff_statistic |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1792 ) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1793 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1794 param_df_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1795 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1796 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1797 ) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1798 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1799 k <- k[selector < ksea_cutoff_threshold, ] |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1800 nrow_k <- nrow(k) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1801 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1802 #ACE nbe(see_variable(fdr_barplot_dataframe <- k)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1803 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1804 if (nrow_k > 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1805 max_nchar_rowname <- max(nchar(rownames(k))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1806 my_cex_names <- 1.0 / (1 + nrow_k / 50) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1807 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1808 if (print_trace_messages) cat_margins("Initially") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1809 if (print_trace_messages) cat_variable(nrow_k, "\n\n", 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1810 if (print_trace_messages) cat_variable(my_cex_names, "\n\n", 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1811 if (print_trace_messages) cat_variable(max_nchar_rowname, "\n\n", 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1812 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1813 # fin: The figure region dimensions, (width, height), in inches. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1814 # mar: A numerical vector of the form c(bottom, left, top, right) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1815 # that gives the number of lines of margin to be specified |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1816 # on the four sides of the plot; default: c(5, 4, 4, 2) + 0.1 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1817 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1818 # mar: The figure region dimensions, (width, height), in inches. |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1819 numeric_z_score <- as.numeric(k$z_score) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1820 bar_order <- order(-as.numeric(k$p_value)) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1821 kinase_name <- k$kinase_gene |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1822 long_caption <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1823 sprintf( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1824 "Kinase z-score, %s, KSEA %s < %s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1825 caption, |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1826 ksea_cutoff_statistic, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1827 ksea_cutoff_threshold |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1828 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1829 my_cex_caption <- 65.0 / max(65.0, nchar(long_caption)) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1830 # return a function that draws the plot |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1831 function() { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1832 par_fin <- par("fin") # vector of width_in_inches and height_in_inches) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1833 op <- par( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1834 bg = if (print_trace_messages) "yellow" else "white", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1835 fin = c(par_fin[1], min(par_fin[2], 2.5 + nrow_k / 6)), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1836 mar = par("mar") + |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1837 c(3 / nrow_k, (1 + max_nchar_rowname * my_cex_names) / 2, 0, 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1838 # bottom, left, top, right |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1839 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1840 on.exit(par(op)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1841 if (print_trace_messages) cat_margins("Eventually") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1842 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1843 barplot( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1844 height = numeric_z_score[bar_order], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1845 border = NA, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1846 xpd = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1847 cex.names = my_cex_names, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1848 main = long_caption, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1849 cex.main = my_cex_caption, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1850 names.arg = kinase_name[bar_order], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1851 horiz = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1852 srt = 45, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1853 las = 1, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1854 cex.axis = 0.9 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1855 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1856 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1857 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1858 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1859 no_op |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1860 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1861 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1862 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1863 # note that this adds elements to the global variable `ksea_asterisk_hash` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1864 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1865 ksea_low_fdr_print <- function( |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1866 rslt, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1867 i_cntrst, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1868 i, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1869 a_level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1870 b_level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1871 fold_change, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1872 caption, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1873 write_db = TRUE, # if TRUE, write to DB, else print table |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1874 anchor = c(const_table_anchor_p, const_table_anchor_t) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1875 ) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1876 rslt_score_list_i <- rslt$score_list[[i]] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1877 if (!is.null(rslt_score_list_i)) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1878 rslt_score_list_i_nrow <- nrow(rslt_score_list_i) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1879 k <- contrast_ksea_scores <- data.frame( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1880 contrast = as.integer(i_cntrst), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1881 a_level = rep.int(a_level, rslt_score_list_i_nrow), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1882 b_level = rep.int(b_level, rslt_score_list_i_nrow), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1883 kinase_gene = rslt_score_list_i$Kinase.Gene, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1884 mean_log2_fc = rslt_score_list_i$mS, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1885 enrichment = rslt_score_list_i$Enrichment, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1886 substrate_count = rslt_score_list_i$m, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1887 z_score = rslt_score_list_i$z.score, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1888 p_value = rslt_score_list_i$p.value, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1889 fdr = rslt_score_list_i$FDR |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1890 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1891 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1892 selector <- switch( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1893 ksea_cutoff_statistic, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1894 "FDR" = { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1895 k$fdr |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1896 }, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1897 "p.value" = { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1898 k$p_value |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1899 }, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1900 { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1901 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1902 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1903 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1904 ksea_cutoff_statistic |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1905 ) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1906 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1907 param_df_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1908 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1909 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1910 ) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1911 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1912 k <- k[selector < ksea_cutoff_threshold, ] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1913 # save kinase names to ksea_asterisk_hash |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1914 for (kinase_name in k$kinase_gene) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1915 ksea_asterisk_hash[[kinase_name]] <- 1 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1916 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1917 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1918 if (write_db) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1919 db_write_table_overwrite <- (i_cntrst < 2) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1920 db_write_table_append <- !db_write_table_overwrite |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1921 RSQLite::dbWriteTable( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1922 conn = db, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1923 name = "contrast_ksea_scores", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1924 value = contrast_ksea_scores, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1925 append = db_write_table_append |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1926 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1927 "" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1928 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1929 selector <- switch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1930 ksea_cutoff_statistic, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1931 "FDR" = { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1932 contrast_ksea_scores$fdr |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1933 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1934 "p.value" = { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1935 contrast_ksea_scores$p_value |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1936 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1937 { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1938 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1939 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1940 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1941 ksea_cutoff_statistic |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1942 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1943 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1944 param_df_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1945 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1946 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
1947 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1948 if (print_nb_messages) nbe(see_variable(contrast_ksea_scores)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1949 output_df <- contrast_ksea_scores[ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1950 selector < ksea_cutoff_threshold, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1951 c("kinase_gene", "mean_log2_fc", "enrichment", "substrate_count", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1952 "z_score", "p_value", "fdr") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1953 ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1954 output_df$kinase_gene <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1955 gsub( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1956 "_", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1957 "\\\\_", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1958 output_df$kinase_gene |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1959 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1960 colnames(output_df) <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1961 c( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1962 colnames(output_df)[1], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1963 colnames(output_df)[2], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1964 "enrichment", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1965 "m_s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1966 "z_score", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1967 "p_value", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1968 "fdr" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1969 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1970 #ACE output_order <- with(output_df, order(fdr)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1971 output_order <- with(output_df, order(p_value)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1972 output_df <- output_df[output_order, ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1973 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1974 output_df[, 2] <- sprintf("%0.3g", output_df[, 2]) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1975 output_df$fdr <- sprintf("%0.4f", output_df$fdr) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1976 output_df$p_value <- sprintf("%0.2e", output_df$p_value) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1977 output_df$z_score <- sprintf("%0.2f", output_df$z_score) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1978 output_df$m_s <- sprintf("%d", output_df$m_s) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1979 output_df$enrichment <- sprintf("%0.3g", output_df$enrichment) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1980 output_ncol <- ncol(output_df) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1981 colnames(output_df) <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1982 c( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1983 "Kinase", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1984 "\\(\\overline{{\\lvert}\\log_2 (\\text{fold-change}){\\rvert}}\\)", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1985 "Enrichment", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1986 "Substrates", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1987 "z-score", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1988 "p-value", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1989 "FDR" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1990 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1991 selector <- switch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1992 ksea_cutoff_statistic, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1993 "FDR" = { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1994 rslt$score_list[[i]]$FDR |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1995 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1996 "p.value" = { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1997 rslt$score_list[[i]]$p.value |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1998 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
1999 { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2000 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2001 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2002 "Unexpected cutoff statistic %s rather than 'FDR' or 'p.value'", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2003 ksea_cutoff_statistic |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2004 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2005 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2006 param_df_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2007 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2008 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2009 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2010 if (sum(selector < ksea_cutoff_threshold) > 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2011 if (print_nb_messages) nbe(see_variable(output_df)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2012 math_caption <- gsub("{", "\\{", caption, fixed = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2013 math_caption <- gsub("}", "\\}", math_caption, fixed = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2014 # with ( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2015 # output_df, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2016 # ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2017 if (TRUE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2018 output_df$Kinase <- whack_underscores(output_df$Kinase) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2019 data_frame_tabbing_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2020 x = output_df, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2021 # vector of tab stops, in inches |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2022 tabstops = c(1.0, 1.2, 1.0, 1.0, 1.0, 1.0), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2023 # vector of headings, registered with tab-stops |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2024 headings = colnames(output_df), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2025 # digits to pass to format.data.frame |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2026 digits = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2027 # maximumn number of rows to print |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2028 max = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2029 # optional caption |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2030 caption = sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2031 "\\text{%s}, KSEA %s < %s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2032 math_caption, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2033 ksea_cutoff_statistic, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2034 ksea_cutoff_threshold |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2035 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2036 # set underscore_whack to TRUE to escape underscores |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2037 underscore_whack = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2038 # flag for landscape mode |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2039 landscape = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2040 # flag indicating that subsubsection should be used for caption |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2041 # rather than subsection |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2042 use_subsubsection_header = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2043 # character-size indicator; for possible values, see: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2044 # https://tug.org/texinfohtml/latex2e.html#Font-sizes |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2045 charactersize = "small", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2046 # set verbatim to TRUE to debug output |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2047 verbatim = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2048 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2049 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2050 data_frame_table_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2051 x = output_df, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2052 justification = "l c c c c c c", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2053 centered = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2054 caption = sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2055 "\\text{%s}, KSEA %s < %s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2056 math_caption, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2057 ksea_cutoff_statistic, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2058 ksea_cutoff_threshold |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2059 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2060 anchor = anchor, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2061 underscore_whack = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2062 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2063 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2064 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2065 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2066 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2067 "\\break |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2068 No kinases had |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2069 \\(\\text{KSEA %s}_\\text{enrichment} < %s\\) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2070 for contrast %s\\hfill\\break\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2071 ksea_cutoff_statistic, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2072 ksea_cutoff_threshold, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2073 caption |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2074 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2075 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2076 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2077 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2078 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2079 "" |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2080 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2081 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2082 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2083 # create_breaks is a helper for ksea_heatmap |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2084 create_breaks <- function(merged_scores) { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2085 if (sum(!is.na(merged_scores)) < 2) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2086 return(NULL) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2087 if (min(merged_scores, na.rm = TRUE) < -1.6) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2088 breaks_neg <- seq(-1.6, 0, length.out = 30) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2089 breaks_neg <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2090 append( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2091 seq(min(merged_scores, na.rm = TRUE), -1.6, length.out = 10), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2092 breaks_neg |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2093 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2094 breaks_neg <- sort(unique(breaks_neg)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2095 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2096 breaks_neg <- seq(-1.6, 0, length.out = 30) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2097 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2098 if (max(merged_scores, na.rm = TRUE) > 1.6) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2099 breaks_pos <- seq(0, 1.6, length.out = 30) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2100 breaks_pos <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2101 append( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2102 breaks_pos, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2103 seq(1.6, max(merged_scores, na.rm = TRUE), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2104 length.out = 10) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2105 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2106 breaks_pos <- sort(unique(breaks_pos)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2107 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2108 breaks_pos <- seq(0, 1.6, length.out = 30) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2109 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2110 breaks_all <- unique(append(breaks_neg, breaks_pos)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2111 mycol_neg <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2112 gplots::colorpanel(n = length(breaks_neg), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2113 low = "blue", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2114 high = "white") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2115 mycol_pos <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2116 gplots::colorpanel(n = length(breaks_pos) - 1, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2117 low = "white", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2118 high = "red") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2119 mycol <- unique(append(mycol_neg, mycol_pos)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2120 color_breaks <- list(breaks_all, mycol) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2121 return(color_breaks) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2122 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2123 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2124 hm2plus <- function( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2125 x, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2126 mat = matrix( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2127 c( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2128 c(0, 4, 0), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2129 c(0, 3, 3), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2130 c(2, 1, 1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2131 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2132 nrow = 3, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2133 ncol = 3, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2134 byrow = TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2135 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2136 denwid = 0.5, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2137 denhgt = 0.15, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2138 widths = c(0.5, 2.5, 1.5), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2139 heights = c(0.4, 0.15, 3.95), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2140 divergent = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2141 notecol = "grey50", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2142 trace = "none", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2143 margins = c(6, 20), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2144 srtcol = 90, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2145 srtrow = 0, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2146 density_info = "none", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2147 key_xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2148 key_par = list(), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2149 hclustfun = hclust, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2150 ... |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2151 ) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2152 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2153 varargs <- list(...) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2154 if (FALSE) # this is to avoid commenting out code to pass linting... |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2155 my_hm2 <- latex_show_invocation(heatmap.2, head_patch = FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2156 else |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2157 my_hm2 <- heatmap.2 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2158 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2159 x <- as.matrix(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2160 if (sum(!is.na(x)) < 1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2161 return(NULL) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2162 color_count <- 1 + max(64, length(as.vector(x))) # 8 was not enough |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2163 break_count <- 1 + color_count |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2164 min_nonax <- min(x, na.rm = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2165 max_nonax <- max(x, na.rm = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2166 if (print_nb_messages) nb("within hm2plus", see_variable(divergent), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2167 if (divergent) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2168 zlim <- max(abs(min_nonax), abs(max_nonax)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2169 if (print_nb_messages) nb(see_variable(pre_zlim <- zlim, "\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2170 breaks <- (zlim) / (break_count:1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2171 if (print_nb_messages) nb(see_variable(breaks, "\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2172 breaks <- breaks - median(breaks) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2173 zlim <- c(-zlim, zlim) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2174 if (print_nb_messages) nb(see_variable(zlim, "\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2175 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2176 zlim <- max(abs(min_nonax), abs(max_nonax)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2177 if (print_nb_messages) nb(see_variable(pre_zlim <- zlim, "\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2178 breaks <- zlim / (break_count:1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2179 if (print_nb_messages) nb(see_variable(breaks, "\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2180 if (max_nonax < 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2181 breaks <- breaks - zlim |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2182 zlim <- c(-zlim, 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2183 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2184 zlim <- c(0, zlim) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2185 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2186 if (print_nb_messages) nb(see_variable(zlim, "\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2187 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2188 nonax <- x |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2189 nonax[is.na(x)] <- min_nonax |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2190 if (is.null(widths)) widths <- c(denwid, 4 - denwid, 1.5) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2191 if (is.null(heights)) heights <- c(0.4, denhgt, 4.0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2192 colors <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2193 if (divergent && min_nonax < 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2194 # divergent colors on both sides of zero |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2195 colorRampPalette(c("red", "white", "blue"))(color_count) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2196 } else if (divergent && min_nonax > 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2197 # "divergent" colors > zero |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2198 colorRampPalette(c("white", "blue"))(color_count) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2199 } else if (divergent && max_nonax < 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2200 # "divergent" colors < zero |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2201 colorRampPalette(c("red", "white"))(color_count) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2202 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2203 # "non-divergent" colors including zero |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2204 hcl.colors(color_count, "YlOrRd", rev = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2205 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2206 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2207 #ACE if (print_nb_messages) nb("within hm2plus", see_variable(key_par), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2208 #ACE if (print_nb_messages) nb(see_variable(colors, "\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2209 #ACE key_par$col = colors |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2210 #ACE key_par$breaks = breaks |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2211 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2212 if (print_nb_messages) nb(see_variable(par(), "\n")) #ACE TODO remove me |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2213 if (print_nb_messages) cat("\\leavevmode\n\\linebreak\n") #ACE TODO remove me |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2214 suppressWarnings( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2215 my_hm2( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2216 x = x, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2217 col = colors, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2218 #ACE symkey = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2219 density.info = density_info, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2220 srtCol = srtcol, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2221 srtRow = srtrow, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2222 margins = margins, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2223 lwid = widths, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2224 lhei = heights, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2225 key.title = NA, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2226 key.xlab = key_xlab, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2227 key.par = key_par, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2228 lmat = mat, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2229 notecol = notecol, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2230 trace = trace, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2231 bg = "yellow", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2232 hclustfun = hclustfun, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2233 #ACE breaks = breaks, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2234 oldstyle = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2235 ... # varargs |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2236 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2237 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2238 # implicitly returning value returned by heatmap.2 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2239 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2240 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2241 # draw_kseaapp_summary_heatmap is a helper function for ksea_heatmap |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2242 draw_kseaapp_summary_heatmap <- function( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2243 x, # matrix with row/col names already formatted |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2244 sample_cluster, # a binary input of TRUE or FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2245 # indicating whether or not to perform |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2246 # hierarchical clustering of the sample columns |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2247 merged_asterisk, # matrix having dimensions of x, values "*" or "" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2248 color_breaks, # breaks for color gradation, from create_breaks |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2249 # passed to `breaks` argument of `image` |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2250 margins = c(8, 15), # two integers setting the bottom and right margins |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2251 # to accommodate row and column labels |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2252 master_cex = 0.7, # basis for text sizes |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2253 ... |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2254 ) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2255 merged_scores <- x |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2256 if (!is.matrix(x)) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2257 cat( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2258 paste0( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2259 "No plot because \\texttt{typeof(x)} is '", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2260 typeof(x), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2261 "' rather than 'matrix'.\n\n" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2262 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2263 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2264 cat_variable(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2265 return(FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2266 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2267 if (print_trace_messages) cat(sprintf("master_cex = %03f\n\n", master_cex)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2268 nrow_x <- nrow(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2269 ncol_x <- ncol(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2270 #if (nrow_x < 2) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2271 if (nrow_x < 1) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2272 cat("No plot because matrix has no rows.\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2273 return(FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2274 } else if (nrow_x < 2) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2275 cat("No plot because matrix has one row. Matrix looks like this:\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2276 cat("\n\\begin{verbatim}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2277 print(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2278 cat("\n\\end{verbatim}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2279 return(FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2280 } else if (ncol_x < 2) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2281 cat("No plot because matrix x has ", ncol_x, " columns.\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2282 cat_variable(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2283 return(FALSE) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2284 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2285 max_nchar_rowname <- max(nchar(rownames(x))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2286 max_nchar_colname <- max(nchar(colnames(x))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2287 my_limit <- g_intensity_hm_rows |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2288 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2289 my_row_cex_scale <- master_cex * 150 / nrow_x |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2290 my_col_cex_scale <- 3.0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2291 my_asterisk_scale <- 0.4 * my_row_cex_scale |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2292 my_row_warp <- 1 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2293 my_note_warp <- 2 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2294 my_row_warp <- 1 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2295 my_row_cex_asterisk <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2296 master_cex * my_row_warp * my_asterisk_scale |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2297 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2298 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2299 my_col_cex <- my_col_cex_scale * master_cex |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2300 my_row_cex <- min(3.5 * my_row_cex_asterisk, my_col_cex) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2301 my_key_cex <- 1.286 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2302 my_hm2_cex <- 1 * master_cex |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2303 my_offset <- (4.8 / (9 + nrow_x / 10)) - 0.4 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2304 if (print_trace_messages) cat(sprintf("nrow_x = %03f\n\n", nrow_x)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2305 if (print_trace_messages) cat(sprintf("my_offset = %03f\n\n", my_offset)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2306 my_offset <- 0.05 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2307 if (print_trace_messages) cat(sprintf("my_offset = %03f\n\n", my_offset)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2308 my_scale <- 3.0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2309 if (ncol_x < 10 && nrow_x < 10) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2310 my_scale <- my_scale * 10 / (10 - nrow_x) * 10 / (10 - ncol_x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2311 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2312 my_heights <- c( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2313 0.15, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2314 3.85 - my_offset, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2315 0.5 + my_offset |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2316 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2317 my_margins <- c(1, 1) + |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2318 c( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2319 margins[1] * 0.08 * max_nchar_colname * my_col_cex, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2320 margins[2] * 0.04 * max_nchar_rowname * my_row_cex |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2321 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2322 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2323 my_notecex <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2324 my_scale * |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2325 min( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2326 1.1, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2327 my_row_cex_asterisk * my_note_warp, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2328 my_col_cex * my_note_warp |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2329 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2330 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2331 if (print_trace_messages) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2332 cat_variable(my_heights, suffix = "; ") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2333 cat_variable(my_margins, suffix = "\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2334 cat_variable(my_row_cex_scale, suffix = "; ") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2335 cat_variable(my_col_cex_scale, suffix = "\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2336 cat_variable(my_row_cex_asterisk, suffix = "\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2337 cat_variable(my_row_cex, suffix = "; ") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2338 cat_variable(my_col_cex, suffix = "\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2339 cat_variable(my_row_cex, suffix = "; ") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2340 cat_variable(my_col_cex, suffix = "\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2341 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2342 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2343 hm2plus( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2344 x = merged_scores, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2345 Colv = sample_cluster, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2346 cellnote = merged_asterisk, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2347 cex = my_hm2_cex, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2348 cexCol = my_col_cex, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2349 cexRow = my_row_cex, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2350 denhgt = 0.15, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2351 density_info = "none", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2352 denwid = 0.5, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2353 divergent = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2354 key_par = list(cex = my_key_cex), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2355 key_xlab = "Z-score", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2356 margins = my_margins, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2357 notecex = my_scale * min( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2358 1.5, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2359 my_row_cex_asterisk * my_note_warp, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2360 my_col_cex * my_note_warp |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2361 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2362 notecol = "white", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2363 scale = "none", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2364 srtcol = 90, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2365 srtrow = 0, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2366 trace = "none", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2367 mat = matrix( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2368 c( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2369 c(0, 3, 3), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2370 c(2, 1, 1), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2371 c(0, 4, 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2372 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2373 nrow = 3, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2374 ncol = 3, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2375 byrow = TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2376 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2377 widths = c(0.5, 3.1, 0.9), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2378 heights = my_heights, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2379 ... |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2380 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2381 return(TRUE) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2382 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2383 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2384 # function drawing heatmap of contrast fold-change for each kinase, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2385 # adapted from KSEAapp::KSEA.Heatmap |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2386 ksea_heatmap <- function( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2387 # the data frame outputs from the KSEA.Scores() function, in list format |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2388 score_list, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2389 # a character vector of all the sample names for heatmap annotation: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2390 # - the names must be in the same order as the data in score_list |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2391 # - please avoid long names, as they may get cropped in the final image |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2392 sample_labels, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2393 # character string of either "p.value" or "FDR" indicating the data column |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2394 # to use for marking statistically significant scores |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2395 stats, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2396 # a numeric value between 0 and infinity indicating the min. number of |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2397 # substrates a kinase must have to be included in the heatmap |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2398 m_cutoff, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2399 # a numeric value between 0 and 1 indicating the p-value/FDR cutoff |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2400 # for indicating significant kinases in the heatmap |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2401 p_cutoff = { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2402 cat("argument 'p_cutoff' is required for function 'ksea_heatmap'") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2403 param_df_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2404 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2405 }, |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2406 # a binary input of TRUE or FALSE, indicating whether or not to perform |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2407 # hierarchical clustering of the sample columns |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2408 sample_cluster, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2409 # a binary input of TRUE or FALSE, indicating whether or not to export |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2410 # the heatmap as a .png image into the working directory |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2411 export = FALSE, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2412 # bottom and right margins; adjust as needehttps://tex.stackexchange.com/a/56795d if contrast names are too long |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2413 margins = c(6, 6), |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2414 # print which kinases? |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2415 # - Mandatory argument, must be one of const_ksea_.*_kinases |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2416 which_kinases, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2417 # additional arguments to gplots::heatmap.2, such as: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2418 # - main: main title of plot |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2419 # - xlab: x-axis label |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2420 # - ylab: y-axis label |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2421 ... |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2422 ) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2423 filter_m <- function(dataset, m_cutoff) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2424 filtered <- dataset[(dataset$m >= m_cutoff), ] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2425 return(filtered) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2426 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2427 score_list_m <- lapply(score_list, function(...) filter_m(..., m_cutoff)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2428 for (i in seq_len(length(score_list_m))) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2429 names <- colnames(score_list_m[[i]])[c(2:7)] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2430 colnames(score_list_m[[i]])[c(2:7)] <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2431 paste(names, i, sep = ".") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2432 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2433 master <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2434 Reduce( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2435 f = function(...) { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2436 base::merge(..., by = "Kinase.Gene", all = TRUE) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2437 }, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2438 x = score_list_m |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2439 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2440 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2441 row.names(master) <- master$Kinase.Gene |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2442 columns <- as.character(colnames(master)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2443 merged_scores <- as.matrix(master[, grep("z.score", columns), drop = FALSE]) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2444 colnames(merged_scores) <- sample_labels |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2445 merged_stats <- as.matrix(master[, grep(stats, columns)]) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2446 asterisk <- function(mtrx, p_cutoff) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2447 new <- data.frame() |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2448 for (i in seq_len(nrow(mtrx))) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2449 for (j in seq_len(ncol(mtrx))) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2450 my_value <- mtrx[i, j] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2451 if (!is.na(my_value) && my_value < p_cutoff) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2452 new[i, j] <- "*" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2453 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2454 new[i, j] <- "" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2455 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2456 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2457 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2458 return(new) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2459 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2460 merged_asterisk <- as.matrix(asterisk(merged_stats, p_cutoff)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2461 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2462 asterisk_rows <- rowSums(merged_asterisk == "*") > 0 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2463 all_rows <- rownames(merged_stats) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2464 names(asterisk_rows) <- all_rows |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2465 non_asterisk_rows <- names(asterisk_rows[asterisk_rows == FALSE]) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2466 asterisk_rows <- names(asterisk_rows[asterisk_rows == TRUE]) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2467 merged_scores_asterisk <- merged_scores[names(asterisk_rows), , drop = FALSE] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2468 merged_scores_non_asterisk <- merged_scores[names(non_asterisk_rows), , drop = FALSE] |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2469 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2470 row_list <- list() |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2471 row_list[[const_ksea_astrsk_kinases]] <- asterisk_rows |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2472 row_list[[const_ksea_all_kinases]] <- all_rows |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2473 row_list[[const_ksea_nonastrsk_kinases]] <- non_asterisk_rows |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2474 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2475 i <- which_kinases |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2476 my_row_names <- row_list[[i]] |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2477 scrs <- merged_scores[my_row_names, , drop = FALSE] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2478 stts <- merged_stats[my_row_names, , drop = FALSE] |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2479 merged_asterisk <- as.matrix(asterisk(stts, p_cutoff)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2480 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2481 color_breaks <- create_breaks(scrs) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2482 if (is.null(color_breaks)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2483 cat("No plot because matrix has too few rows.\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2484 return(NULL) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2485 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2486 plot_height <- nrow(scrs) ^ 0.55 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2487 plot_width <- ncol(scrs) ^ 0.7 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2488 if (export == "TRUE") { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2489 png( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2490 "KSEA.Merged.Heatmap.png", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2491 width = plot_width * 300, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2492 height = 2 * plot_height * 300, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2493 res = 300, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2494 pointsize = 14 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2495 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2496 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2497 did_draw <- draw_kseaapp_summary_heatmap( |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2498 x = scrs, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2499 sample_cluster = sample_cluster, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2500 merged_asterisk = merged_asterisk, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2501 color_breaks = color_breaks, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2502 margins = margins |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2503 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2504 if (export == "TRUE") { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2505 dev.off() |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2506 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2507 if (!did_draw) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2508 return(NULL) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2509 return(my_row_names) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2510 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2511 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2512 # helpers for heatmaps of phosphopeptide intensities |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2513 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2514 # factory producing function to truncate string after n characters |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2515 trunc_n <- function(n) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2516 function(x) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2517 sapply( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2518 X = x, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2519 FUN = function(s) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2520 if (is.na(s)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2521 return("NA") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2522 cond <- try_catch_w_e(nchar(s) > n) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2523 if (!is.logical(cond$value)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2524 return(cond$value$message) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2525 } else if (cond$value) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2526 paste0( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2527 strtrim(s, n), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2528 "..." |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2529 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2530 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2531 s |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2532 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2533 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2534 USE.NAMES = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2535 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2536 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2537 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2538 trunc_long_ppep <- function(x) trunc_n(40)(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2539 trunc_ppep <- function(x) trunc_n(g_ppep_trunc_n)(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2540 trunc_subgene <- function(x) trunc_n(g_subgene_trunc_n)(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2541 trunc_enriched_substrate <- function(x) trunc_n(g_sbstr_trunc_n)(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2542 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2543 # factory producing a function that returns a covariance |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2544 # matrix's rows (and columns) having variance > v_min |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2545 keep_cov_w_var_gtr_min <- function(v_min) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2546 function(x) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2547 if (!is.matrix(x)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2548 return(NULL) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2549 keepers <- sapply( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2550 X = seq_len(nrow(x)), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2551 FUN = function(i) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2552 if (x[i, i] < v_min) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2553 NA |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2554 else |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2555 x[i, i] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2556 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2557 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2558 names(keepers) <- rownames(x) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2559 keepers <- keepers[!is.na(keepers)] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2560 keepers <- names(keepers) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2561 if (length(keepers) == 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2562 return(NULL) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2563 x[keepers, keepers] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2564 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2565 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2566 # function that returns a matrix's rows having variance > 1 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2567 keep_cov_w_var_gtr_1 <- keep_cov_w_var_gtr_min(1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2568 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2569 # factory producing a function that returns |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2570 # - either a matrix's rows (rows = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2571 # - or a matrix's columns (rows = FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2572 # having variance > v_min |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2573 keep_var_gtr_min <- function(v_min) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2574 function(x, rows = TRUE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2575 nrowcol <- if (rows) nrow else ncol |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2576 if (!is.matrix(x)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2577 return(NULL) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2578 keepers <- sapply( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2579 X = seq_len(nrowcol(x)), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2580 FUN = function(i) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2581 row_var <- var( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2582 if (rows) x[i, ] else x[, i], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2583 na.rm = TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2584 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2585 if (is.na(row_var) || row_var <= v_min) NA else i |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2586 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2587 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2588 keepers <- keepers[!is.na(keepers)] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2589 if (rows) x[keepers, ] else x[, keepers] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2590 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2591 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2592 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2593 keep_var_gtr_0 <- keep_var_gtr_min(0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2594 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2595 # function drawing heatmap of phosphopeptide intensities |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2596 ppep_heatmap <- |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2597 function( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2598 m, # matrix with rownames already formatted |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2599 cutoff, # cutoff used by hm_heading_function |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2600 hm_heading_function, # construct $ cat heading from m and cutoff |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2601 hm_main_title, # main title for plot (drawn below heading) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2602 suppress_row_dendrogram = TRUE, # set to false to show dendrogram |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2603 max_peptide_count = # experimental: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2604 g_intensity_hm_rows, # values of 50 and 75 worked well |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2605 master_cex = 1.0, # basis for text sizes |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2606 margins = NULL, # optional margins (bottom, right) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2607 cellnote = NULL, # optional matrix of character; dim = dim(m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2608 adj = 0.5, # adjust text: 0 left, 0.5 middle, 1 right |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2609 ... # passthru to hm2plus or heatmap.2 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2610 ) { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2611 use_heatmap_1 <- FALSE |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2612 peptide_count <- 0 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2613 # emit the heading for the heatmap |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2614 if (hm_heading_function(m, cutoff)) { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2615 nrow_m <- nrow(m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2616 peptide_count <- min(max_peptide_count, nrow_m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2617 if (nrow_m > 1) { |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2618 m_margin <- m[peptide_count:1, ] |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2619 # Margin was heuristically derived to accommodate the widest label |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2620 row_mchar_max <- max(nchar(rownames(m_margin))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2621 col_mchar_max <- max(nchar(colnames(m_margin))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2622 row_margin <- master_cex * row_mchar_max * 2.6 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2623 col_margin <- master_cex * col_mchar_max * 2.6 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2624 if (print_trace_messages) cat(sprintf("row_margin = %0.3f; ", row_margin)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2625 if (print_trace_messages) cat(sprintf("col_margin = %0.3f; ", col_margin)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2626 hm_call <- NULL |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2627 tryCatch( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2628 { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2629 # set non-argument parameters for hm_call inner function |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2630 my_row_cex <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2631 master_cex * 200000 / ( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2632 (max(nchar(rownames(m_margin)))^2) * g_intensity_hm_rows |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2633 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2634 m_hm <- m[peptide_count:1, , drop = FALSE] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2635 if (is.null(cellnote)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2636 cellnote <- matrix("", nrow = nrow(m_hm), ncol = ncol(m_hm)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2637 cellnote[is.na(m_hm)] <- "NA" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2638 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2639 cellnote <- cellnote[peptide_count:1, , drop = FALSE] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2640 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2641 m_hm[is.na(m_hm)] <- 0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2642 nrow_m_hm <- nrow(m_hm) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2643 ncol_m_hm <- ncol(m_hm) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2644 if (nrow_m_hm < 1 || ncol_m_hm < 1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2645 return(peptide_count) # return zero as initialized above |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2646 my_limit <- g_intensity_hm_rows |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2647 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2648 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2649 my_row_cex <- master_cex * (100 / (2 + row_mchar_max)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2650 my_col_cex <- master_cex * 6 * row_margin / col_margin |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2651 my_col_adj <- min(my_col_cex, my_row_cex) / my_col_cex |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2652 my_col_cex <- min(my_col_cex, my_row_cex) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2653 col_margin <- sqrt(my_col_adj) * col_margin |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2654 if (print_trace_messages) cat(sprintf("my_row_cex = %0.3f; ", my_row_cex)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2655 if (print_trace_messages) cat(sprintf("my_col_cex = %0.3f; ", my_col_cex)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2656 if (is.null(margins)) my_margins <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2657 c( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2658 (my_col_cex + col_margin), # col |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2659 (my_row_cex + row_margin) / my_row_cex # row |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2660 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2661 else |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2662 my_margins <- margins |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2663 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2664 if (print_trace_messages) cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2665 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2666 "my_margins = c(%s)\n\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2667 paste(my_margins, collapse = ", ") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2668 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2669 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2670 my_hm2_cex <- 2 * master_cex |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2671 my_key_cex <- 0.9 - 0.1 * (g_intensity_hm_rows + nrow_m_hm) / g_intensity_hm_rows |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2672 my_key_warp <- 1.5 * 22.75 / row_margin |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2673 my_key_cex <- min(1.10, my_key_warp * my_key_cex) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2674 my_hgt_scale <- 3.70 - 0.4 * (max(1, 0.9 * my_row_cex) - 1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2675 my_hgt_scale <- 3.75 # 3.615 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2676 my_hgt_scale <- 3.60 # 3.615 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2677 if (print_trace_messages) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2678 cat_variable(my_hgt_scale, "\n\n", 3) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2679 my_warp <- max(0.1, 1.4 * (7.5 + nrow_m) / g_intensity_hm_rows) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2680 if (print_trace_messages) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2681 cat_variable(my_warp, "\n\n", 3) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2682 # added 0.9 heuristically... |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2683 my_plot_height <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2684 (0.566 + 0.354 * (nrow_m / g_intensity_hm_rows)) * |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2685 min(my_hgt_scale, my_hgt_scale * my_warp) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2686 my_plot_height <- min(3.65, my_plot_height * g_intensity_hm_rows / 50) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2687 my_heights <- c( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2688 0.3, # title and top dendrogram |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2689 my_plot_height, # plot and bottom margin |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2690 4.15 - my_hgt_scale, # legend |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2691 0.05 + my_hgt_scale - my_plot_height # whitespace below legend |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2692 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2693 my_note_cex <- min(0.8, my_row_cex, my_col_cex) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2694 if (print_trace_messages) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2695 cat_variable(my_plot_height, "\n\n", 3) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2696 cat_variable(4.19 - my_hgt_scale, "\n\n", 3) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2697 cat_variable(nrow_m_hm, "; ", 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2698 cat_variable(ncol_m_hm, "; ", 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2699 cat_variable(my_row_cex, "; ", 3) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2700 cat_variable(my_col_cex, "; ", 3) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2701 cat_variable(my_note_cex, "; ", 3) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2702 cat_variable(my_key_cex, "\n\n", 3) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2703 cat_variable(my_hgt_scale, "; ", 3) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2704 cat_variable(my_plot_height, "; ", 3) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2705 cat_variable(my_warp, "\n\n", 3) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2706 cat_variable(my_heights, "; ", 2) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2707 cat_variable(sum(my_heights), "\n\n", 3) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2708 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2709 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2710 # define hm_call inner function |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2711 hm_call <- function(x, scaling, title) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2712 my_cex_main <- min(5.0, 220 / nchar(title)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2713 op <- par( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2714 cex.main = my_cex_main * master_cex, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2715 adj = adj |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2716 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2717 if ( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2718 !is.null( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2719 hm2plus( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2720 x, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2721 Colv = NA, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2722 Rowv = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2723 cexRow = my_row_cex, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2724 cexCol = my_col_cex, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2725 dendrogram = "row", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2726 las = 1, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2727 main = title, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2728 key_xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2729 cex = my_hm2_cex, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2730 key_par = list(cex = my_key_cex), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2731 margins = my_margins, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2732 widths = c(0.4, 2.6, 1.5), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2733 heights = my_heights, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2734 mat = matrix( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2735 c( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2736 c(0, 3, 3), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2737 c(2, 1, 1), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2738 c(0, 4, 0), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2739 c(0, 0, 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2740 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2741 nrow = 4, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2742 ncol = 3, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2743 byrow = TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2744 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2745 na.rm = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2746 scale = scaling, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2747 srtcol = 90, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2748 srtrow = 0, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2749 xlab = "", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2750 cellnote = cellnote, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2751 notecex = my_note_cex, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2752 ... |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2753 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2754 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2755 ) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2756 if (print_trace_messages) cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2757 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2758 "my_heights = c(%s); sum = %0.3f\n\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2759 paste( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2760 sprintf("%0.3f", my_heights), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2761 collapse = ", " |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2762 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2763 sum(my_heights) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2764 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2765 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2766 if (print_trace_messages) cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2767 sprintf("my_key_cex = %0.3f\n\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2768 my_key_cex) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2769 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2770 if (print_trace_messages) cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2771 sprintf("my_key_cex/my_heights[3] = %0.3f\n\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2772 my_key_cex / my_heights[3]) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2773 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2774 if (print_trace_messages) cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2775 sprintf("my_heights[2]/my_heights[3] = %0.3f\n\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2776 my_heights[2] / my_heights[3]) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2777 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2778 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2779 par(op) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2780 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2781 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2782 # invoke hm_call inner function |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2783 if (sum(rowSums(!is.na(m_hm)) < 2)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2784 hm_call( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2785 m_hm, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2786 "none", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2787 "log(intensities), unscaled, unimputed, and unnormalized" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2788 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2789 else |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2790 hm_call( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2791 m_hm, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2792 "row", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2793 "log(intensities), row-scaled, unimputed, and unnormalized" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2794 ) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2795 }, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2796 error = function(e) { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2797 if (!is.null(hm_call)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2798 m_hm[is.na(m_hm)] <- 0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2799 tryCatch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2800 { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2801 if (nrow(m_hm) > 1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2802 hm_call( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2803 m_hm, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2804 "none", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2805 paste( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2806 "log(intensities), unscaled,", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2807 "zero-imputed, unnormalized" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2808 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2809 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2810 else |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2811 cat("\nThere are too few peptides to produce a heatmap.\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2812 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2813 error = function(r) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2814 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2815 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2816 "\n%s %s Internal message: %s\n\\newline\n\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2817 "Failure drawing heatmap,", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2818 "possibly because of too many missing values.\n\\newline\n\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2819 r$message |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2820 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2821 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2822 cat_margins() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2823 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2824 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2825 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2826 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2827 "\nFailure drawing heatmap, possibly because of too many missing values.\n" |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2828 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2829 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2830 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2831 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2832 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2833 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2834 # return value: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2835 peptide_count |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
2836 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2837 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2838 # function drawing heatmap of correlations if they exist, else covariances |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2839 cov_heatmap <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2840 function( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2841 m, # matrix with rownames already formatted |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2842 top_substrates = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2843 ... # passthru to hm2plus or heatmap.2 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2844 ) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2845 if (print_nb_messages) nbe(see_variable(m), " [", nrow(m), "x", ncol(m), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2846 #ACE nb(rowSums(m, na.rm = TRUE)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2847 #ACE bad_rows <- (rowSums(m, na.rm = TRUE) == 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2848 #ACE nb(see_variable(bad_rows)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2849 #ACE m <- m[-bad_rows, , drop = FALSE] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2850 colnames_m <- colnames(m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2851 is_na_m <- is.na(m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2852 tmp <- m |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2853 tmp[is_na_m] <- 0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2854 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2855 tmp <- m[, 0 < colSums(x = tmp)] # by default, na.rm is FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2856 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2857 colnames_tmp <- colnames(tmp) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2858 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2859 my_low_p_seq <- seq( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2860 from = min(g_intensity_hm_rows, nrow(m)), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2861 to = 1, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2862 by = -1 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2863 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2864 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2865 if (g_correlate_substrates) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2866 # zap samples having zero or near-zero variance |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2867 tmp[is.na(tmp)] <- 0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2868 nzv <- caret::nearZeroVar( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2869 tmp, # matrix of values, samples x variables |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2870 freqCut = 1.01, # min(freq most prevalent value / |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2871 # freq second most prevalent) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2872 uniqueCut = 99 # max(number of unique values / |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2873 # total number of samples) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2874 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2875 tmp <- if (length(nzv) > 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2876 m[, -nzv, drop = FALSE] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2877 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2878 m |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2879 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2880 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2881 tmp <- m[my_low_p_seq, , drop = FALSE] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2882 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2883 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2884 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2885 t_m <- t(tmp) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2886 t_m[is.na(t_m)] <- 0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2887 prefiltered_nrow <- ncol(t_m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2888 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2889 my_corcov <- cov(t_m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2890 did_filter_rows <- did_filter_cols <- FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2891 if (g_correlate_substrates && !is_positive_definite(my_corcov)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2892 my_correlate_substrates <- FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2893 t_m <- t(m[my_low_p_seq, , drop = FALSE]) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2894 t_m[is.na(t_m)] <- 0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2895 unfiltered_row_count <- ncol(t_m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2896 unfiltered_col_count <- nrow(t_m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2897 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2898 # zap empty samples |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2899 t_m <- t_m[0 < rowSums(x = t_m), ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2900 # zap substrates present in fewer than two samples |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2901 foo <- t_m > 0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2902 foo <- colSums(x = foo) > 1 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2903 t_m <- t_m[, foo] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2904 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2905 did_filter_rows <- unfiltered_row_count > ncol(t_m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2906 did_filter_cols <- unfiltered_col_count > nrow(t_m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2907 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2908 colnames_tmp <- rownames(t_m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2909 my_corcov <- cov(t_m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2910 if (g_filter_cov_var_gt_1) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2911 my_corcov <- keep_cov_w_var_gtr_1(my_corcov) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2912 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2913 } else if (g_correlate_substrates) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2914 my_corcov <- cov2cor(my_corcov) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2915 my_correlate_substrates <- TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2916 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2917 my_correlate_substrates <- FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2918 if (g_filter_cov_var_gt_1) my_corcov <- keep_cov_w_var_gtr_1(my_corcov) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2919 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2920 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2921 omitted_samples <- colnames_m[colnames_m %notin% colnames_tmp] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2922 suffix <- if (length(omitted_samples) > 1) "s" else "" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2923 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2924 f_omissions <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2925 function(is_corr) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2926 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2927 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2928 "Below is the %s plot for %s substrates", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2929 if (is_corr) "correlation" else "covariance", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2930 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2931 if (top_substrates) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2932 "%0.0f \"highest-quality\"" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2933 else |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2934 "%0.0f", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2935 ncol(t_m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2936 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2937 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2938 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2939 if (did_filter_cols) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2940 cat(sprintf(", omitting sample%s ", suffix)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2941 latex_collapsed_vector(", ", omitted_samples) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2942 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2943 cat(".\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2944 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2945 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2946 if (is.null(my_corcov) || sum(!is.na(t_m)) < 2) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2947 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2948 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2949 "\\newline\n%s %s plot.\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2950 "Insufficient covariance to produce", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2951 if (my_correlate_substrates) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2952 "correlation" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2953 else |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2954 "covariance" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2955 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2956 "\\newpage\n" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2957 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2958 return(NULL) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2959 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2960 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2961 cat("\\leavevmode\n", "\\newpage\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2962 f_omissions(my_correlate_substrates) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2963 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2964 master_cex <- 0.4 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2965 max_nchar <- max(nchar(rownames(t_m))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2966 my_limit <- g_intensity_hm_rows |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2967 diminution <- sqrt(my_limit / (my_limit + ncol(t_m))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2968 my_row_cex <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2969 my_col_cex <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2970 min(1.75, master_cex * 9 * diminution ^ 1.5) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2971 my_margin <- 3 + my_row_cex * 64 / (8 + max_nchar) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2972 my_key_cex <- 1.4 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2973 my_hm2_cex <- 1.0 * master_cex |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2974 my_hgt_scale <- 3.50 - 0.26 * (max(0.4, my_key_cex) - 0.4) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2975 my_hgt_scale <- 2.7 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2976 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2977 my_legend_height <- 4.0 - my_hgt_scale |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2978 my_legend_height <- 0.5 * my_key_cex |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2979 my_warp <- 0.65 * (my_limit + ncol(t_m)) / my_limit |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2980 my_warp <- 0.8 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2981 my_legend_height <- 0.77 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2982 my_legend_height <- 0.67 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2983 my_plot_height <- my_hgt_scale + (1 - my_warp) * my_legend_height |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2984 my_legend_height <- my_warp * my_legend_height |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2985 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2986 parjust <- par(adj = 0.5) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2987 on.exit(par(parjust)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2988 my_corcov <- my_corcov[order(rownames(my_corcov)), ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2989 my_main <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2990 sprintf("%s among %s substrates %s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2991 if (my_correlate_substrates) "Correlation" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2992 else "Covariance", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2993 kinase_name, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2994 if (!my_correlate_substrates && |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2995 g_filter_cov_var_gt_1 && |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2996 did_filter_rows |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2997 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2998 "having variance > 1" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
2999 else "" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3000 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3001 my_main_nchar <- nchar(my_main) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3002 my_heights <- c( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3003 0.3, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3004 my_plot_height, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3005 my_legend_height # was 4.0 - my_hgt_scale # was 4.19 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3006 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3007 if (print_trace_messages) cat(sprintf("max_nchar = %0.3f; ", max_nchar)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3008 if (print_trace_messages) cat(sprintf("my_margin = %0.3f; ", my_margin)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3009 if (print_trace_messages) cat(sprintf("my_plot_height = %0.3f\n\n", my_plot_height)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3010 if (print_trace_messages) cat(sprintf("master_cex = %0.3f; ", master_cex)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3011 if (print_trace_messages) cat(sprintf("my_row_cex = %0.3f; ", my_row_cex)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3012 if (print_trace_messages) cat(sprintf("my_col_cex = %0.3f; ", my_col_cex)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3013 if (print_trace_messages) cat(sprintf("my_key_cex = %0.3f\n\n", my_key_cex)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3014 if (print_trace_messages) cat(sprintf("my_hgt_scale = %0.3f\n\n", my_hgt_scale)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3015 if (print_trace_messages) cat(sprintf("legend height = %0.3f\n\n", my_legend_height)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3016 if (print_trace_messages) cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3017 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3018 "my_heights = c(%s); sum = %0.3f\n\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3019 paste( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3020 sprintf("%0.3f", my_heights), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3021 collapse = ", " |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3022 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3023 sum(my_heights) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3024 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3025 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3026 op <- par(cex.main = (30 + my_main_nchar) / my_main_nchar) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3027 on.exit(par(op)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3028 hm2plus( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3029 x = my_corcov, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3030 cex = my_hm2_cex, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3031 cexCol = my_col_cex, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3032 cexRow = my_row_cex, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3033 density_info = "none", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3034 denhgt = 0.15, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3035 denwid = 0.5, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3036 divergent = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3037 key_par = list(cex = my_key_cex), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3038 key_xlab = if (my_correlate_substrates) "Correlation" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3039 else "Covariance", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3040 main = my_main, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3041 mat = matrix( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3042 c( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3043 c(0, 3, 3), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3044 c(2, 1, 1), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3045 c(0, 4, 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3046 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3047 nrow = 3, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3048 ncol = 3, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3049 byrow = TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3050 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3051 heights = my_heights, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3052 margins = c(my_margin, my_margin), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3053 widths = c(0.5, 3.1, 0.9), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3054 scale = "none", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3055 symkey = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3056 symbreaks = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3057 symm = FALSE #TODO evaluate TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3058 # ... |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3059 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3060 } # end cov_heatmap |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3061 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3062 ### FILE IMPORT |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3063 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3064 # function reading bzipped file to data.frame |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3065 bzip2df <- function(d, f, ctor = bzfile) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3066 # read.delim file (by default, compressed by bzip2) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3067 if (file.exists(f)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3068 conn <- NULL |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3069 pf <- parent.frame() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3070 tryCatch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3071 assign( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3072 as.character(substitute(d)), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3073 read.delim(conn <- bzfile(f, open = "r")), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3074 pf |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3075 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3076 finally = if (!is.null(conn)) close(conn) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3077 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3078 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3079 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3080 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3081 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3082 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3083 # Purpose |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3084 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3085 The purpose of this analysis is to perform for phosphopeptides: |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3086 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3087 - imputation of missing values, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3088 - quantile normalization, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3089 - ANOVA (using the R stats::`r params$oneWayManyCategories` function), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3090 - assignment of an FDR-adjusted $p$-value and a "quality score" to each phosphopeptide, and |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3091 - KSEA (Kinase-Substrate Enrichment Analysis) using code adapted from the CRAN `KSEAapp` package to search for kinase substrates from the following databases: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3092 - PhosphoSitesPlus [https://www.phosphosite.org](https://www.phosphosite.org) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3093 - The Human Proteome Database [http://hprd.org](http://hprd.org) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3094 - NetworKIN [http://networkin.science/](http://networkin.science/) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3095 - Phosida [http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx](http://pegasus.biochem.mpg.de/phosida/help/motifs.aspx) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3096 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3097 ```{r include = FALSE} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3098 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3099 if (params$kseaUseAbsoluteLog2FC) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3100 sfc <- "|s|" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3101 pfc <- "|p|" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3102 pfc_txt <- "$\\text{absolute value}({\\log_2 (\\text{fold-change})})$" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3103 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3104 sfc <- "s" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3105 pfc <- "p" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3106 pfc_txt <- "${\\log_2 (\\text{fold-change}})$" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3107 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3108 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3109 ksea_heatmap_titles <- list() |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3110 ksea_heatmap_titles[[const_ksea_astrsk_kinases]] <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3111 sprintf( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3112 "Summary for all kinases enriched in one or more contrasts at %s < %s", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3113 ksea_cutoff_statistic, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3114 ksea_cutoff_threshold |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3115 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3116 ksea_heatmap_titles[[const_ksea_all_kinases]] <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3117 "Summary figure for all contrasts and all kinases" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3118 ksea_heatmap_titles[[const_ksea_nonastrsk_kinases]] <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3119 sprintf( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3120 "Summary for all kinases not enriched at %s < %s in any contrast", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3121 ksea_cutoff_statistic, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3122 ksea_cutoff_threshold |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3123 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3124 # hash to hold names of significantly enriched kinases |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3125 ksea_asterisk_hash <- new_env() |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3126 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3127 # PROCESS (mostly read) PARAMETERS |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3128 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3129 # False discovery rate adjustment for ANOVA |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3130 # Since pY abundance is low, set to 0.10 and 0.20 in addition to 0.05 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3131 val_fdr <- read.table(file = alpha_file, sep = "\t", header = FALSE, quote = "") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3132 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3133 if ( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3134 ncol(val_fdr) != 1 || |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3135 sum(!is.numeric(val_fdr[, 1])) || |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3136 sum(val_fdr[, 1] < 0) || |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3137 sum(val_fdr[, 1] > 1) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3138 ) { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3139 cat("alphaFile should be one column of numbers within the range [0.0,1.0]") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3140 param_df_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3141 knitr::knit_exit() |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3142 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3143 val_fdr <- val_fdr[, 1] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3144 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3145 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3146 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3147 ```{r echo = FALSE, results = 'asis'} |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3148 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3149 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3150 result <- file.copy( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3151 from = preproc_db, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3152 to = ksea_app_prep_db, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3153 overwrite = TRUE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3154 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3155 if (!result) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3156 write( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3157 sprintf( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3158 "fatal error copying initial database '%s' to output '%s'", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3159 preproc_db, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3160 ksea_app_prep_db, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3161 ), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3162 stderr() |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3163 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3164 if (sys.nframe() > 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3165 cat("Cannot continue and quit() failed. Goodbye.") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3166 param_df_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3167 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3168 # in case knit_exit doesn't exit |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3169 quit(save = "no", status = 1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3170 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3171 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3172 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3173 if (FALSE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3174 write.table(x = param_df, file = "test-data/params.txt") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3175 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3176 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3177 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3178 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3179 ```{r echo = FALSE} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3180 ### READ DATA |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3181 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3182 # read.table reads a file in table format and creates a data frame from it. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3183 # - note that `quote = ""` means that quotation marks are treated literally. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3184 full_data <- read.table( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3185 file = input_file, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3186 sep = "\t", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3187 header = TRUE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3188 quote = "", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3189 check.names = FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3190 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3191 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3192 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3193 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3194 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3195 # Extraction of Sample Classes and Names from Input Data |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3196 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3197 ```{r echo = FALSE, results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3198 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3199 data_column_indices <- grep(first_data_column, names(full_data), perl = TRUE) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3200 my_column_names <- names(full_data) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3201 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3202 if (!fdc_is_integer) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3203 if (length(data_column_indices) > 0) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3204 first_data_column <- data_column_indices[1] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3205 } else { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3206 cat(paste("failed to convert firstDataColumn:", first_data_column)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3207 param_df_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3208 knitr::knit_exit() |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3209 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3210 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3211 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3212 cat( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3213 sprintf( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3214 paste( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3215 "\n\nThe input data file has peptide-intensity data", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3216 "in columns %d (\"%s\") through %d (\"%s\")." |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3217 ), |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3218 tmp <- min(data_column_indices), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3219 my_column_names[tmp], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3220 tmp <- max(data_column_indices), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3221 my_column_names[tmp] |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3222 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3223 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3224 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3225 if (TRUE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3226 cat0( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3227 table_offset(i = 1, new = TRUE), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3228 "Sample classes and names are shown in ", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3229 table_href(), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3230 ".\n\n" |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3231 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3232 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3233 cat0( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3234 "\\newcounter{offset}\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3235 "\\setcounter{offset}{\\value{table}}\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3236 "\\stepcounter{offset}\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3237 "Sample classes and names are shown in ", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3238 table_href(), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3239 ".\n\n" |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3240 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3241 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3242 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3243 #TODO remove this unused variable and assignment |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3244 if (FALSE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3245 # Write column names as a LaTeX enumerated list. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3246 column_name_df <- data.frame( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3247 column = seq_len(length(colnames(full_data))), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3248 name = paste0("\\verb@", colnames(full_data), "@") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3249 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3250 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3251 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3252 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3253 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3254 ```{r echo = FALSE, results = 'asis'} |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3255 # extract intensity columns from full_data to quant_data |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3256 quant_data <- full_data[first_data_column:length(full_data)] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3257 quant_data[quant_data == 0] <- NA |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3258 rownames(quant_data) <- rownames(full_data) <- full_data$Phosphopeptide |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3259 full_data_names <- colnames(quant_data) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3260 # Extract factors and trt-replicates using regular expressions. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3261 # Typically: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3262 # regex_sample_names is "\\.\\d+[A-Z]$" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3263 # regex_sample_grouping is "\\d+" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3264 # This would distinguish trt-replicates by terminal letter [A-Z] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3265 # in sample names and group them into trts by the preceding digits. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3266 # e.g.: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3267 # group .1A .1B .1C into group 1; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3268 # group .2A .2B .2C, into group 2; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3269 # etc. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3270 m <- regexpr(regex_sample_names, colnames(quant_data), perl = TRUE) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3271 sample_name_matches <- regmatches(names(quant_data), m) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3272 colnames(quant_data) <- sample_name_matches |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3273 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3274 write_debug_file(quant_data) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3275 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3276 rx_match <- regexpr(regex_sample_grouping, sample_name_matches, perl = TRUE) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3277 smpl_trt <- as.factor(regmatches(sample_name_matches, rx_match)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3278 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3279 if (print_nb_messages) nbe(see_variable(smpl_trt, "\n\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3280 if (print_nb_messages) nbe(see_variable(sample_name_matches, "\n\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3281 if (print_nb_messages) nbe(see_variable(full_data_names, "\n\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3282 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3283 sample_treatment_df <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3284 save_sample_treatment_df <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3285 data.frame( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3286 class = smpl_trt, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3287 sample = sample_name_matches, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3288 full_sample_names = full_data_names |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3289 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3290 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3291 if (print_nb_messages) nbe(see_variable(sample_treatment_df, "\n\n")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3292 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3293 # reorder data |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3294 my_order <- with(sample_treatment_df, order(class, sample)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3295 quant_data <- quant_data[, my_order] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3296 sample_name_matches <- sample_name_matches[my_order] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3297 smpl_trt <- smpl_trt[my_order] |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3298 sample_treatment_df <- data.frame( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3299 class = smpl_trt, |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3300 sample = sample_name_matches |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3301 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3302 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3303 # filter smpl_trt as appropriate |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3304 if (sample_group_filter %in% c("include", "exclude")) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3305 include_sample <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3306 mgrepl( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3307 v = sample_group_filter_patterns, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3308 s = as.character(smpl_trt), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3309 fixed = sample_group_filter_fixed, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3310 perl = sample_group_filter_perl, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3311 ignore.case = sample_group_filter_nocase |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3312 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3313 if (sum(include_sample) < 2) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3314 errmsg <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3315 paste( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3316 "ERROR:", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3317 sum(include_sample), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3318 "samples are too few for analysis;", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3319 "check input parameters for sample-name parsing" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3320 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3321 cat0( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3322 errmsg, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3323 "\\stepcounter{offset}\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3324 " in ", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3325 table_href(), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3326 ".\n\n" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3327 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3328 data_frame_tabbing_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3329 x = save_sample_treatment_df, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3330 tabstops = c(1.25, 1.25), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3331 caption = "Sample classes", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3332 use_subsubsection_header = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3333 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3334 data_frame_tabbing_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3335 x = |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3336 param_df[ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3337 c("regexSampleNames", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3338 "regexSampleGrouping", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3339 "groupFilterPatterns", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3340 "groupFilter", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3341 "groupFilterMode" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3342 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3343 ], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3344 tabstops = c(1.75), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3345 underscore_whack = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3346 caption = "Input parameters for sample-name parsing", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3347 verbatim = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3348 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3349 param_df_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3350 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3351 return(invisible(-1)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3352 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3353 sample_treatment_df <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3354 if (sample_group_filter == "include") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3355 sample_treatment_df[include_sample, ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3356 else |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3357 sample_treatment_df[!include_sample, ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3358 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3359 include_sample <- rep.int(TRUE, length(smpl_trt)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3360 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3361 sample_name_matches <- sample_treatment_df$sample |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3362 rx_match <- regexpr(regex_sample_grouping, sample_name_matches, perl = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3363 smpl_trt <- as.factor(regmatches(sample_name_matches, rx_match)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3364 sample_treatment_df$class <- smpl_trt |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3365 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3366 # filter quant_data as appropriate |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3367 number_of_samples <- length(sample_name_matches) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3368 quant_data <- quant_data[, sample_name_matches] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3369 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3370 sample_level_integers <- as.integer(smpl_trt) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3371 sample_treatment_levels <- levels(smpl_trt) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3372 count_of_treatment_levels <- length(sample_treatment_levels) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3373 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3374 # for each phosphopeptide, across treatment levels, compute minimum |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3375 # count of observed (i.e., non-missing) values |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3376 my_env <- new_env() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3377 for (l in sample_treatment_levels) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3378 my_env[[as.character(l)]] <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3379 as.vector(rowSums(!is.na(quant_data[l == smpl_trt]))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3380 min_group_obs_count <- row_apply( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3381 x = Reduce( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3382 f = function(l, r) cbind(l, my_env[[r]]), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3383 x = sample_treatment_levels, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3384 init = c() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3385 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3386 fun = min |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3387 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3388 names(min_group_obs_count) <- rownames(quant_data) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3389 rm(my_env) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3390 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3391 # display (possibly-filtered) results |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3392 cat("\\newpage\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3393 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3394 if (sum(include_sample) > 1) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3395 data_frame_tabbing_latex( |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3396 x = sample_treatment_df, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3397 tabstops = c(1.25), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3398 caption = "Sample classes", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3399 use_subsubsection_header = FALSE |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3400 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3401 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3402 sample_name_grow <- 10 / (10 + max(nchar(sample_name_matches) + 6)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3403 sample_colsep <- transition_positions(as.integer(sample_treatment_df$class)) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3404 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3405 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3406 ```{r echo = FALSE, results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3407 cat("\\newpage\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3408 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3409 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3410 ## Are the log-transformed sample distributions similar? |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3411 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3412 ```{r echo = FALSE, fig.dim = c(9, 6.5), results = 'asis'} |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3413 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3414 quant_data[quant_data == 0] <- NA #replace 0 with NA |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3415 quant_data_log <- log10(quant_data) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3416 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3417 rownames(quant_data_log) <- rownames(quant_data) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3418 colnames(quant_data_log) <- sample_name_matches |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3419 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3420 write_debug_file(quant_data_log) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3421 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3422 g_ppep_distrib_ctl <- new_env() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3423 g_ppep_distrib_ctl$xlab_line <- 3.5 + 11.86 * (0.67 - sample_name_grow) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3424 g_ppep_distrib_ctl$mai_bottom <- (0.5 + 3.95 * (0.67 - sample_name_grow)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3425 g_ppep_distrib_ctl$axis <- (0.6 + 0.925 * (0.67 - sample_name_grow)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3426 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3427 my_ppep_distrib_bxp <- function( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3428 x |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3429 , sample_name_grow = sample_name_grow |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3430 , main |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3431 , varwidth = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3432 , sub = NULL |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3433 , xlab |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3434 , ylab |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3435 , col = const_boxplot_fill |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3436 , notch = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3437 , ppep_distrib_ctl = g_ppep_distrib_ctl |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3438 , ... |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3439 ) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3440 my_xlab_line <- g_ppep_distrib_ctl$xlab_line |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3441 my_mai_bottom <- g_ppep_distrib_ctl$mai_bottom |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3442 my_axis <- g_ppep_distrib_ctl$axis |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3443 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3444 if (print_trace_messages) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3445 cat_variable(my_xlab_line, suffix = "; ") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3446 cat_variable(my_mai_bottom, suffix = "; ") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3447 cat_variable(my_axis, suffix = "\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3448 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3449 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3450 old_par <- par( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3451 mai = par("mai") + c(my_mai_bottom, 0, 0, 0), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3452 cex.axis = my_axis, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3453 cex.lab = 1.2 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3454 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3455 tryCatch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3456 { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3457 # Vertical plot |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3458 boxplot( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3459 x |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3460 , las = 2 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3461 , col = col |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3462 , main = main |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3463 , sub = NULL |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3464 , ylab = ylab |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3465 , xlab = NULL |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3466 , notch = notch |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3467 , varwidth = varwidth |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3468 , ... |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3469 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3470 title( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3471 sub = sub |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3472 , cex.sub = 1.0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3473 , line = my_xlab_line + 1 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3474 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3475 title( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3476 xlab = xlab |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3477 , line = my_xlab_line |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3478 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3479 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3480 finally = par(old_par) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3481 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3482 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3483 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3484 my_ppep_distrib_bxp( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3485 x = quant_data_log |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3486 , sample_name_grow = sample_name_grow |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3487 , main = "Peptide intensities for each sample" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3488 , varwidth = boxplot_varwidth |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3489 , sub = "Box widths reflect number of peptides for sample" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3490 , xlab = "Sample" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3491 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3492 , col = const_boxplot_fill |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3493 , notch = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3494 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3495 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3496 cat("\n\n\n\n") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3497 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3498 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3499 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3500 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4), results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3501 if (nrow(quant_data_log) > 1) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3502 quant_data_log_stack <- stack(quant_data_log) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3503 ggplot2::ggplot(quant_data_log_stack, ggplot2::aes(x = values)) + |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3504 ggplot2::xlab(latex2exp::TeX("$log_{10}$(peptide intensity)")) + |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3505 ggplot2::ylab("Probability density") + |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3506 ggplot2::geom_density(ggplot2::aes(group = ind, colour = ind), na.rm = TRUE) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3507 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3508 cat("No density plot because there are too few peptides.\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3509 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3510 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3511 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3512 ## Globally, are peptide intensities are approximately unimodal? |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3513 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3514 <!-- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3515 # bquote could be used as an alternative to latex2exp::TeX below particularly |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3516 # and when plotting math expressions generally, at the expense of mastering |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3517 # another syntax, which hardly seems worthwhile when I need to use TeX |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3518 # elsewhere; here's an introduction to bquote: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3519 # https://www.r-bloggers.com/2018/03/math-notation-for-r-plot-titles-expression-and-bquote/ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3520 --> |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3521 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5), results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3522 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3523 # identify the location of missing values |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3524 fin <- is.finite(as.numeric(as.matrix(quant_data_log))) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3525 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3526 logvalues <- as.numeric(as.matrix(quant_data_log))[fin] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3527 logvalues_density <- density(logvalues) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3528 plot( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3529 x = logvalues_density, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3530 main = latex2exp::TeX( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3531 "Smoothed estimated probability density vs. $log_{10}$(peptide intensity)" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3532 ), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3533 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3534 ylab = "Probability density" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3535 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3536 hist( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3537 x = as.numeric(as.matrix(quant_data_log)), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3538 xlim = c(min(logvalues_density$x), max(logvalues_density$x)), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3539 breaks = 100, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3540 main = latex2exp::TeX("Frequency vs. $log_{10}$(peptide intensity)"), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3541 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3542 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3543 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3544 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3545 # Characterization of Input Data |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3546 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3547 ## Distribution of standard deviations of $log_{10}(\text{intensity})$, ignoring missing values |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3548 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3549 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 5), results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3550 # determine quantile |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3551 q1 <- quantile(logvalues, probs = mean_percentile)[1] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3552 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3553 # 1 = row of matrix (ie, phosphopeptide) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3554 sds <- row_apply(quant_data_log, sd_finite) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3555 if (sum(!is.na(sds)) > 2) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3556 plot( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3557 density(sds, na.rm = TRUE) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3558 , main = "Smoothed estimated probability density vs. std. deviation" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3559 , sub = "(probability estimation made with Gaussian smoothing)" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3560 , ylab = "Probability density" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3561 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3562 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3563 cat( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3564 "At least two non-missing values are required to plot", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3565 "probability density.\n\n" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3566 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3567 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3568 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3569 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3570 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3571 ```{r echo = FALSE} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3572 # Determine number of cells to impute |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3573 temp <- quant_data[is.na(quant_data)] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3574 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3575 # Determine number of values to impute |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3576 number_to_impute <- length(temp) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3577 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3578 # Determine percent of missing values |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3579 pct_missing_values <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3580 round(length(temp) / (length(logvalues) + length(temp)) * 100) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3581 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3582 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3583 ```{r echo = FALSE} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3584 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3585 # prep for trt-median based imputation |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3586 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3587 ``` |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3588 # Imputation of Missing Values |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3589 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3590 ```{r echo = FALSE} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3591 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3592 imp_smry_pot_peptides_before <- nrow(quant_data_log) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3593 imp_smry_missing_values_before <- number_to_impute |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3594 imp_smry_pct_missing <- pct_missing_values |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3595 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3596 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3597 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3598 ```{r echo = FALSE} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3599 #Determine number of cells to impute |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3600 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3601 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3602 ```{r echo = FALSE} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3603 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3604 # Identify which values are missing and need to be imputed |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3605 ind <- which(is.na(quant_data), arr.ind = TRUE) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3606 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3607 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3608 ```{r echo = FALSE, results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3609 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3610 # Apply imputation |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3611 switch( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3612 imputation_method |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3613 , "group-median" = { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3614 quant_data_imp <- quant_data |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3615 imputation_method_description <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3616 paste("Substitute missing value with", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3617 "median peptide-intensity for sample group.\n" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3618 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3619 # Take the accurate ln(x+1) because the data are log-normally distributed |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3620 # and because median can involve an average of two measurements. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3621 quant_data_imp <- log1p(quant_data_imp) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3622 for (i in seq_len(count_of_treatment_levels)) { |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3623 # Determine the columns for this factor-level |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3624 level_cols <- i == sample_level_integers |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3625 # Extract those columns |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3626 lvlsbst <- quant_data_imp[, level_cols, drop = FALSE] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3627 # assign to ind the row-column pairs corresponding to each NA |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3628 ind <- which(is.na(lvlsbst), arr.ind = TRUE) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3629 # No group-median exists if there is only one sample |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3630 # a given ppep has no measurement; otherwise, proceed. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3631 if (ncol(lvlsbst) > 1) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3632 the_centers <- |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3633 row_apply(lvlsbst, median, na.rm = TRUE) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3634 for (j in seq_len(nrow(lvlsbst))) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3635 for (k in seq_len(ncol(lvlsbst))) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3636 if (is.na(lvlsbst[j, k])) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3637 lvlsbst[j, k] <- the_centers[j] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3638 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3639 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3640 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3641 quant_data_imp[, level_cols] <- lvlsbst |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3642 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3643 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3644 # Take the accurate e^x - 1 to match scaling of original input. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3645 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3646 good_rows <- !is.na(rowMeans(quant_data_imp)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3647 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3648 , "median" = { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3649 quant_data_imp <- quant_data |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3650 imputation_method_description <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3651 paste("Substitute missing value with", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3652 "median peptide-intensity across all sample classes.\n" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3653 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3654 # Take the accurate ln(x+1) because the data are log-normally distributed |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3655 # and because median can involve an average of two measurements. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3656 quant_data_imp <- log1p(quant_data_imp) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3657 quant_data_imp[ind] <- row_apply(quant_data_imp, median, na.rm = TRUE)[ind[, 1]] |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3658 # Take the accurate e^x - 1 to match scaling of original input. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3659 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3660 good_rows <- !is.nan(rowMeans(quant_data_imp)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3661 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3662 , "mean" = { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3663 quant_data_imp <- quant_data |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3664 imputation_method_description <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3665 paste("Substitute missing value with", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3666 "geometric-mean peptide intensity across all sample classes.\n" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3667 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3668 # Take the accurate ln(x+1) because the data are log-normally distributed, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3669 # so arguments to mean should be previously transformed. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3670 # this will have to be |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3671 quant_data_imp <- log1p(quant_data_imp) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3672 # Assign to NA cells the mean for the row |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3673 quant_data_imp[ind] <- row_apply(quant_data_imp, mean, na.rm = TRUE)[ind[, 1]] |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3674 # Take the accurate e^x - 1 to match scaling of original input. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3675 quant_data_imp <- round(expm1(quant_data_imp_ln <- quant_data_imp)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3676 good_rows <- !is.nan(rowMeans(quant_data_imp)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3677 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3678 , "random" = { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3679 quant_data_imp <- quant_data |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3680 m1 <- median(sds, na.rm = TRUE) * sd_percentile #sd to be used is the median sd |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3681 # If you want results to be reproducible, you will want to call |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3682 # base::set.seed before calling stats::rnorm |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3683 imputation_method_description <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3684 paste("Substitute each missing value with random intensity", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3685 sprintf( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3686 "random intensity $N \\sim (%0.2f, %0.2f)$.\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3687 q1, m1 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3688 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3689 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3690 cat(sprintf("mean_percentile (from input parameter) is %2.0f\n\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3691 100 * mean_percentile)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3692 cat(sprintf("sd_percentile (from input parameter) is %0.2f\n\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3693 sd_percentile)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3694 quant_data_imp[ind] <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3695 10 ^ rnorm(number_to_impute, mean = q1, sd = m1) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3696 quant_data_imp_ln <- log1p(quant_data_imp) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3697 good_rows <- !is.nan(rowMeans(quant_data_imp)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3698 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3699 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3700 quant_data_imp_log10 <- quant_data_imp_ln * const_log10_e |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3701 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3702 if (length(good_rows) < 1) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3703 print("ERROR: Cannot impute data; there are no good rows!") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3704 return(-1) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3705 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3706 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3707 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3708 ```{r echo = FALSE, results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3709 cat("\\quad\n\nImputation method:\n\n\n", imputation_method_description) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3710 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3711 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3712 ```{r echo = FALSE} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3713 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3714 imp_smry_pot_peptides_after <- sum(good_rows) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3715 imp_smry_rejected_after <- sum(!good_rows) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3716 imp_smry_missing_values_after <- sum(is.na(quant_data_imp[good_rows, ])) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3717 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3718 # From ?`%in%`, %in% is currently defined as function(x, table) match(x, table, nomatch = 0) > 0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3719 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3720 sink(stderr()) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3721 print("`%in%`:") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3722 print(`%in%`) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3723 sink() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3724 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3725 stock_in <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3726 names(good_rows) %in% |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3727 names(min_group_obs_count[g_intensity_min_per_class <= min_group_obs_count]) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3728 if (print_nb_messages) nbe(see_variable(stock_in), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3729 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3730 explicit_in <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3731 0 < match( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3732 names(good_rows), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3733 names(min_group_obs_count[g_intensity_min_per_class <= min_group_obs_count]) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3734 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3735 if (print_nb_messages) nbe(see_variable(explicit_in), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3736 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3737 great_enough_row_names <- good_rows[ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3738 names(good_rows) %in% |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3739 names(min_group_obs_count[g_intensity_min_per_class <= min_group_obs_count]) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3740 ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3741 if (print_nb_messages) nbe(see_variable(great_enough_row_names), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3742 great_enough_row_names <- great_enough_row_names[great_enough_row_names] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3743 if (print_nb_messages) nbe(see_variable(great_enough_row_names), "\n") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3744 ``` |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3745 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3746 ```{r echo = FALSE, results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3747 # ref: http://www1.maths.leeds.ac.uk/latex/TableHelp1.pdf |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3748 tabular_lines_fmt <- paste( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3749 "\\begin{table}[hb]", # h(inline); b(bottom); t (top) or p (separate page) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3750 " \\leavevmode", |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3751 " \\caption{Imputation Results}", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3752 " \\centering", # \centering centers the table on the page |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3753 " \\begin{tabular}{l c c c}", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3754 " \\hline\\hline", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3755 " \\ & potential peptides & missing values & rejected", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3756 " peptides \\\\ [0.5ex]", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3757 " \\hline", |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3758 " before imputation & %d & %d (%d\\%s) & \\\\", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3759 " after imputation & %d & %d & %d \\\\", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3760 " after keep comparable & %d & & %d \\\\ [1ex]", |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3761 " \\hline", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3762 " \\end{tabular}", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3763 #" \\label{table:nonlin}", # may be used to refer this table in the text |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3764 "\\end{table}", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3765 sep = "\n" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3766 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3767 tabular_lines <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3768 sprintf( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3769 tabular_lines_fmt, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3770 imp_smry_pot_peptides_before, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3771 imp_smry_missing_values_before, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3772 imp_smry_pct_missing, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3773 "%", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3774 imp_smry_pot_peptides_after, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3775 imp_smry_missing_values_after, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3776 imp_smry_rejected_after, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3777 length(great_enough_row_names), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3778 imp_smry_pot_peptides_before - |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3779 length(great_enough_row_names) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3780 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3781 cat(tabular_lines) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3782 ``` |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3783 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3784 ```{r filter_good_rows, echo = FALSE} |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3785 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3786 if (print_nb_messages) nbe("before name extraction, ", see_variable(length(good_rows)), " ", see_variable(good_rows), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3787 good_rows <- names(good_rows[names(great_enough_row_names)]) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3788 if (print_nb_messages) nbe("after name extraction, ", see_variable(length(good_rows)), see_variable(good_rows), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3789 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3790 #ACE min_group_obs_count <- min_group_obs_count[names(great_enough_row_names)] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3791 #ACE nbe("good_rows") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3792 #ACE nbe(see_variable(good_rows)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3793 #ACE nbe("names(min_group_obs_count) before filter for good rows") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3794 #ACE nbe(see_variable(names(min_group_obs_count))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3795 min_group_obs_count <- min_group_obs_count[good_rows] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3796 #ACE nbe("min_group_obs_count after filter for good rows") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3797 #ACE nbe(see_variable(names(min_group_obs_count))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3798 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3799 # Zap rows where imputation was insufficiently effective |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3800 full_data <- full_data [good_rows, ] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3801 quant_data <- quant_data [good_rows, ] |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3802 quant_data_log <- quant_data_log [good_rows, ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3803 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3804 if (print_nb_messages) nbe("before row filter, ", see_variable(nrow(quant_data_imp)), "\n") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3805 quant_data_imp <- quant_data_imp[good_rows, ] |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3806 if (print_nb_messages) nbe("after row filter, ", see_variable(nrow(quant_data_imp)), "\n") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3807 write_debug_file(quant_data_imp) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3808 quant_data_imp_good_rows <- quant_data_imp |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3809 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3810 write_debug_file(quant_data_imp_good_rows) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3811 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3812 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3813 ```{r echo = FALSE, results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3814 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3815 can_plot_before_after_imp <- TRUE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3816 d_combined <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3817 as.numeric( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3818 as.matrix( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3819 log10(quant_data_imp) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3820 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3821 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3822 d_original <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3823 as.numeric( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3824 as.matrix( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3825 log10(quant_data_imp[!is.na(quant_data)]) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3826 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3827 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3828 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3829 if (sum(!is.na(d_original)) > 2) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3830 d_original <- density(d_original) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3831 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3832 can_plot_before_after_imp <- FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3833 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3834 if (can_plot_before_after_imp && sum(is.na(d_combined)) < 1) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3835 d_combined <- density(d_combined) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3836 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3837 can_plot_before_after_imp <- FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3838 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3839 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3840 if (sum(is.na(quant_data)) > 0) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3841 # There ARE missing values |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3842 d_imputed <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3843 as.numeric( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3844 as.matrix( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3845 log10(quant_data_imp[is.na(quant_data)]) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3846 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3847 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3848 if (can_plot_before_after_imp && sum(is.na(d_imputed)) < 1) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3849 d_imputed <- (density(d_imputed)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3850 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3851 can_plot_before_after_imp <- FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3852 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3853 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3854 # There are NO missing values |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3855 d_imputed <- d_combined |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3856 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3857 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3858 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3859 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3860 ```{r echo = FALSE, fig.dim = c(9, 6.5), results = 'asis'} |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3861 zero_sd_rownames <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3862 rownames(quant_data_imp)[ |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3863 is.na((row_apply(quant_data_imp, sd, na.rm = TRUE)) == 0) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3864 ] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3865 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3866 if (length(zero_sd_rownames) >= nrow(quant_data_imp)) { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3867 cat("All peptides have zero standard deviation. Cannot continue.") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3868 param_df_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3869 knitr::knit_exit() |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3870 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3871 if (length(zero_sd_rownames) > 0) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3872 cat( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3873 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3874 "%d %s %s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3875 length(zero_sd_rownames), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3876 "peptides with zero variance", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3877 "were removed from statistical consideration" |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3878 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3879 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3880 zap_named_rows <- function(df, nms) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3881 return(df[!(row.names(df) %in% nms), ]) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3882 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3883 quant_data_imp <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3884 zap_named_rows(quant_data_imp, zero_sd_rownames) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3885 quant_data <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3886 zap_named_rows(quant_data, zero_sd_rownames) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3887 full_data <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3888 zap_named_rows(full_data, zero_sd_rownames) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3889 min_group_obs_count <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3890 min_group_obs_count[names(min_group_obs_count) %notin% zero_sd_rownames] |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3891 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3892 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3893 if (sum(is.na(quant_data)) > 0) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3894 cat("\\leavevmode\\newpage\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3895 # Copy quant data to x |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3896 x <- quant_data |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3897 # x gets to have values of: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3898 # - NA for observed values |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3899 # - 1 for missing values |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3900 x[is.na(x)] <- 0 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3901 x[x > 1] <- NA |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3902 x[x == 0] <- 1 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3903 # Log-transform imputed data |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3904 # update variable because rows may have been eliminated from quant_data_imp |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3905 quant_data_imp_log10 <- log10(quant_data_imp) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3906 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3907 write_debug_file(quant_data_imp_log10) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3908 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3909 # Set blue_dots to log of quant data or NA for NA quant data |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3910 blue_dots <- log10(quant_data) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3911 # Set red_dots to log of imputed data or NA for observed quant data |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3912 red_dots <- quant_data_imp_log10 * x |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3913 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3914 count_red <- sum(!is.na(red_dots)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3915 count_blue <- sum(!is.na(blue_dots)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3916 ylim_save <- ylim <- c( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3917 min(red_dots, blue_dots, na.rm = TRUE), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3918 max(red_dots, blue_dots, na.rm = TRUE) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3919 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3920 show_stripchart <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3921 50 > (count_red + count_blue) / length(sample_name_matches) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3922 if (show_stripchart) { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3923 boxplot_sub <- "Light blue = data before imputation; Red = imputed data;" |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3924 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3925 boxplot_sub <- "" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3926 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3927 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3928 # Vertical plot |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3929 colnames(blue_dots) <- sample_name_matches |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3930 my_ppep_distrib_bxp( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3931 x = blue_dots |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3932 , sample_name_grow = sample_name_grow |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3933 , main = "Peptide intensities after eliminating unusable peptides" |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3934 , varwidth = boxplot_varwidth |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3935 , sub = paste(boxplot_sub, "Box widths reflect number of peptides for sample") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3936 , xlab = "Sample" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3937 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3938 , col = const_boxplot_fill |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3939 , notch = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3940 , ylim = ylim |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3941 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3942 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3943 if (show_stripchart) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3944 # Points |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3945 # ref: https://r-charts.com/distribution/add-points-boxplot/ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3946 # NA values are not plotted |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3947 stripchart( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3948 blue_dots, # Data |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3949 method = "jitter", # Random noise |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3950 jitter = const_stripchart_jitter, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3951 pch = 19, # Pch symbols |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3952 cex = const_stripchart_cex, # Size of symbols reduced |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3953 col = "lightblue", # Color of the symbol |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3954 vertical = TRUE, # Vertical mode |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3955 add = TRUE # Add it over |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3956 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3957 stripchart( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3958 red_dots, # Data |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3959 method = "jitter", # Random noise |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3960 jitter = const_stripchart_jitter, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3961 pch = 19, # Pch symbols |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3962 cex = const_stripchart_cex, # Size of symbols reduced |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3963 col = "red", # Color of the symbol |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3964 vertical = TRUE, # Vertical mode |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3965 add = TRUE # Add it over |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3966 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3967 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3968 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3969 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3970 ``` |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3971 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3972 ```{r echo = FALSE, fig.dim = c(9, 5.5), results = 'asis'} |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3973 if (sum(is.na(quant_data)) > 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3974 # show measured values in blue on left half-violin plot |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3975 cat("\\leavevmode\n\\quad\n\n\\quad\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3976 old_par <- par( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3977 mai = par("mai") + c(g_ppep_distrib_ctl$mai_bottom, 0, 0, 0), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3978 cex.axis = g_ppep_distrib_ctl$axis, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3979 cex.lab = 1.2 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3980 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3981 tryCatch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3982 { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3983 vioplot::vioplot( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3984 x = lapply(blue_dots, function(x) x[!is.na(x)]), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3985 col = "lightblue1", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3986 side = "left", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3987 plotCentre = "line", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3988 ylim = ylim_save, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3989 main = "Distributions of observed and imputed data", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3990 sub = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3991 las = 2, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3992 xlab = NULL, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3993 ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3994 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3995 title( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3996 sub = "Light blue = observed data; Pink = imputed data", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3997 cex.sub = 1.0, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
3998 line = g_ppep_distrib_ctl$xlab_line + 1 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
3999 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4000 title( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4001 xlab = "Sample", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4002 line = g_ppep_distrib_ctl$xlab_line |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4003 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4004 red_violins <- lapply(red_dots, function(x) x[!is.na(x)]) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4005 cols_to_delete <- c() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4006 for (ix in seq_len(length(red_violins))) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4007 if (length(red_violins[[ix]]) < 1) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4008 cols_to_delete <- c(cols_to_delete, ix) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4009 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4010 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4011 # destroy any unimputable columns |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4012 if (!is.null(cols_to_delete)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4013 red_violins <- red_violins[-cols_to_delete] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4014 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4015 # plot imputed values in red on right half-violin plot |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4016 vioplot::vioplot( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4017 x = red_violins, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4018 col = "lightpink1", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4019 side = "right", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4020 plotCentre = "line", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4021 add = TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4022 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4023 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4024 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4025 finally = par(old_par) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4026 ) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4027 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4028 # density plot |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4029 cat("\\leavevmode\n\n\n\n\n\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4030 if (can_plot_before_after_imp) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4031 ylim <- c( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4032 0, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4033 max( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4034 if (is.list(d_combined)) d_combined$y else d_combined, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4035 if (is.list(d_original)) d_original$y else d_original, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4036 if (is.list(d_imputed)) d_imputed$y else d_imputed, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4037 na.rm = TRUE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4038 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4039 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4040 plot( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4041 d_combined, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4042 ylim = ylim, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4043 sub = |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4044 paste( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4045 "Blue = data before imputation; Red = imputed data;", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4046 "Black = combined" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4047 ), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4048 main = "Density of peptide intensity before and after imputation", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4049 xlab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4050 ylab = "Probability density" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4051 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4052 lines(d_original, col = "blue") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4053 lines(d_imputed, col = "red") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4054 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4055 cat( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4056 "There are too few points to plot the density of peptide intensity", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4057 "before and after imputation." |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4058 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4059 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4060 cat("\\leavevmode\\newpage\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4061 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4062 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4063 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4064 # Quantile Normalization |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4065 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4066 The excellent `normalize.quantiles` function from |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4067 *[the `preprocessCore` Bioconductor package](http://bioconductor.org/packages/release/bioc/html/preprocessCore.html)* |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4068 performs "quantile normalization" as described Bolstad *et al.* (2003), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4069 DOI *[10.1093/bioinformatics/19.2.185](https://doi.org/10.1093%2Fbioinformatics%2F19.2.185)* |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4070 and its supplementary material [http://bmbolstad.com/misc/normalize/normalize.html](http://bmbolstad.com/misc/normalize/normalize.html), |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4071 i.e., it assumes that the goal is to detect |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4072 subtle differences among grossly similar samples (having similar distributions) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4073 by equalizing intra-quantile quantitations^[Unfortunately, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4074 one software library upon which `preprocessCore` depends |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4075 *[suffers from a concurrency defect](https://support.bioconductor.org/p/122925/#9135989)* |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4076 that requires that a specific, non-concurrent version of the library (`openblas` version $0.3.3$) be |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4077 installed. The installation command equivalent to what was used to install the library to produce the results presented here is: |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4078 \linebreak |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4079 ` conda install bioconductor-preprocesscore openblas=0.3.3`]. |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4080 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4081 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4082 <!-- |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4083 # Apply quantile normalization using preprocessCore::normalize.quantiles |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4084 # --- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4085 # tool repository: http://bioconductor.org/packages/release/bioc/html/preprocessCore.html |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4086 # except this: https://support.bioconductor.org/p/122925/#9135989 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4087 # says to install it like this: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4088 # ``` |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4089 # BiocManager::install("preprocessCore", configure.args="--disable-threading", force = TRUE, lib=.libPaths()[1]) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4090 # ``` |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4091 # conda installation (necessary because of a bug in recent openblas): |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4092 # conda install bioconductor-preprocesscore openblas=0.3.3 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4093 # ... |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4094 # --- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4095 # normalize.quantiles {preprocessCore} -- Quantile Normalization |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4096 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4097 # Description: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4098 # Using a normalization based upon quantiles, this function normalizes a |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4099 # matrix of probe level intensities. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4100 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4101 # THIS FUNCTIONS WILL HANDLE MISSING DATA (ie NA values), based on the |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4102 # assumption that the data is missing at random. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4103 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4104 # Usage: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4105 # normalize.quantiles(x, copy = TRUE, keep.names = FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4106 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4107 # Arguments: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4108 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4109 # - x: A matrix of intensities where each column corresponds to a chip and each row is a probe. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4110 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4111 # - copy: Make a copy of matrix before normalizing. Usually safer to work with a copy, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4112 # but in certain situations not making a copy of the matrix, but instead normalizing |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4113 # it in place will be more memory friendly. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4114 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4115 # - keep.names: Boolean option to preserve matrix row and column names in output. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4116 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4117 # Details: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4118 # This method is based upon the concept of a quantile-quantile plot extended to n dimensions. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4119 # No special allowances are made for outliers. If you make use of quantile normalization |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4120 # please cite Bolstad et al, Bioinformatics (2003). |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4121 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4122 # This functions will handle missing data (ie NA values), based on |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4123 # the assumption that the data is missing at random. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4124 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4125 # Note that the current implementation optimizes for better memory usage |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4126 # at the cost of some additional run-time. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4127 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4128 # Value: A normalized matrix. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4129 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4130 # Author: Ben Bolstad, bmbolstad.com |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4131 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4132 # References |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4133 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4134 # - Bolstad, B (2001) Probe Level Quantile Normalization of High Density Oligonucleotide |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4135 # Array Data. Unpublished manuscript http://bmbolstad.com/stuff/qnorm.pdf |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4136 # |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4137 # - Bolstad, B. M., Irizarry R. A., Astrand, M, and Speed, T. P. (2003) A Comparison of |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4138 # Normalization Methods for High Density Oligonucleotide Array Data Based on Bias |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4139 # and Variance. Bioinformatics 19(2), pp 185-193. DOI 10.1093/bioinformatics/19.2.185 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4140 # http://bmbolstad.com/misc/normalize/normalize.html |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4141 # ... |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4142 --> |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4143 ```{r echo = FALSE, results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4144 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4145 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp)), "\n") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4146 if (nrow(quant_data_imp) > 0) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4147 quant_data_imp_qn <- preprocessCore::normalize.quantiles( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4148 as.matrix(quant_data_imp), keep.names = TRUE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4149 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4150 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4151 quant_data_imp_qn <- as.matrix(quant_data_imp) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4152 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4153 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4154 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp_qn)), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4155 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4156 quant_data_imp_qn <- as.data.frame(quant_data_imp_qn) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4157 write_debug_file(quant_data_imp_qn) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4158 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4159 quant_data_imp_qn_log <- log10(quant_data_imp_qn) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4160 write_debug_file(quant_data_imp_qn_log) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4161 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4162 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp_qn_log)), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4163 if (print_nb_messages) nbe(see_variable(ncol(quant_data_imp_qn_log)), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4164 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4165 quant_data_imp_qn_ls <- t(scale(t(log10(quant_data_imp_qn)))) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4166 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4167 sel <- row_apply(quant_data_imp_qn_ls, any_nan) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4168 quant_data_imp_qn_ls2 <- quant_data_imp_qn_ls |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4169 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4170 quant_data_imp_qn_ls2 <- quant_data_imp_qn_ls2[which(sel), ] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4171 quant_data_imp_qn_ls2 <- as.data.frame(quant_data_imp_qn_ls2) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4172 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4173 quant_data_imp_qn_ls <- as.data.frame(quant_data_imp_qn_ls) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4174 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4175 write_debug_file(quant_data_imp_qn_ls) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4176 write_debug_file(quant_data_imp_qn_ls2) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4177 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4178 # Create data.frame used by ANOVA analysis |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4179 data_table_imp_qn_lt <- cbind(full_data[1:9], quant_data_imp_qn_log) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4180 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4181 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4182 ## Are normalized, imputed, log-transformed sample distributions similar? |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4183 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4184 ```{r echo = FALSE, fig.dim = c(9, 6.5), results = 'asis'} |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4185 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4186 # Save unimputed quant_data_log for plotting below |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4187 unimputed_quant_data_log <- quant_data_log |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4188 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4189 # log10 transform (after preparing for zero values, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4190 # which should never happen...) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4191 quant_data_imp_qn[quant_data_imp_qn == 0] <- .000000001 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4192 quant_data_log <- log10(quant_data_imp_qn) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4193 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4194 how_many_peptides <- nrow(quant_data_log) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4195 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4196 if ((how_many_peptides) > 0) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4197 cat( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4198 sprintf( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4199 "Intensities for %d peptides:\n\n\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4200 how_many_peptides |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4201 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4202 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4203 cat("\n\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4204 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4205 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4206 # data visualization |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4207 if (TRUE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4208 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4209 my_ppep_distrib_bxp( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4210 x = quant_data_log |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4211 , sample_name_grow = sample_name_grow |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4212 , main = "Peptide intensities for each sample" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4213 , varwidth = boxplot_varwidth |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4214 , sub = NULL |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4215 , xlab = "Sample" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4216 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4217 , col = const_boxplot_fill |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4218 , notch = boxplot_notch |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4219 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4220 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4221 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4222 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4223 old_par <- par( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4224 mai = par("mai") + c(0.5, 0, 0, 0) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4225 , oma = par("oma") + c(0.5, 0, 0, 0) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4226 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4227 # ref: https://r-charts.com/distribution/add-points-boxplot/ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4228 # Vertical plot |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4229 colnames(quant_data_log) <- sample_name_matches |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4230 boxplot( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4231 quant_data_log |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4232 , las = 2 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4233 , cex.axis = 0.9 * sample_name_grow |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4234 , col = const_boxplot_fill |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4235 , ylab = latex2exp::TeX("$log_{10}$(peptide intensity)") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4236 , xlab = "Sample" |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4237 , notch = boxplot_notch |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4238 , varwidth = boxplot_varwidth |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4239 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4240 par(old_par) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4241 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4242 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4243 cat("There are no peptides to plot\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4244 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4245 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4246 cat("\n\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4247 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4248 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4249 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4250 ```{r echo = FALSE, fig.align = "left", fig.dim = c(9, 4), results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4251 if (nrow(quant_data_log) > 1) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4252 quant_data_log_stack <- stack(quant_data_log) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4253 ggplot2::ggplot(quant_data_log_stack, ggplot2::aes(x = values)) + |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4254 ggplot2::xlab(latex2exp::TeX("$log_{10}$(peptide intensity)")) + |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4255 ggplot2::ylab("Probability density") + |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4256 ggplot2::geom_density(ggplot2::aes(group = ind, colour = ind), na.rm = TRUE) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4257 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4258 cat("No density plot because there are fewer than two peptides to plot.\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4259 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4260 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4261 ```{r echo = FALSE, results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4262 cat("\\leavevmode\\newpage\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4263 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4264 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4265 # ANOVA Analysis |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4266 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4267 ## Assignment of $p$-value and quality score |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4268 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4269 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. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4270 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4271 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). |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4272 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4273 Furthermore, to give more weight to phosphopeptides having fewer missing values, an (arbitrarily defined) quality score was assigned to each, defined as: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4274 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4275 $$ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4276 \textit{quality}_j |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4277 = \frac{1 + o_{j}}{v_{j}(1 + o_{j}) + 0.005} |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4278 $$ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4279 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4280 where: |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4281 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4282 - $o_j$ is the minimum number of non-missing observations per sample group for substrate $j$ for all sample groups, and |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4283 - $v_j$ is the FDR-adjusted ANOVA $p$-value for substrate $j$. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4284 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4285 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4286 ```{r, echo = FALSE, results = 'asis'} |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4287 cat("\\newpage\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4288 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4289 # Make new data frame containing only Phosphopeptides |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4290 # to connect preANOVA to ANOVA (connect_df) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4291 connect_df <- data.frame( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4292 data_table_imp_qn_lt$Phosphopeptide |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4293 , data_table_imp_qn_lt[, first_data_column] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4294 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4295 colnames(connect_df) <- c("Phosphopeptide", "Intensity") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4296 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4297 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4298 ```{r anova, echo = FALSE, fig.dim = c(10, 12), results = 'asis'} |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4299 g_can_run_ksea <- FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4300 old_oma <- par("oma") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4301 if (count_of_treatment_levels < 2) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4302 cat( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4303 "ERROR!!!! Cannot perform ANOVA analysis", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4304 "(see next page)\\newpage\n" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4305 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4306 cat( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4307 "ERROR: ANOVA analysis", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4308 "requires two or more factor levels!\n\n\n" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4309 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4310 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4311 cat("\n\n\n\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4312 cat("Unparsed sample names are:\n\n\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4313 "\\begin{quote}\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4314 paste(names(quant_data_imp_qn_log), collapse = "\n\n\n"), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4315 "\n\\end{quote}\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4316 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4317 regex_sample_names <- latex_printable_control_seqs(regex_sample_names) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4318 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4319 cat("\\leavevmode\n\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4320 cat("Parsing rule for SampleNames is", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4321 "\n\n\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4322 "\\text{'", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4323 regex_sample_names, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4324 "'}\n\n\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4325 sep = "" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4326 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4327 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4328 cat("\nParsed sample names are:\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4329 "\\begin{quote}\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4330 paste(sample_name_matches, collapse = "\n\n\n"), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4331 "\n\\end{quote}\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4332 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4333 regex_sample_grouping <- latex_printable_control_seqs(regex_sample_grouping) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4334 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4335 cat("\\leavevmode\n\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4336 cat("Parsing rule for SampleGrouping is", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4337 "\n\n\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4338 "\\text{'", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4339 regex_sample_grouping, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4340 "'}\n\n\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4341 sep = "" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4342 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4343 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4344 cat("\n\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4345 cat("Sample group assignments are:\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4346 "\\begin{quote}\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4347 paste(regmatches(sample_name_matches, rx_match), collapse = "\n\n\n"), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4348 "\n\\end{quote}\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4349 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4350 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4351 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4352 if (print_nb_messages) nbe("computing p_value_data_anova_ps\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4353 if (print_nb_messages) nbe(see_variable(nrow(quant_data_imp_qn_log)), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4354 if (print_nb_messages) nbe(see_variable(ncol(quant_data_imp_qn_log)), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4355 if (print_nb_messages) nbe(see_variable(quant_data_imp_qn_log[, ".NE.7C"]), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4356 if (print_nb_messages) nbe(see_variable(quant_data_imp_qn_log), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4357 if (print_nb_messages) nbe(see_variable(anova_func), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4358 if (print_nb_messages) nbe(see_variable(smpl_trt), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4359 if (print_nb_messages) nbe(see_variable(one_way_all_categories), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4360 tryCatch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4361 { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4362 p_value_data_anova_ps <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4363 row_apply( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4364 quant_data_imp_qn_log, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4365 anova_func, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4366 grouping_factor = smpl_trt, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4367 one_way_f = one_way_all_categories |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4368 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4369 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4370 error = function(e) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4371 mesg <- paste("Could not compute ANOVA because", e$message) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4372 cat("\n\n", mesg, "\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4373 param_df_noexit(e) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4374 sink(stderr()) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4375 cat("\n\n", mesg, "\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4376 values <- paste(param_df$parameter, "=", param_df$value, collapse = "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4377 cat(values) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4378 sink() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4379 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4380 exit(code = 1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4381 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4382 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4383 if (print_nb_messages) nbe(see_variable(p_value_data_anova_ps), "\n") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4384 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4385 p_value_data_anova_ps_fdr <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4386 p.adjust(p_value_data_anova_ps, method = "fdr") |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4387 my_ppep_v <- full_data[, 1] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4388 p_value_data <- list( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4389 phosphopeptide = my_ppep_v, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4390 raw_anova_p = p_value_data_anova_ps, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4391 fdr_adjusted_anova_p = p_value_data_anova_ps_fdr, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4392 missing_values = rowSums(is.na(quant_data)), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4393 min_group_obs_count = min_group_obs_count |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4394 ) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4395 p_value_data <- data.frame( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4396 phosphopeptide = my_ppep_v, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4397 raw_anova_p = p_value_data_anova_ps, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4398 fdr_adjusted_anova_p = p_value_data_anova_ps_fdr, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4399 missing_values = rowSums(is.na(quant_data)), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4400 min_group_obs_count = min_group_obs_count |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4401 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4402 p_value_data$quality <- 1.0 / with( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4403 p_value_data, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4404 fdr_adjusted_anova_p + 0.005 / (1 + min_group_obs_count) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4405 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4406 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4407 p_value_data$ranking <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4408 with( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4409 p_value_data, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4410 switch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4411 g_intensity_hm_criteria, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4412 "quality" = order(-quality), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4413 "na_count" = order(missing_values, fdr_adjusted_anova_p), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4414 # the default is "p_value" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4415 order(fdr_adjusted_anova_p) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4416 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4417 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4418 p_value_data <- p_value_data[p_value_data$ranking, , drop = FALSE] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4419 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4420 write.table( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4421 p_value_data, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4422 file = "p_value_data.txt", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4423 sep = "\t", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4424 col.names = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4425 row.names = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4426 quote = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4427 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4428 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4429 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4430 # output ANOVA file to constructed filename, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4431 # e.g. "Outputfile_pST_ANOVA_STEP5.txt" |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4432 # becomes "Outputfile_pST_ANOVA_STEP5_FDR0.05.txt" |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4433 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4434 # Re-output datasets to include p-values |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4435 metadata_plus_p <- cbind(full_data[1:9], p_value_data[, 2:ncol(p_value_data)]) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4436 write.table( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4437 cbind(metadata_plus_p, quant_data_imp), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4438 file = imputed_data_filename, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4439 sep = "\t", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4440 col.names = TRUE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4441 row.names = FALSE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4442 quote = FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4443 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4444 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4445 write.table( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4446 cbind(metadata_plus_p, quant_data_imp_qn_log), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4447 file = imp_qn_lt_data_filenm, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4448 sep = "\t", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4449 col.names = TRUE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4450 row.names = FALSE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4451 quote = FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4452 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4453 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4454 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4455 first_page_suppress <- 1 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4456 number_of_peptides_found <- 0 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4457 cutoff <- val_fdr[1] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4458 for (cutoff in val_fdr) { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4459 #loop through FDR cutoffs |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4460 if (number_of_peptides_found > g_intensity_hm_rows - 1) { |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4461 cat("\\leavevmode\n\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4462 break |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4463 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4464 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4465 bool_1 <- (p_value_data$fdr_adjusted_anova_p < cutoff) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4466 bool_2 <- (p_value_data$min_group_obs_count >= g_intensity_min_per_class) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4467 g_can_run_ksea <- g_can_run_ksea || (sum(bool_2) > 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4468 bool_4 <- (p_value_data$quality >= params$minQuality) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4469 bool_3 <- as.logical( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4470 as.integer(bool_1) * |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4471 as.integer(bool_2) * |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4472 as.integer(bool_4) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4473 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4474 if (print_trace_messages) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4475 if (length(bool_1) > 30) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4476 cat_variable(bool_1, force_str = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4477 cat_variable(bool_2, force_str = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4478 cat_variable(bool_3, force_str = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4479 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4480 cat_variable(bool_1, suffix = "\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4481 cat_variable(bool_2, suffix = "\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4482 cat_variable(bool_3, suffix = "\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4483 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4484 cat_variable(length(bool_3), digits = 0, suffix = "; ") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4485 cat_variable(sum(bool_3), digits = 0, suffix = "\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4486 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4487 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4488 filtered_p <- |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4489 p_value_data[bool_3, , drop = FALSE] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4490 filtered_p <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4491 filtered_p[!is.na(filtered_p$phosphopeptide), , drop = FALSE] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4492 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4493 if (print_trace_messages) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4494 cat_variable(filtered_p, force_str = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4495 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4496 have_remaining_peptides <- sum(bool_3, na.rm = TRUE) > 0 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4497 filter_result_string <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4498 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4499 "%s, %s of %0.0f peptides remained having both %s and %s.\n\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4500 "After filtering for ANOVA results", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4501 if (have_remaining_peptides) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4502 as.character(sum(bool_3, na.rm = TRUE)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4503 else |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4504 "none", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4505 length(bool_3), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4506 sprintf("adjusted p-value < %s", as.character(signif(cutoff, 2))), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4507 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4508 "more than %0.0f observations in some groups", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4509 max(0, g_intensity_min_per_class - 1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4510 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4511 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4512 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4513 filtered_data_filtered <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4514 quant_data_imp_qn_log[ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4515 rownames(filtered_p), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4516 , drop = FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4517 ] |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4518 # order by p-value |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4519 filtered_data_filtered <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4520 filtered_data_filtered[ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4521 order(filtered_p$fdr_adjusted_anova_p), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4522 , drop = FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4523 ] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4524 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4525 if (have_remaining_peptides && nrow(filtered_p) > 0 && nrow(filtered_data_filtered) > 0) { |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4526 if (first_page_suppress == 1) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4527 first_page_suppress <- 0 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4528 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4529 cat("\\newpage\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4530 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4531 latex_samepage({ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4532 cat(filter_result_string) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4533 if (nrow(filtered_data_filtered) > 1) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4534 cat(subsection_header(sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4535 "Intensity distributions for %d phosphopeptides\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4536 nrow(filtered_data_filtered) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4537 ))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4538 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4539 cat(subsection_header(sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4540 "Intensity distribution for one phosphopeptide (%s)\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4541 rownames(filtered_data_filtered)[1] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4542 ))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4543 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4544 }) # end latex_samepage |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4545 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4546 old_par <- par( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4547 mai = (par("mai") + c(0.7, 0, 0, 0)) * c(1, 1, 0.3, 1), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4548 oma = old_oma * c(1, 1, 0.3, 1), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4549 cex.main = 0.9, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4550 cex.axis = 0.7, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4551 fin = c(9, 7.25) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4552 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4553 # Vertical plot |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4554 colnames(filtered_data_filtered) <- sample_name_matches |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4555 tryCatch( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4556 boxplot( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4557 filtered_data_filtered, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4558 main = "Imputed, normalized intensities", # no line plot |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4559 las = 2, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4560 cex.axis = 0.9 * sample_name_grow, |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4561 col = const_boxplot_fill, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4562 ylab = latex2exp::TeX("$log_{10}$(peptide intensity)"), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4563 notch = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4564 varwidth = boxplot_varwidth |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4565 ), |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4566 error = function(e) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4567 print(e) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4568 cat_margins() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4569 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4570 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4571 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4572 par(old_par) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4573 } else { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4574 cat(sprintf( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4575 "%s < %0.2f\n\n\n\n\n", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4576 "No peptides were found to have cutoff adjusted p-value", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4577 cutoff |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4578 )) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4579 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4580 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4581 if (have_remaining_peptides && nrow(filtered_data_filtered) > 0) { |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4582 # Add Phosphopeptide column to anova_filtered table |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4583 # The assumption here is that the first intensity is unique; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4584 # this is a hokey assumption but almost definitely will |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4585 # be true in the real world unless there is a computation |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4586 # error upstream. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4587 anova_filtered_merge <- base::merge( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4588 x = connect_df, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4589 y = filtered_data_filtered, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4590 by.x = "Intensity", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4591 by.y = 1 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4592 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4593 anova_filtered_merge_order <- rownames(filtered_p) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4594 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4595 anova_filtered <- data.frame( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4596 ppep = anova_filtered_merge$Phosphopeptide, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4597 intense = anova_filtered_merge$Intensity, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4598 data = anova_filtered_merge[, 2:number_of_samples + 1] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4599 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4600 colnames(anova_filtered) <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4601 c("Phosphopeptide", colnames(filtered_data_filtered)) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4602 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4603 # Merge qualitative columns into the ANOVA data |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4604 output_table <- data.frame(anova_filtered$Phosphopeptide) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4605 output_table <- base::merge( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4606 x = output_table, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4607 y = data_table_imp_qn_lt, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4608 by.x = "anova_filtered.Phosphopeptide", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4609 by.y = "Phosphopeptide" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4610 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4611 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4612 # Produce heatmap to visualize significance and the effect of imputation |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4613 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4614 cat_hm_heading <- function(m, cutoff) { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4615 if (nrow(m) > g_intensity_hm_rows) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4616 cat("\\clearpage\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4617 cat(subsection_header( |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4618 paste( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4619 sprintf("Heatmap for the %d most-significant peptides", |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4620 g_intensity_hm_rows), |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4621 sprintf("whose adjusted p-value < %0.2f\n", cutoff) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4622 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4623 )) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4624 } else { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4625 if (nrow(m) == 0) { |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4626 return(FALSE) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4627 } else { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4628 cat(subsection_header( |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4629 paste( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4630 sprintf("Heatmap for %d usable peptide genes whose", nrow(m)), |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4631 sprintf("adjusted p-value < %0.2f\n", cutoff) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4632 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4633 )) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4634 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4635 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4636 cat("\n\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4637 cat("\n\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4638 return(TRUE) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4639 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4640 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4641 # construct matrix with appropriate rownames |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4642 m <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4643 as.matrix(unimputed_quant_data_log[anova_filtered_merge_order, ]) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4644 nrow_m <- nrow(m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4645 ncol_m <- ncol(m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4646 if (nrow_m > 0) { |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4647 rownames_m <- rownames(m) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4648 q <- data.frame(pepname = rownames_m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4649 g <- sqldf(" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4650 SELECT q.pepname, substr(met.Gene_Name, 1, 30) AS gene_name |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4651 FROM q, metadata_plus_p AS met |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4652 WHERE q.pepname = met.Phosphopeptide |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4653 ORDER BY q.rowid |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4654 ") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4655 tmp <- sapply( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4656 X = seq_len(nrow(g)), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4657 FUN = function(i) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4658 pre <- strsplit(g$gene_name[i], "; ")[[1]] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4659 rslt <- paste(unique(pre), sep = "; ") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4660 return(rslt) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4661 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4662 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4663 tmp <- unlist(tmp) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4664 tmp <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4665 make.names(tmp, unique = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4666 tmp <- sub( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4667 "No_Gene_Name", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4668 "not_found", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4669 tmp, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4670 fixed = TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4671 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4672 ten_trunc_names <- trunc_ppep(rownames_m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4673 tmp <- sapply( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4674 X = seq_len(nrow_m), |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4675 FUN = function(i) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4676 sprintf( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4677 "(%s) %s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4678 tmp[i], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4679 ten_trunc_names[i] |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4680 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4681 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4682 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4683 rownames(m) <- tmp |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4684 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4685 # draw the heading and heatmap |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4686 if (nrow_m > 0) { |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4687 number_of_peptides_found <- |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4688 ppep_heatmap( |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4689 m = m, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4690 cutoff = cutoff, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4691 hm_heading_function = cat_hm_heading, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4692 hm_main_title = |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4693 "log(intensities), row-scaled, unimputed, unnormalized", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4694 suppress_row_dendrogram = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4695 master_cex = 0.35, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4696 sepcolor = "black", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4697 colsep = sample_colsep |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4698 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4699 if (number_of_peptides_found > 1) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4700 cat("\\leavevmode\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4701 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4702 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4703 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4704 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4705 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4706 cat(filter_result_string) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4707 cat("\\leavevmode\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4708 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4709 if (!g_can_run_ksea) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4710 errmsg <- paste("Cannot proceed with KSEA analysis", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4711 "because too many values are missing.") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4712 if (FALSE) cat0( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4713 errmsg, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4714 "\\stepcounter{offset}\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4715 "\\stepcounter{offset}\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4716 "\\stepcounter{offset}\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4717 " in ", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4718 table_href(), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4719 ".\n\n" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4720 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4721 if (FALSE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4722 if (print_nb_messages) nbe(see_variable(p_value_data)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4723 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4724 if (print_nb_messages) nbe(see_variable(p_value_data)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4725 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4726 display_p_value_data <- p_value_data |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4727 display_p_value_data$raw_anova_p <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4728 sprintf("%0.3g", display_p_value_data$raw_anova_p) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4729 display_p_value_data$fdr_adjusted_anova_p <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4730 sprintf("%0.3g", display_p_value_data$fdr_adjusted_anova_p) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4731 display_p_value_data$quality <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4732 sprintf("%0.3g", display_p_value_data$quality) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4733 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4734 headers_1st_line <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4735 c("", "Raw ANOVA", "FDR-adj.", "Missing", "Min. #", "", "") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4736 headers_2nd_line <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4737 c("Phosphopeptide", "p-value", "p-value", "values", "group-obs", "Quality", "Ranking") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4738 data_frame_tabbing_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4739 x = display_p_value_data, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4740 tabstops = c(2.75, 0.80, 0.80, 0.5, 0.6, 0.60), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4741 use_subsubsection_header = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4742 headings = c(headers_1st_line, headers_2nd_line), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4743 caption = "ANOVA results" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4744 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4745 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4746 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4747 data_frame_tabbing_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4748 x = save_sample_treatment_df, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4749 tabstops = c(1.25, 1.25), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4750 caption = "Sample classes", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4751 use_subsubsection_header = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4752 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4753 param_df_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4754 knitr::knit_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4755 return(invisible(-1)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4756 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4757 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4758 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4759 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4760 ```{r sqlite, echo = FALSE, fig.dim = c(9, 10), results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4761 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4762 if (g_can_run_ksea && count_of_treatment_levels > 1) { |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4763 # Prepare two-way contrasts with adjusted p-values |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4764 # Strategy: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4765 # - use imputed, log-transformed data: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4766 # - remember this when computing log2(fold-change) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4767 # - each contrast is between a combination of trt levels |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4768 # - for each contrast, compute samples that are members |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4769 # - compute one-way test: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4770 # - use `oneway.test` (Welch test) if numbers of samples |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4771 # are not equivalent between trt levels |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4772 # - otherwise, aov is fine but offers no advantage |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4773 # - adjust p-value, assuming that |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4774 # (# of pppeps)*(# of contrasts) tests were performed |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4775 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4776 # Each contrast is between a combination of trt levels |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4777 m2 <- combn( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4778 x = seq_len(length(levels(smpl_trt))), |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4779 m = 2, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4780 simplify = TRUE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4781 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4782 contrast_count <- ncol(m2) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4783 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4784 # For each contrast, compute samples that are members |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4785 # - local function to construct a data.frame for each contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4786 # - the contrast in the first "column" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4787 f_m2 <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4788 function(cntrst, lvl1, lvl2) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4789 return( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4790 data.frame( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4791 contrast = cntrst, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4792 level = smpl_trt[ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4793 smpl_trt %in% |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4794 levels(smpl_trt)[c(lvl1, lvl2)] |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4795 ], |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4796 label = sample_name_matches[ |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4797 smpl_trt %in% |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4798 levels(smpl_trt)[c(lvl1, lvl2)] |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4799 ] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4800 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4801 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4802 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4803 # - compute a df for each contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4804 sample_level_dfs <- lapply( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4805 X = 1:contrast_count, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4806 FUN = function(i) f_m2(i, m2[1, i], m2[2, i]) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4807 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4808 # - compute a single df for all contrasts |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4809 combined_contrast_df <- Reduce(f = rbind, x = sample_level_dfs) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4810 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4811 # - dispose objects to free resources |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4812 rm(sample_level_dfs) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4813 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4814 # - write the df to a DB for later join-per-contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4815 db <- RSQLite::dbConnect(RSQLite::SQLite(), ksea_app_prep_db) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4816 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4817 RSQLite::dbWriteTable( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4818 conn = db, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4819 name = "contrast", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4820 value = combined_contrast_df, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4821 overwrite = TRUE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4822 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4823 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4824 # Create UK for insert |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4825 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4826 CREATE UNIQUE INDEX IF NOT EXISTS contrast__uk__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4827 ON contrast(contrast, label); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4828 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4829 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4830 # Create indexes for join |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4831 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4832 -- index for join in contrast_ppep_smpl_qnlt on a.label < b.label |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4833 CREATE INDEX IF NOT EXISTS contrast__label__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4834 ON contrast(label); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4835 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4836 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4837 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4838 -- index for joining two contrast_lvl_ppep_avg_quant on contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4839 CREATE INDEX IF NOT EXISTS contrast__contrast__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4840 ON contrast(contrast); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4841 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4842 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4843 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4844 -- index for joining two contrast_lvl_ppep_avg_quant on phophospep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4845 CREATE INDEX IF NOT EXISTS contrast__level__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4846 ON contrast(level); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4847 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4848 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4849 # - dispose objects to free resources |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4850 rm(combined_contrast_df) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4851 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4852 # Use imputed, log-transformed data |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4853 # - remember that this was donoe when computing log2(fold-change) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4854 # - melt data matrix for use in later join-per-contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4855 casted <- cbind( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4856 data.frame(vrbl = rownames(quant_data_imp_qn_log)), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4857 quant_data_imp_qn_log |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4858 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4859 quant_data_imp_qn_log_melted <- reshape2::melt( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4860 casted, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4861 id.vars = "vrbl" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4862 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4863 colnames(quant_data_imp_qn_log_melted) <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4864 c("phosphopep", "sample", "quant") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4865 # - dispose objects to free resources |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4866 rm(casted) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4867 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4868 # - write the df to a DB for use in later join-per-contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4869 RSQLite::dbWriteTable( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4870 conn = db, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4871 name = "ppep_smpl_qnlt", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4872 value = quant_data_imp_qn_log_melted, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4873 overwrite = TRUE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4874 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4875 # Create UK for insert |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4876 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4877 CREATE UNIQUE INDEX IF NOT EXISTS ppep_smpl_qnlt__uk__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4878 ON ppep_smpl_qnlt(phosphopep, sample); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4879 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4880 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4881 # Create index for join |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4882 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4883 -- index for join in contrast_ppep_smpl_qnlt |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4884 CREATE INDEX IF NOT EXISTS ppep_smpl_qnlt__sample__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4885 ON ppep_smpl_qnlt(sample); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4886 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4887 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4888 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4889 -- index for joining two contrast_lvl_ppep_avg_quant on phopho.pep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4890 CREATE INDEX IF NOT EXISTS ppep_smpl_qnlt__phosphopep__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4891 ON ppep_smpl_qnlt(phosphopep); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4892 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4893 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4894 # - dispose objects to free resources |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4895 rm(quant_data_imp_qn_log_melted) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4896 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4897 # - drop views if exist |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4898 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4899 -- drop view dependent on contrast_lvl_ppep_avg_quant |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4900 DROP VIEW IF EXISTS v_contrast_log2_fc; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4901 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4902 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4903 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4904 -- drop table dependent on contrast_ppep_smpl_qnlt |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4905 DROP TABLE IF EXISTS contrast_lvl_ppep_avg_quant; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4906 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4907 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4908 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4909 DROP TABLE IF EXISTS contrast_lvl_lvl_metadata; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4910 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4911 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4912 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4913 DROP VIEW IF EXISTS v_contrast_lvl_metadata; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4914 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4915 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4916 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4917 -- drop view dependent on contrast_ppep_smpl_qnlt |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4918 DROP VIEW IF EXISTS v_contrast_lvl_ppep_avg_quant; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4919 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4920 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4921 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4922 DROP VIEW IF EXISTS v_contrast_lvl_lvl; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4923 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4924 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4925 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4926 -- drop view upon which other views depend |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4927 DROP VIEW IF EXISTS contrast_ppep_smpl_qnlt; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4928 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4929 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4930 # - create view |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4931 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4932 -- view contrast_ppep_smpl_qnlt is used for each phopshopep to |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4933 -- compute p-value for test of trt effect for two trt levels |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4934 CREATE VIEW contrast_ppep_smpl_qnlt |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4935 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4936 SELECT contrast, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4937 level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4938 phosphopep, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4939 sample, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4940 quant |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4941 FROM contrast AS c, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4942 ppep_smpl_qnlt AS q |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4943 WHERE q.sample = c.label |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4944 ORDER BY contrast, level, phosphopep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4945 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4946 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4947 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4948 # - create simplification views |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4949 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4950 CREATE VIEW v_contrast_lvl_metadata |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4951 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4952 SELECT contrast, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4953 level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4954 group_concat(label, ';') AS samples |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4955 FROM contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4956 GROUP BY contrast, level |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4957 /* view v_contrast_lvl_metadata is used |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4958 to simplify creation of table contrast_lvl_lvl_metadata */ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4959 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4960 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4961 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4962 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4963 CREATE VIEW v_contrast_lvl_ppep_avg_quant |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4964 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4965 SELECT contrast, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4966 level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4967 phosphopep, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4968 avg(quant) AS avg_quant |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4969 FROM contrast_ppep_smpl_qnlt |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4970 GROUP BY contrast, level, phosphopep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4971 /* view v_contrast_lvl_ppep_avg_quant is used |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4972 to simplify view v_contrast_log2_fc */ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4973 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4974 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4975 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4976 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4977 # - create contrast-metadata table |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
4978 if (print_nb_messages) nbe("CREATE TABLE contrast_lvl_lvl_metadata") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4979 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4980 CREATE TABLE contrast_lvl_lvl_metadata |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4981 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4982 SELECT DISTINCT |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4983 a.contrast AS ab_contrast, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4984 a.level AS a_level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4985 b.level AS b_level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4986 a.samples AS a_samples, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4987 b.samples AS b_samples, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4988 'log2(level_'||a.level||'/level_'||b.level||')' |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4989 AS fc_description |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4990 FROM v_contrast_lvl_metadata AS a, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4991 v_contrast_lvl_metadata AS b |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4992 WHERE a.contrast = b.contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4993 AND a.level > b.level |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4994 /* view v_contrast_lvl_lvl is used |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4995 to simplify view v_contrast_log2_fc */ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4996 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4997 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4998 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
4999 # - create pseudo-materialized view table |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5000 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5001 CREATE VIEW v_contrast_lvl_lvl |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5002 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5003 SELECT DISTINCT |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5004 a.contrast AS ab_contrast, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5005 a.level AS a_level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5006 b.level AS b_level |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5007 FROM contrast AS a, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5008 contrast AS b |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5009 WHERE a.contrast = b.contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5010 AND a.level > b.level |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5011 /* view v_contrast_lvl_lvl is used |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5012 to simplify view v_contrast_log2_fc */ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5013 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5014 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5015 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5016 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5017 # - create view to compute log2(fold-change) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5018 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5019 CREATE VIEW v_contrast_log2_fc |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5020 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5021 SELECT ab.ab_contrast AS contrast, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5022 m.a_level AS a_level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5023 c.avg_quant AS a_quant, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5024 m.a_samples AS a_samples, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5025 ab.b_level AS b_level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5026 d.avg_quant AS b_quant, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5027 m.b_samples AS b_samples, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5028 m.fc_description AS fc_description, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5029 3.32193 * ( d.avg_quant - c.avg_quant) AS log2_fc, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5030 d.phosphopep AS phosphopep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5031 FROM contrast_lvl_lvl_metadata AS m, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5032 v_contrast_lvl_ppep_avg_quant AS d, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5033 v_contrast_lvl_lvl AS ab |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5034 INNER JOIN v_contrast_lvl_ppep_avg_quant AS c |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5035 ON c.contrast = ab.ab_contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5036 AND c.level = ab.a_level |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5037 WHERE d.contrast = ab.ab_contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5038 AND m.ab_contrast = ab.ab_contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5039 AND d.level = ab.b_level |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5040 AND d.phosphopep = c.phosphopep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5041 /* view to compute log2(fold-change) */ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5042 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5043 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5044 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5045 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5046 # For each contrast, compute samples that are members |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5047 # compute one-way test: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5048 # - use `oneway.test` (Welch test) if numbers of samples |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5049 # are not equivalent between trt levels |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5050 # - otherwise, aov is fine but offers no advantage |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5051 for (contrast in contrast_count:2) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5052 invisible(contrast) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5053 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5054 for (contrast in 1:contrast_count) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5055 contrast_df <- sqldf::sqldf( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5056 x = paste0(" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5057 SELECT level, phosphopep, sample, quant |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5058 FROM contrast_ppep_smpl_qnlt |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5059 WHERE contrast = ", contrast, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5060 ORDER BY phosphopep, level, sample |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5061 "), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5062 connection = db |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5063 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5064 contrast_cast <- reshape2::dcast( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5065 data = contrast_df, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5066 formula = phosphopep ~ sample, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5067 value.var = "quant" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5068 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5069 contrast_cast_ncol <- ncol(contrast_cast) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5070 contrast_cast_data <- contrast_cast[, 2:contrast_cast_ncol] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5071 contrast_cast_samples <- colnames(contrast_cast_data) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5072 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5073 # - order grouping_factor by order of sample columns of contrast_cast_data |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5074 grouping_factor <- sqldf::sqldf( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5075 x = paste0(" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5076 SELECT sample, level |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5077 FROM contrast_ppep_smpl_qnlt |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5078 WHERE contrast = ", contrast, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5079 ORDER BY phosphopep, level, sample |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5080 LIMIT ", contrast_cast_ncol - 1 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5081 ), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5082 connection = db |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5083 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5084 rownames(grouping_factor) <- grouping_factor$sample |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5085 grouping_factor <- grouping_factor[, "level", drop = FALSE] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5086 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5087 # - run the two-level (one-way) test |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5088 p_value_data_contrast_ps <- |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5089 row_apply( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5090 x = contrast_cast_data, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5091 fun = anova_func, |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5092 grouping_factor = |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5093 as.factor(grouping_factor$level), # anova_func arg2 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5094 one_way_f = one_way_two_categories, # anova_func arg3 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5095 simplify = TRUE # TRUE is the default for simplify |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5096 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5097 contrast_data_adj_p_values <- p.adjust( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5098 p = p_value_data_contrast_ps, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5099 method = "fdr", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5100 n = length(p_value_data_contrast_ps) # this is the default, length(p) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5101 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5102 # - compute the fold-change |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5103 contrast_p_df <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5104 data.frame( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5105 contrast = contrast, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5106 phosphopep = contrast_cast$phosphopep, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5107 p_value_raw = p_value_data_contrast_ps, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5108 p_value_adj = contrast_data_adj_p_values |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5109 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5110 db_write_table_overwrite <- (contrast < 2) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5111 db_write_table_append <- !db_write_table_overwrite |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5112 RSQLite::dbWriteTable( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5113 conn = db, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5114 name = "contrast_ppep_p_val", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5115 value = contrast_p_df, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5116 append = db_write_table_append |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5117 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5118 # Create UK for insert |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5119 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5120 CREATE UNIQUE INDEX IF NOT EXISTS contrast_ppep_p_val__uk__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5121 ON contrast_ppep_p_val(phosphopep, contrast); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5122 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5123 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5124 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5125 # Perhaps this could be done more elegantly using unique keys |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5126 # or creating the tables before saving data to them, but this |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5127 # is fast and, if the database exists on disk rather than in |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5128 # memory, it doesn't stress memory. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5129 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5130 CREATE TEMP table contrast_log2_fc |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5131 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5132 SELECT * |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5133 FROM v_contrast_log2_fc |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5134 ORDER BY contrast, phosphopep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5135 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5136 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5137 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5138 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5139 CREATE TEMP table ppep_p_val |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5140 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5141 SELECT p_value_raw, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5142 p_value_adj, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5143 contrast AS p_val_contrast, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5144 phosphopep AS p_val_ppep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5145 FROM contrast_ppep_p_val |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5146 ORDER BY contrast, phosphopep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5147 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5148 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5149 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5150 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5151 DROP TABLE IF EXISTS contrast_log2_fc_p_val |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5152 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5153 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5154 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5155 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5156 CREATE TABLE contrast_log2_fc_p_val |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5157 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5158 SELECT a.*, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5159 b.p_value_raw, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5160 b.p_value_adj, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5161 b.p_val_contrast, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5162 b.p_val_ppep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5163 FROM contrast_log2_fc a, ppep_p_val b |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5164 WHERE a.rowid = b.rowid |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5165 AND a.phosphopep = b.p_val_ppep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5166 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5167 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5168 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5169 # Create UK |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5170 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5171 CREATE UNIQUE INDEX IF NOT EXISTS contrast_log2_fc_p_val__uk__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5172 ON contrast_log2_fc_p_val(phosphopep, contrast); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5173 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5174 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5175 # Create indices for future queries |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5176 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5177 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__contrast__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5178 ON contrast_log2_fc_p_val(contrast); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5179 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5180 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5181 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5182 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__phosphopep__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5183 ON contrast_log2_fc_p_val(phosphopep); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5184 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5185 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5186 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5187 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__p_value_raw__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5188 ON contrast_log2_fc_p_val(p_value_raw); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5189 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5190 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5191 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5192 CREATE INDEX IF NOT EXISTS contrast_log2_fc_p_val__p_value_adj__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5193 ON contrast_log2_fc_p_val(p_value_adj); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5194 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5195 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5196 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5197 DROP VIEW IF EXISTS v_contrast_log2_fc_p_val |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5198 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5199 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5200 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5201 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5202 CREATE VIEW v_contrast_log2_fc_p_val |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5203 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5204 SELECT contrast, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5205 a_level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5206 a_samples, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5207 b_level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5208 b_samples, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5209 a_quant, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5210 b_quant, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5211 fc_description, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5212 log2_fc, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5213 p_value_raw, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5214 p_value_adj, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5215 phosphopep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5216 FROM contrast_log2_fc_p_val |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5217 ORDER BY contrast, phosphopep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5218 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5219 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5220 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5221 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5222 DROP TABLE IF EXISTS kseaapp_metadata |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5223 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5224 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5225 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5226 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5227 CREATE TABLE kseaapp_metadata |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5228 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5229 WITH extended(deppep, ppep, gene_name, uniprot_id, phosphoresidue) AS ( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5230 SELECT DISTINCT |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5231 deppep.seq, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5232 ppep.seq, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5233 GeneName||';', |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5234 UniProtID||';', |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5235 PhosphoResidue||';' |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5236 FROM |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5237 ppep, deppep, mrgfltr_metadata |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5238 WHERE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5239 mrgfltr_metadata.ppep_id = ppep.id |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5240 AND |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5241 ppep.deppep_id = deppep.id |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5242 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5243 SELECT |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5244 ppep AS `ppep`, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5245 SUBSTR(uniprot_id, 1, INSTR(uniprot_id,';') - 1 ) AS `Protein`, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5246 SUBSTR(gene_name, 1, INSTR(gene_name,';') - 1 ) AS `Gene`, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5247 deppep AS `Peptide`, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5248 REPLACE( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5249 REPLACE( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5250 SUBSTR(phosphoresidue, 1, INSTR(phosphoresidue,';') - 1 ), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5251 'p', |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5252 '' |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5253 ), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5254 ', ', |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5255 ';' |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5256 ) AS `Residue.Both` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5257 FROM extended |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5258 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5259 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5260 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5261 # Create indexes for join |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5262 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5263 CREATE INDEX IF NOT EXISTS kseaapp_metadata__ppep__idx |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5264 ON kseaapp_metadata(ppep); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5265 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5266 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5267 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5268 DROP VIEW IF EXISTS v_kseaapp_contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5269 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5270 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5271 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5272 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5273 CREATE VIEW v_kseaapp_contrast |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5274 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5275 SELECT a.*, b.Protein, b.Gene, b.Peptide, b.`Residue.Both` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5276 FROM v_contrast_log2_fc_p_val a, kseaapp_metadata b |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5277 WHERE b.ppep = a.phosphopep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5278 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5279 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5280 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5281 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5282 DROP VIEW IF EXISTS v_kseaapp_input |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5283 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5284 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5285 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5286 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5287 CREATE VIEW v_kseaapp_input |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5288 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5289 SELECT v.contrast, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5290 v.phosphopep, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5291 m.`Protein`, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5292 m.`Gene`, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5293 m.`Peptide`, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5294 m.`Residue.Both`, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5295 v.p_value_raw AS `p`, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5296 v.log2_fc AS `FC` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5297 FROM kseaapp_metadata AS m, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5298 v_contrast_log2_fc_p_val AS v |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5299 WHERE m.ppep = v.phosphopep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5300 AND NOT m.`Gene` = 'No_Gene_Name' |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5301 AND NOT v.log2_fc = 0 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5302 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5303 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5304 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5305 # We are done with DDL and insertion |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5306 RSQLite::dbDisconnect(db) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5307 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5308 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5309 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5310 ```{r echo = FALSE, results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5311 cat("\\newpage\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5312 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5313 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5314 # KSEA Analysis Summaries |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5315 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5316 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: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5317 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5318 - The package is available on CRAN, at https:/cran.r-project.org/package=KSEAapp |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5319 - 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). |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5320 - An online alternative (supporting only analysis of human data) is available at [https:/casecpb.shinyapps.io/ksea/](https:/casecpb.shinyapps.io/ksea/). |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5321 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5322 For each kinase, $i$, and each two-way contrast of treatments, $j$, an enrichment $z$-score is computed as: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5323 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5324 $$ |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5325 \text{kinase enrichment }z\text{-score}_{j,i} = \frac{(\overline{`r sfc`}_{j,i} - \overline{`r pfc`}_j)\sqrt{m_{j,i}}}{\delta_j} |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5326 $$ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5327 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5328 and fold-enrichment is computed as: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5329 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5330 $$ |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5331 \text{Enrichment}_{j,i} = \frac{\overline{`r sfc`}_{j,i}}{\overline{`r pfc`}_j} |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5332 $$ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5333 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5334 where: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5335 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5336 - $\overline{`r sfc`}_{j,i}$ is the mean `r pfc_txt` in intensities of known substrates of the kinase $i$ in contrast $j$, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5337 - $\overline{`r pfc`}_j$ is the mean `r pfc_txt` of all phosphosites identified in contrast $j$, and |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5338 - $m_{j,i}$ is the total number of phosphosite substrates of kinase $i$ identified in contrast $j$, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5339 - $\delta_j$ is the standard deviation of the $\log_2 (\text{fold-change})$ for contrast $j$ across all phosphosites in the dataset. |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5340 - 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. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5341 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5342 $\text{FDR}_{j,i}$ is the False Discovery Rate corrected kinase enrichment score. |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5343 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5344 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). |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5345 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5346 Asterisks in heatmaps reflect enrichments that are significant at `r ksea_cutoff_statistic` < `r ksea_cutoff_threshold`. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5347 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5348 - 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. |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5349 - 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
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5350 - 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). |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5351 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5352 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". |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5353 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5354 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. |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5355 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5356 ```{r ksea, echo = FALSE, fig.dim = c(12, 14.5), results = 'asis'} |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5357 cat("\\clearpage\n") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5358 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5359 db <- RSQLite::dbConnect(RSQLite::SQLite(), ksea_app_prep_db) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5360 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5361 # -- eliminate the table that's about to be defined |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5362 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5363 DROP TABLE IF EXISTS site_metadata; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5364 ") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5365 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5366 # -- define the site_metadata table |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5367 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5368 CREATE TABLE site_metadata( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5369 id INTEGER PRIMARY KEY |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5370 , site_type_id INTEGER REFERENCES site_type(id) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5371 , full TEXT UNIQUE ON CONFLICT IGNORE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5372 , abbrev TEXT |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5373 , pattern TEXT |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5374 , motif TEXT |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5375 ); |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5376 ") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5377 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5378 # -- populate the table with initial values |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5379 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5380 INSERT INTO site_metadata(full, abbrev, site_type_id) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5381 SELECT DISTINCT kinase_map, kinase_map, site_type_id |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5382 FROM ppep_gene_site |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5383 ORDER BY kinase_map; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5384 ") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5385 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5386 # -- drop bogus KSData view if exists |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5387 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5388 DROP VIEW IF EXISTS ks_data_v; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5389 ") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5390 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5391 # -- create view to serve as an impostor for KSEAapp::KSData |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5392 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5393 CREATE VIEW IF NOT EXISTS ks_data_v |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5394 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5395 SELECT |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5396 'NA' AS KINASE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5397 'NA' AS KIN_ACC_ID, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5398 kinase_map AS GENE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5399 'NA' AS KIN_ORGANISM, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5400 'NA' AS SUBSTRATE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5401 0 AS SUB_GENE_ID, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5402 'NA' AS SUB_ACC_ID, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5403 gene_names AS SUB_GENE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5404 'NA' AS SUB_ORGANISM, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5405 phospho_peptide AS SUB_MOD_RSD, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5406 0 AS SITE_GROUP_ID, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5407 'NA' AS 'SITE_7AA', |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5408 2 AS networkin_score, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5409 type_name AS Source |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5410 FROM ppep_gene_site_view; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5411 ") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5412 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5413 contrast_metadata_df <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5414 sqldf::sqldf("select * from contrast_lvl_lvl_metadata", connection = db) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5415 rslt <- new_env() |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5416 rslt$score_list <- list() |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5417 rslt$name_list <- list() |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5418 rslt$longname_list <- list() |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5419 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5420 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5421 DROP TABLE IF EXISTS contrast_ksea_scores; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5422 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5423 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5424 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5425 next_index <- 0 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5426 err_na_subscr_df_const <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5427 "missing values are not allowed in subscripted assignments of data frames" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5428 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5429 for (i_cntrst in seq_len(nrow(contrast_metadata_df))) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5430 cntrst_a_level <- contrast_metadata_df[i_cntrst, "a_level"] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5431 cntrst_b_level <- contrast_metadata_df[i_cntrst, "b_level"] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5432 cntrst_fold_change <- contrast_metadata_df[i_cntrst, 6] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5433 contrast_label <- sprintf("%s -> %s", cntrst_b_level, cntrst_a_level) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5434 contrast_longlabel <- ( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5435 sprintf( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5436 "Class %s -> Class %s", |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5437 contrast_metadata_df[i_cntrst, "b_level"], |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5438 contrast_metadata_df[i_cntrst, "a_level"] |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5439 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5440 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5441 kseaapp_input <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5442 sqldf::sqldf( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5443 x = sprintf(" |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5444 SELECT `Protein`, `Gene`, `Peptide`, phosphopep AS `Residue.Both`, `p`, `FC` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5445 FROM v_kseaapp_input |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5446 WHERE contrast = %d |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5447 ", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5448 i_cntrst |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5449 ), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5450 connection = db |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5451 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5452 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5453 pseudo_ksdata <- dbReadTable(db, "ks_data_v") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5454 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5455 # This hack is because SQL table has the log2-transformed values |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5456 kseaapp_input[, "FC"] <- 2 ** kseaapp_input[, "FC", drop = TRUE] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5457 main_title <- ( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5458 sprintf( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5459 "Change from treatment %s to treatment %s", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5460 contrast_metadata_df[i_cntrst, "b_level"], |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5461 contrast_metadata_df[i_cntrst, "a_level"] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5462 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5463 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5464 sub_title <- contrast_longlabel |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5465 tryCatch( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5466 expr = { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5467 ksea_scores_rslt <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5468 ksea_scores( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5469 ksdata = pseudo_ksdata, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5470 px = kseaapp_input, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5471 networkin = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5472 networkin_cutoff = 2, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5473 minimum_substrate_count = ksea_min_substrate_count |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5474 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5475 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5476 if (FALSE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5477 ksea_scores_rslt <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5478 ksea_scores_rslt[ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5479 ksea_scores_rslt$m >= ksea_min_substrate_count, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5480 , |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5481 drop = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5482 ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5483 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5484 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5485 if (FALSE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5486 data_frame_tabbing_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5487 x = ksea_scores_rslt, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5488 tabstops = c(0.8, 0.8, 0.8, 0.8, 0.8, 0.8), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5489 caption = paste("KSEA scores for contrast ", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5490 cntrst_b_level, "to", cntrst_a_level), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5491 use_subsubsection_header = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5492 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5493 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5494 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5495 if (FALSE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5496 if (print_nb_messages) nbe("Output contents of `ksea_scores_rslt` table\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5497 cat_variable(ksea_scores_rslt) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5498 cat("\n\\clearpage\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5499 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5500 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5501 if (0 < sum(!is.nan(ksea_scores_rslt$FDR))) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5502 next_index <- 1 + next_index |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5503 rslt$score_list[[next_index]] <- ksea_scores_rslt |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5504 rslt$name_list[[next_index]] <- contrast_label |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5505 rslt$longname_list[[next_index]] <- contrast_longlabel |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5506 ksea_low_fdr_print( |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5507 rslt = rslt, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5508 i_cntrst = i_cntrst, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5509 i = next_index, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5510 a_level = cntrst_a_level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5511 b_level = cntrst_b_level, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5512 fold_change = cntrst_fold_change, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5513 caption = contrast_longlabel |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5514 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5515 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5516 }, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5517 error = function(e) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5518 str(e) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5519 cat_margins() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5520 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5521 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5522 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5523 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5524 plotted_kinases <- NULL |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5525 if (g_can_run_ksea && length(rslt$score_list) > 1) { |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5526 for (i in seq_len(length(ksea_heatmap_titles))) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5527 hdr <- ksea_heatmap_titles[[i]] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5528 which_kinases <- i |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5529 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5530 cat("\\clearpage\n\\begin{center}\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5531 if (i == const_ksea_astrsk_kinases) { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5532 cat(subsection_header(hdr)) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5533 } else { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5534 cat(subsection_header(hdr)) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5535 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5536 cat("\\end{center}\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5537 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5538 plotted_kinases <- ksea_heatmap( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5539 # the data frame outputs from the KSEA.Scores() function, in list format |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5540 score_list = rslt$score_list, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5541 # a character vector of all the sample names for heatmap annotation: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5542 # - the names must be in the same order as the data in score_list |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5543 # - please avoid long names, as they may get cropped in the final image |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5544 sample_labels = rslt$name_list, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5545 # character string of either "p.value" or "FDR" indicating the data column |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5546 # to use for marking statistically significant scores |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5547 stats = c("p.value", "FDR")[2], |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5548 # a numeric value between 0 and infinity indicating the min. number of |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5549 # substrates a kinase must have to be included in the heatmap |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5550 m_cutoff = 1, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5551 # a numeric value between 0 and 1 indicating the p-value/FDR cutoff |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5552 # for indicating significant kinases in the heatmap |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5553 p_cutoff = params$kseaCutoffThreshold, |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5554 # a binary input of TRUE or FALSE, indicating whether or not to perform |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5555 # hierarchical clustering of the sample columns |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5556 sample_cluster = TRUE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5557 # a binary input of TRUE or FALSE, indicating whether or not to export |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5558 # the heatmap as a .png image into the working directory |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5559 export = FALSE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5560 # additional arguments to gplots::heatmap.2, such as: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5561 # - main: main title of plot |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5562 # - xlab: x-axis label |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5563 # - ylab: y-axis label |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5564 xlab = "Contrast", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5565 ylab = "Kinase", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5566 # print which kinases: |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5567 # - 1 : all kinases |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5568 # - 2 : significant kinases |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5569 # - 3 : non-significant kinases |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5570 which_kinases = which_kinases, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5571 margins = c(7, 15) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5572 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5573 if (!is.null(plotted_kinases)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5574 cat("\\begin{center}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5575 if (which_kinases != const_ksea_nonastrsk_kinases) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5576 cat("Asterisks reflect significance.\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5577 cat("\\end{center}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5578 } |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5579 } # end for (i in ... |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5580 } # end if (length ... |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5581 ``` |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5582 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5583 ```{r kseabar_calc, echo = FALSE, fig.dim = c(9.5, 6), results = 'asis'} |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5584 ksea_prints <- list() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5585 ksea_barplots <- list() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5586 for (i_cntrst in seq_len(length(rslt$score_list))) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5587 next_index <- i_cntrst |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5588 cntrst_a_level <- contrast_metadata_df[i_cntrst, "a_level"] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5589 cntrst_b_level <- contrast_metadata_df[i_cntrst, "b_level"] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5590 cntrst_fold_change <- contrast_metadata_df[i_cntrst, 6] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5591 contrast_label <- sprintf("%s -> %s", cntrst_b_level, cntrst_a_level) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5592 contrast_longlabel <- ( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5593 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5594 "Class %s -> Class %s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5595 contrast_metadata_df[i_cntrst, "b_level"], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5596 contrast_metadata_df[i_cntrst, "a_level"] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5597 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5598 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5599 main_title <- ( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5600 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5601 "Change from treatment %s to treatment %s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5602 contrast_metadata_df[i_cntrst, "b_level"], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5603 contrast_metadata_df[i_cntrst, "a_level"] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5604 ) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5605 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5606 sub_title <- contrast_longlabel |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5607 tryCatch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5608 expr = { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5609 ksea_scores_rslt <- rslt$score_list[[next_index]] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5610 if (print_nb_messages) nbe(see_variable(ksea_scores_rslt)) #ACE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5611 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5612 if (0 < sum(!is.nan(ksea_scores_rslt$FDR))) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5613 sink(deferred <- file()) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5614 ksea_low_fdr_print( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5615 rslt = rslt, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5616 i_cntrst = i_cntrst, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5617 i = next_index, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5618 a_level = cntrst_a_level, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5619 b_level = cntrst_b_level, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5620 fold_change = cntrst_fold_change, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5621 caption = contrast_longlabel, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5622 write_db = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5623 anchor = const_table_anchor_t |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5624 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5625 cat("\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5626 sink() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5627 lines <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5628 paste( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5629 readLines(deferred, warn = FALSE), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5630 collapse = "\n" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5631 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5632 close(deferred) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5633 sq_put(ksea_prints, lines) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5634 sink(stderr()) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5635 cat("\n---\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5636 cat_variable(ksea_prints) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5637 barplot_closure <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5638 ksea_low_fdr_barplot_factory( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5639 rslt = rslt, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5640 i_cntrst = i_cntrst, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5641 i = next_index, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5642 a_level = cntrst_a_level, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5643 b_level = cntrst_b_level, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5644 fold_change = cntrst_fold_change, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5645 caption = contrast_longlabel |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5646 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5647 if (rlang::is_closure(barplot_closure)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5648 sq_put(ksea_barplots, barplot_closure) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5649 else |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5650 sq_put(ksea_barplots, no_op) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5651 str(ksea_barplots) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5652 cat("\n...\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5653 sink() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5654 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5655 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5656 error = function(e) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5657 str(e) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5658 cat_margins() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5659 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5660 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5661 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5662 ``` |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5663 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5664 ```{r phosphoelm_kinase_upid_desc, echo = FALSE, fig.dim = c(12, 13.7), results = 'asis'} |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5665 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5666 have_kinase_descriptions <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5667 if (!is.null(bzip2df(kinase_uprt_desc_lut, kinase_uprt_desc_lut_bz2)) && |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5668 !is.null(bzip2df(kinase_name_uprt_lut, kinase_name_uprt_lut_bz2)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5669 ) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5670 rownames(kinase_uprt_desc_lut) <- kinase_uprt_desc_lut$UniProtID |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5671 kinase_name_to_desc_uprt <- function(s) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5672 rslt <- NULL |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5673 tryCatch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5674 { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5675 which_rows <- eval(s == kinase_name_uprt_lut$kinase) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5676 kinase_uprtid <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5677 kinase_name_uprt_lut[which_rows, 2] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5678 # filter for first _HUMAN match if any |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5679 grepl_human <- grepl("_HUMAN$", kinase_uprtid) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5680 if (0 < sum(grepl_human)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5681 kinase_uprtid <- kinase_uprtid[grepl_human] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5682 # filter for first match if any |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5683 if (0 < length(kinase_uprtid)) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5684 kinase_uprtid <- kinase_uprtid[1] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5685 kinase_desc <- kinase_uprt_desc_lut[kinase_uprtid, 2] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5686 if (!is.na(kinase_desc)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5687 rslt <- c(kinase_desc, kinase_uprtid) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5688 else |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5689 rslt <- c(kinase_desc, "") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5690 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5691 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5692 warning = str |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5693 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5694 rslt |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5695 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5696 TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5697 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5698 kinase_name_to_desc_uprt <- function(s) NULL |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5699 FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5700 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5701 ``` |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5702 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5703 ```{r write_params, echo = FALSE, results = 'asis'} |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5704 # perhaps this should be moved into the functions section, eventually ... |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5705 write_params <- function(db) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5706 # write parameters to report |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5707 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5708 # write parameters to SQLite output |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5709 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5710 mqppep_anova_script_param_df <- data.frame( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5711 script = "mqppep_anova_script.Rmd", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5712 parameter = names(param_unlist), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5713 value = param_unlist |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5714 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5715 ddl_exec(db, " |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5716 DROP TABLE IF EXISTS script_parameter; |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5717 " |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5718 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5719 ddl_exec(db, " |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5720 CREATE TABLE IF NOT EXISTS script_parameter( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5721 script TEXT, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5722 parameter TEXT, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5723 value ANY, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5724 UNIQUE (script, parameter) ON CONFLICT REPLACE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5725 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5726 ; |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5727 " |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5728 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5729 RSQLite::dbWriteTable( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5730 conn = db, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5731 name = "script_parameter", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5732 value = mqppep_anova_script_param_df, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5733 append = TRUE |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5734 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5735 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5736 loaded_packages_df <- sessioninfo::package_info("loaded") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5737 loaded_packages_df[, "library"] <- as.character(loaded_packages_df$library) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5738 loaded_packages_df <- data.frame( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5739 package = loaded_packages_df$package, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5740 version = loaded_packages_df$loadedversion, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5741 date = loaded_packages_df$date |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5742 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5743 #ACE cat("\\clearpage\n\\section{R package versions}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5744 #ACE data_frame_tabbing_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5745 #ACE x = loaded_packages_df, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5746 #ACE tabstops = c(2.5, 1.25), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5747 #ACE caption = "R package versions" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5748 #ACE ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5749 cat("\\clearpage\n\\section{Input parameter settings}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5750 data_frame_tabbing_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5751 x = param_df, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5752 tabstops = c(1.75), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5753 underscore_whack = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5754 caption = "Input parameters", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5755 verbatim = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5756 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5757 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5758 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5759 if (!have_kinase_descriptions) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5760 write_params(db) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5761 # We are done with output |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5762 RSQLite::dbDisconnect(db) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5763 param_df_exit() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5764 knitr::knit_exit() |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5765 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5766 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5767 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5768 ```{r kseabar, echo = FALSE, fig.dim = c(9.5, 12.3), results = 'asis'} |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5769 if (have_kinase_descriptions) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5770 my_section_header <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5771 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5772 "inases whose KSEA %s < %s\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5773 ksea_cutoff_statistic, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5774 signif(ksea_cutoff_threshold, 2) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5775 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5776 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5777 # Use enriched kinases to find enriched kinase-substrate pairs |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5778 enriched_kinases <- data.frame(kinase = ls(ksea_asterisk_hash)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5779 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5780 enriched_kinase_descs <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5781 Reduce( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5782 f = function(l, r) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5783 lkup <- kinase_name_to_desc_uprt(r) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5784 if (is.null(lkup)) l |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5785 else r2 <- rbind( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5786 l, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5787 data.frame( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5788 kinase = r, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5789 uniprot_id = lkup[2], |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5790 description = lkup[1] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5791 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5792 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5793 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5794 x = enriched_kinases$kinase, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5795 init = NULL |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5796 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5797 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5798 if (length(enriched_kinase_descs) > 0 && nrow(enriched_kinase_descs) > 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5799 cat("\n\\clearpage\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5800 data_frame_tabbing_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5801 x = enriched_kinase_descs, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5802 tabstops = c(0.9, 1.3), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5803 headings = c("Kinase", "UniProt ID", "Description"), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5804 caption = paste0("Descriptions of k", my_section_header) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5805 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5806 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5807 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5808 if (FALSE) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5809 cat_variable(sqldf("SELECT kinase FROM enriched_kinases")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5810 cat_variable(sqldf(" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5811 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5812 FROM pseudo_ksdata |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5813 WHERE gene IN (SELECT kinase FROM enriched_kinases) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5814 ")) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5815 data_frame_table_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5816 x = sqldf(" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5817 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5818 FROM pseudo_ksdata |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5819 WHERE gene IN (SELECT kinase FROM enriched_kinases) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5820 "), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5821 justification = "l l l", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5822 centered = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5823 caption = "substrates of enriched kinases", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5824 anchor = c(const_table_anchor_p, const_table_anchor_t), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5825 underscore_whack = TRUE |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5826 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5827 data_frame_table_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5828 x = sqldf(" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5829 SELECT |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5830 gene AS kinase, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5831 ppep, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5832 sub_gene, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5833 '('||group_concat(gene||'-'||sub_gene)||') '||ppep AS label, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5834 fdr_adjusted_anova_p, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5835 quality, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5836 min_group_obs_count |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5837 FROM ( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5838 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5839 FROM pseudo_ksdata |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5840 WHERE gene IN (SELECT kinase FROM enriched_kinases) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5841 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5842 p_value_data |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5843 WHERE ppep = phosphopeptide |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5844 GROUP BY kinase, ppep |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5845 ORDER BY kinase, ppep, p_value_data.quality DESC |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5846 "), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5847 justification = "l l l l l l l", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5848 centered = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5849 caption = "labeled substrates of enriched kinases", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5850 anchor = c(const_table_anchor_p, const_table_anchor_t), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5851 underscore_whack = TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5852 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5853 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5854 all_enriched_substrates <- sqldf(" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5855 SELECT |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5856 gene AS kinase, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5857 ppep, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5858 sub_gene, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5859 '('||group_concat(gene||'-'||sub_gene)||') '||ppep AS label, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5860 fdr_adjusted_anova_p, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5861 quality, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5862 min_group_obs_count |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5863 FROM ( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5864 SELECT DISTINCT gene, sub_gene, SUB_MOD_RSD AS ppep |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5865 FROM pseudo_ksdata |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5866 WHERE gene IN (SELECT kinase FROM enriched_kinases) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5867 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5868 p_value_data |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5869 WHERE ppep = phosphopeptide |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5870 GROUP BY kinase, ppep |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5871 ORDER BY kinase, ppep, p_value_data.quality DESC |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5872 ") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5873 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5874 all_enriched_substrates <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5875 all_enriched_substrates[ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5876 all_enriched_substrates$quality >= params$minQuality, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5877 , |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5878 drop = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5879 ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5880 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5881 all_enriched_substrates$sub_gene <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5882 sub( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5883 " ///.*", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5884 " ...", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5885 all_enriched_substrates$sub_gene |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5886 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5887 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5888 all_enriched_substrates$label <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5889 with( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5890 all_enriched_substrates, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5891 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5892 "(%s-%s) %s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5893 kinase, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5894 trunc_subgene(sub_gene), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5895 ppep |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5896 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5897 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5898 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5899 # this global is set to TRUE by cat_enriched_heading immediately below |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5900 g_neednewpage <- FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5901 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5902 # helper used to label per-kinase substrate enrichment figure |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5903 cat_enriched_heading <- function(m, cut_args) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5904 cutoff <- cut_args$cutoff |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5905 kinase <- cut_args$kinase |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5906 if (g_neednewpage) cat("\\newpage\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5907 g_neednewpage <- TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5908 if (nrow(m) > g_intensity_hm_rows) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5909 cat(subsection_header( |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5910 sprintf( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5911 "Highest-quality %d (of %d) enriched %s-substrates", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5912 g_intensity_hm_rows, |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5913 nrow(m), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5914 kinase |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5915 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5916 )) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5917 } else { |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5918 if (nrow(m) == 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5919 return(FALSE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5920 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5921 nrow_m <- nrow(m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5922 cat(subsection_header( |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5923 sprintf( |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5924 "%d enriched %s-substrate%s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5925 nrow_m, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5926 kinase, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5927 if (nrow_m > 1) "s" else "" |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5928 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5929 )) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5930 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5931 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5932 cat("\n\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5933 cat("\n\n\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5934 return(TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5935 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5936 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5937 # -------------------------------- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5938 # hack begin - show all substrates |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5939 enriched_substrates <- all_enriched_substrates |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5940 # add "FALSE &&" to prevent listing of substrates |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5941 if (show_enriched_substrates && nrow(enriched_substrates) > 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5942 short_row_names <- sub( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5943 "$FAILED_MATCH_GENE_NAME", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5944 "not_found", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5945 enriched_substrates$sub_gene, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5946 fixed = TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5947 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5948 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5949 if (print_nb_messages) nbe(see_variable(enriched_substrates)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5950 substrates_df <- with( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5951 enriched_substrates, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5952 data.frame( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5953 kinase = kinase, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5954 substrate = sub(" ///*", "...", short_row_names), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5955 anova_p_value = signif(fdr_adjusted_anova_p, 2), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5956 min_group_obs_count = signif(min_group_obs_count, 0), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5957 quality = signif(quality, 3), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5958 sequence = trunc_n(30)(ppep) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5959 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5960 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5961 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5962 substrates_df <- substrates_df[ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5963 with(substrates_df, order(kinase, -quality)), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5964 , |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5965 drop = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5966 ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5967 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5968 if (print_nb_messages) nbe(see_variable(substrates_df)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5969 if (nrow(substrates_df) < 1) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5970 substrates_df$sequence <- c() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5971 if (print_nb_messages) nbe(see_variable(substrates_df)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5972 names(substrates_df) <- headers_2nd_line <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5973 c("Kinase", "Substrate", "p-value", "per group)", "quality", "Sequence") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5974 headers_1st_line <- c("", "", "ANOVA", "min(values", "", "") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5975 data_frame_tabbing_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5976 x = substrates_df, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5977 tabstops = c(1.2, 0.8, 0.5, 0.65, 0.5), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5978 headings = c(headers_1st_line, headers_2nd_line), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5979 caption = "Details for all enriched substrates of enriched kinases" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5980 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5981 rm( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5982 enriched_substrates, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5983 substrates_df, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5984 short_row_names, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5985 headers_1st_line, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5986 headers_2nd_line |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5987 ) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
5988 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5989 cat("\\clearpage\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5990 # hack end - show all substrates |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5991 # -------------------------------- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5992 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5993 # print deferred tables and graphs for kinases from contrasts |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5994 for (i_cntrst in seq_len(length(ksea_prints))) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5995 #latex_samepage({ |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5996 cat(ksea_prints[[i_cntrst]]) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5997 cat("\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5998 ksea_barplots[[i_cntrst]]() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
5999 cat("\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6000 cat("\\clearpage\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6001 #}) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6002 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6003 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6004 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6005 ``` |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6006 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6007 ```{r enriched, echo = FALSE, fig.dim = c(12, 13.7), results = 'asis'} |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6008 if (g_can_run_ksea) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6009 g_did_enriched_header <- FALSE |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6010 for (kinase_name in sort(enriched_kinases$kinase)) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6011 enriched_substrates <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6012 all_enriched_substrates[ |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6013 all_enriched_substrates$kinase == kinase_name, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6014 , |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6015 drop = FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6016 ] |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6017 ten_trunc_ppep <- trunc_enriched_substrate(enriched_substrates$ppep) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6018 enriched_substrates$label <- with( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6019 enriched_substrates, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6020 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6021 "(%s) %s", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6022 make.names( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6023 sub("$FAILED_MATCH_GENE_NAME", "not_found", sub_gene, fixed = TRUE), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6024 unique = TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6025 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6026 ten_trunc_ppep |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6027 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6028 ) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6029 # Get the intensity values for the heatmap |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6030 enriched_intensities <- |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6031 as.matrix(unimputed_quant_data_log[enriched_substrates$ppep, , drop = FALSE]) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6032 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6033 # Remove rows having too many NA values to be relevant |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6034 good_rows <- (rowSums(enriched_intensities, na.rm = TRUE) != 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6035 #ACE nbe(see_variable(good_rows), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6036 enriched_substrates <- enriched_substrates[good_rows, , drop = FALSE] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6037 enriched_intensities <- enriched_intensities[good_rows, , drop = FALSE] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6038 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6039 # Rename the rows with the display-name for the heatmap |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6040 short_row_names <- sub( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6041 "$FAILED_MATCH_GENE_NAME", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6042 "not_found", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6043 enriched_substrates$sub_gene, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6044 fixed = TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6045 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6046 short_row_names <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6047 make.names(short_row_names, unique = TRUE) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6048 long_row_names <- |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6049 sapply( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6050 X = rownames(enriched_intensities), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6051 FUN = function(rn) { |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6052 enriched_substrates[enriched_substrates$ppep == rn, "label"] |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6053 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6054 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6055 rownames(enriched_intensities) <- long_row_names |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6056 # Format as matrix for heatmap |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6057 m <- as.matrix(enriched_intensities) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6058 rownames(m) <- trunc_enriched_substrate(rownames(m)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6059 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6060 #ACE nb("m with bad rows: ", see_variable(m), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6061 #ACE good_rows <- (rowSums(m, na.rm = TRUE) != 0) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6062 #ACE nb(see_variable(good_rows), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6063 #ACE m <- m[good_rows, , drop = FALSE] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6064 #ACE nb("m without(?) bad rows: ", see_variable(m), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6065 #ACE nb(see_variable(short_row_names), "\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6066 #ACE local_short_row_names <- short_row_names[good_rows] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6067 #ACE local_long_row_names <- long_row_names[good_rows] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6068 #ACE local_enriched_intensities <- enriched_intensities[local_long_row_names, ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6069 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6070 # Draw the heading and heatmap |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6071 nrow_m <- nrow(m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6072 if (nrow_m > 0) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6073 if (!g_did_enriched_header) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6074 cat("\n\\clearpage\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6075 cat(section_header(paste0("K", my_section_header))) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6076 g_did_enriched_header <- TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6077 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6078 is_na_m <- is.na(m) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6079 cellnote_m <- is_na_m |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6080 cellnote_m[!is_na_m] <- "" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6081 cellnote_m[is_na_m] <- "NA" |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6082 cut_args <- new_env() |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6083 cut_args$cutoff <- cutoff |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6084 cut_args$kinase <- kinase_name |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6085 cut_args$statistic <- ksea_cutoff_statistic |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6086 cut_args$threshold <- ksea_cutoff_threshold |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6087 number_of_peptides_found <- |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6088 ppep_heatmap( |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6089 m = m, |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6090 cellnote = cellnote_m, |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6091 cutoff = cut_args, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6092 hm_heading_function = cat_enriched_heading, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6093 hm_main_title |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6094 = "Unnormalized (zero-imputed) intensities of enriched kinase-substrates", |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6095 suppress_row_dendrogram = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6096 master_cex = 0.35, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6097 sepcolor = "black", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6098 colsep = sample_colsep |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6099 ) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6100 if (number_of_peptides_found > 1) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6101 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6102 tryCatch( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6103 { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6104 rownames(m) <- short_row_names |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6105 cov_heatmap(m, nrow_m > g_intensity_hm_rows) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6106 }, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6107 error = function(e) { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6108 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6109 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6110 "ERROR: %s\n\\newline\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6111 mget("e") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6112 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6113 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6114 cat( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6115 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6116 "message: %s\n\\newline\n", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6117 e$message |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6118 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6119 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6120 cat_margins() |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6121 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6122 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6123 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6124 substrates_df <- with( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6125 enriched_substrates, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6126 data.frame( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6127 substrate = sub(" ///*", "...", short_row_names), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6128 sequence = trunc_long_ppep(ppep), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6129 anova_p_value = signif(fdr_adjusted_anova_p, 2), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6130 min_group_obs_count = signif(min_group_obs_count, 0), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6131 quality = signif(quality, 3) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6132 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6133 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6134 excess_substrates <- nrow(substrates_df) > g_intensity_hm_rows |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6135 if (excess_substrates) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6136 substrates_df <- substrates_df[1:g_intensity_hm_rows, ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6137 names(substrates_df) <- headers_2nd_line <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6138 c("Substrate", "Sequence", "p-value", "per group)", "quality") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6139 headers_1st_line <- c("", "", "ANOVA", "min(values", "") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6140 if (1 < nrow(enriched_substrates)) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6141 cat("\n\\newpage\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6142 cat(subsubsection_header( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6143 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6144 "Details for %s%s-substrates", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6145 if (excess_substrates) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6146 sprintf( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6147 "%s \"highest quality\" ", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6148 g_intensity_hm_rows |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6149 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6150 else "", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6151 kinase_name |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6152 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6153 )) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6154 substrates_df <- substrates_df[order(-substrates_df$quality), ] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6155 data_frame_tabbing_latex( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6156 x = substrates_df, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6157 tabstops = c(0.8, 3.8, 0.6, 0.8), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6158 headings = c(headers_1st_line, headers_2nd_line) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6159 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6160 } else { |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6161 if (print_nb_messages) nbe(see_variable(nrow_m > 0), "\n") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6162 } |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6163 if (print_nb_messages) nb("end kinase ", kinase_name, "\n") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6164 } |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6165 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6166 # Write output tabular files |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6167 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6168 # get kinase, ppep, concat(kinase) tuples for enriched kinases |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6169 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6170 if (print_nb_messages) nb("kinase_ppep_label <- ...\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6171 if (print_nb_messages) nbe("kinase_ppep_label <- ...\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6172 kinase_ppep_label <- sqldf(" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6173 WITH |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6174 t(ppep, label) AS |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6175 ( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6176 SELECT DISTINCT |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6177 SUB_MOD_RSD AS ppep, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6178 group_concat(gene, '; ') AS label |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6179 FROM pseudo_ksdata |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6180 WHERE GENE IN (SELECT kinase FROM enriched_kinases) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6181 GROUP BY ppep |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6182 ), |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6183 k(kinase, ppep_join) AS |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6184 ( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6185 SELECT DISTINCT gene AS kinase, SUB_MOD_RSD AS ppep_join |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6186 FROM pseudo_ksdata |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6187 WHERE GENE IN (SELECT kinase FROM enriched_kinases) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6188 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6189 SELECT k.kinase, t.ppep, t.label |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6190 FROM t, k |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6191 WHERE t.ppep = k.ppep_join |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6192 ORDER BY k.kinase, t.ppep |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6193 ") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6194 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6195 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6196 # extract what we need from full_data |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6197 impish <- cbind(rownames(quant_data_imp), quant_data_imp) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6198 colnames(impish)[1] <- "Phosphopeptide" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6199 data_table_imputed_sql <- " |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6200 SELECT |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6201 f.*, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6202 k.label AS KSEA_enrichments, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6203 q.* |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6204 FROM |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6205 metadata_plus_p f |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6206 LEFT JOIN kinase_ppep_label k |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6207 ON f.Phosphopeptide = k.ppep, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6208 impish q |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6209 WHERE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6210 f.Phosphopeptide = q.Phosphopeptide |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6211 " |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6212 data_table_imputed <- sqldf(data_table_imputed_sql) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6213 # Zap the duplicated 'Phosphopeptide' column named 'ppep' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6214 data_table_imputed <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6215 data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6216 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6217 # Output imputed, un-normalized data |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6218 if (print_nb_messages) nb("Output imputed, un-normalized data tabular file\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6219 if (print_nb_messages) nbe("Output imputed, un-normalized data tabular file\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6220 write.table( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6221 data_table_imputed |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6222 , file = imputed_data_filename |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6223 , sep = "\t" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6224 , col.names = TRUE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6225 , row.names = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6226 , quote = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6227 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6228 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6229 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6230 #output quantile normalized data |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6231 impish <- cbind(rownames(quant_data_imp_qn_log), quant_data_imp_qn_log) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6232 colnames(impish)[1] <- "Phosphopeptide" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6233 data_table_imputed <- sqldf(data_table_imputed_sql) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6234 # Zap the duplicated 'Phosphopeptide' column named 'ppep' |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6235 data_table_imputed <- |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6236 data_table_imputed[, c(1:12, 14:ncol(data_table_imputed))] |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6237 if (print_nb_messages) nb("Output quantile normalized data tabular file\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6238 if (print_nb_messages) nbe("Output quantile normalized data tabular file\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6239 write.table( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6240 data_table_imputed, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6241 file = imp_qn_lt_data_filenm, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6242 sep = "\t", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6243 col.names = TRUE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6244 row.names = FALSE, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6245 quote = FALSE |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6246 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6247 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6248 ppep_kinase <- sqldf(" |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6249 SELECT DISTINCT k.ppep, k.kinase |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6250 FROM ( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6251 SELECT DISTINCT gene AS kinase, SUB_MOD_RSD AS ppep |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6252 FROM pseudo_ksdata |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6253 WHERE GENE IN (SELECT kinase FROM enriched_kinases) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6254 ) k |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6255 ORDER BY k.ppep, k.kinase |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6256 ") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6257 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6258 RSQLite::dbWriteTable( |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6259 conn = db, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6260 name = "ksea_enriched_ks", |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6261 value = ppep_kinase, |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6262 append = FALSE |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6263 ) |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6264 } |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6265 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6266 if (print_nb_messages) nb("RSQLite::dbWriteTable anova_signif\n") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6267 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6268 RSQLite::dbWriteTable( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6269 conn = db, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6270 name = "anova_signif", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6271 value = p_value_data, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6272 append = FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6273 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6274 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6275 ddl_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6276 DROP VIEW IF EXISTS stats_metadata_v; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6277 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6278 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6279 dml_no_rows_exec(db, " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6280 CREATE VIEW stats_metadata_v |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6281 AS |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6282 SELECT DISTINCT m.*, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6283 p.raw_anova_p, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6284 p.fdr_adjusted_anova_p, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6285 kek.kinase AS ksea_enrichments |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6286 FROM |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6287 mrgfltr_metadata_view m |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6288 LEFT JOIN anova_signif p |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6289 ON m.phospho_peptide = p.phosphopeptide |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6290 LEFT JOIN ksea_enriched_ks kek |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6291 ON m.phospho_peptide = kek.ppep |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6292 ; |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6293 " |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6294 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6295 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6296 if (print_nb_messages) nb("Output contents of `stats_metadata_v` table to tabular file\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6297 if (print_nb_messages) nbe("Output contents of `stats_metadata_v` table to tabular file\n") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6298 write.table( |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6299 dbReadTable(db, "stats_metadata_v"), |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6300 file = anova_ksea_mtdt_file, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6301 sep = "\t", |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6302 col.names = TRUE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6303 row.names = FALSE, |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6304 quote = FALSE |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6305 ) |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6306 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6307 cat("\n\\clearpage\n") |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6308 |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6309 ``` |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6310 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6311 # Data-processing summary flowchart |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6312 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6313  |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6314 |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6315 ```{r parmlist, echo = FALSE, fig.dim = c(9, 10), results = 'asis'} |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6316 cat("\\leavevmode\n\n\n") |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6317 |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6318 write_params(db) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6319 # We are done with output |
|
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6320 RSQLite::dbDisconnect(db) |
|
1
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6321 |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6322 cat("\\clearpage\n\\section{R package versions}\n") |
|
b76c75521d91
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 43e7a43b545c24b2dc33d039198551c032aa79be
galaxyp
parents:
0
diff
changeset
|
6323 utils::toLatex(utils::sessionInfo()) |
|
0
8dfd5d2b5903
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 3a7b3609d6e514c9e8f980ecb684960c6b2252fe
galaxyp
parents:
diff
changeset
|
6324 ``` |