Mercurial > repos > iuc > limma_voom
annotate limma_voom.R @ 20:0921444c832d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
author | iuc |
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date | Wed, 29 May 2019 10:31:41 -0400 |
parents | c9c6427edfe9 |
children | 58c35179ebf0 |
rev | line source |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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1 # This tool takes in a matrix of feature counts as well as gene annotations and |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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2 # outputs a table of top expressions as well as various plots for differential |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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3 # expression analysis |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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4 # |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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5 # ARGS: htmlPath", "R", 1, "character" -Path to html file linking to other outputs |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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6 # outPath", "o", 1, "character" -Path to folder to write all output to |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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7 # filesPath", "j", 2, "character" -JSON list object if multiple files input |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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8 # matrixPath", "m", 2, "character" -Path to count matrix |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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9 # factFile", "f", 2, "character" -Path to factor information file |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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10 # factInput", "i", 2, "character" -String containing factors if manually input |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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11 # annoPath", "a", 2, "character" -Path to input containing gene annotations |
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c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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12 # contrastFile", "C", 1, "character" -Path to contrasts information file |
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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13 # contrastInput", "D", 1, "character" -String containing contrasts of interest |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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14 # cpmReq", "c", 2, "double" -Float specifying cpm requirement |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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15 # cntReq", "z", 2, "integer" -Integer specifying minimum total count requirement |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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16 # sampleReq", "s", 2, "integer" -Integer specifying cpm requirement |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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17 # normCounts", "x", 0, "logical" -String specifying if normalised counts should be output |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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18 # rdaOpt", "r", 0, "logical" -String specifying if RData should be output |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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19 # lfcReq", "l", 1, "double" -Float specifying the log-fold-change requirement |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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20 # pValReq", "p", 1, "double" -Float specifying the p-value requirement |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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21 # pAdjOpt", "d", 1, "character" -String specifying the p-value adjustment method |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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22 # normOpt", "n", 1, "character" -String specifying type of normalisation used |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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23 # robOpt", "b", 0, "logical" -String specifying if robust options should be used |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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24 # trend", "t", 1, "double" -Float for prior.count if limma-trend is used instead of voom |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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25 # weightOpt", "w", 0, "logical" -String specifying if voomWithQualityWeights should be used |
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e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
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26 # topgenes", "G", 1, "integer" -Integer specifying no. of genes to highlight in volcano and heatmap |
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00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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27 # treatOpt", "T", 0, "logical" -String specifying if TREAT function should be used |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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28 # plots, "P", 1, "character" -String specifying additional plots to be created |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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29 # |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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30 # OUT: |
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e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
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31 # Density Plots (if filtering) |
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
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32 # Box Plots (if normalising) |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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33 # MDS Plot |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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34 # Voom/SA plot |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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35 # MD Plot |
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e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
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36 # Volcano Plot |
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
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37 # Heatmap |
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76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
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38 # Expression Table |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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39 # HTML file linking to the ouputs |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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40 # Optional: |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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41 # Normalised counts Table |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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42 # RData file |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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43 # |
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bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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44 # |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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45 # Author: Shian Su - registertonysu@gmail.com - Jan 2014 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
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46 # Modified by: Maria Doyle - Jun 2017, Jan 2018, May 2018 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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47 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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48 # Record starting time |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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49 timeStart <- as.character(Sys.time()) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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50 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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51 # Load all required libraries |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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52 library(methods, quietly=TRUE, warn.conflicts=FALSE) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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53 library(statmod, quietly=TRUE, warn.conflicts=FALSE) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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54 library(splines, quietly=TRUE, warn.conflicts=FALSE) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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55 library(edgeR, quietly=TRUE, warn.conflicts=FALSE) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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56 library(limma, quietly=TRUE, warn.conflicts=FALSE) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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57 library(scales, quietly=TRUE, warn.conflicts=FALSE) |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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58 library(getopt, quietly=TRUE, warn.conflicts=FALSE) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
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59 library(gplots, quietly=TRUE, warn.conflicts=FALSE) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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60 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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61 ################################################################################ |
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62 ### Function Declaration |
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63 ################################################################################ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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64 # Function to sanitise contrast equations so there are no whitespaces |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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65 # surrounding the arithmetic operators, leading or trailing whitespace |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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66 sanitiseEquation <- function(equation) { |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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67 equation <- gsub(" *[+] *", "+", equation) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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68 equation <- gsub(" *[-] *", "-", equation) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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69 equation <- gsub(" *[/] *", "/", equation) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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70 equation <- gsub(" *[*] *", "*", equation) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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71 equation <- gsub("^\\s+|\\s+$", "", equation) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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72 return(equation) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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73 } |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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74 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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75 # Function to sanitise group information |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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76 sanitiseGroups <- function(string) { |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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77 string <- gsub(" *[,] *", ",", string) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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78 string <- gsub("^\\s+|\\s+$", "", string) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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79 return(string) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
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80 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
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81 |
20
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
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82 # Function to make contrast contain valid R names |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
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83 sanitiseContrast <- function(string) { |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
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84 string <- strsplit(string, split="-") |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
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85 string <- lapply(string, make.names) |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
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86 string <- lapply(string, paste, collapse="-") |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
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87 return(string) |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
parents:
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changeset
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88 } |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
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89 |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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diff
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90 # Function to change periods to whitespace in a string |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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91 unmake.names <- function(string) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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92 string <- gsub(".", " ", string, fixed=TRUE) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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93 return(string) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
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94 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
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changeset
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95 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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96 # Generate output folder and paths |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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97 makeOut <- function(filename) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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98 return(paste0(opt$outPath, "/", filename)) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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99 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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100 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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101 # Generating design information |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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102 pasteListName <- function(string) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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103 return(paste0("factors$", string)) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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104 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
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105 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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106 # Create cata function: default path set, default seperator empty and appending |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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107 # true by default (Ripped straight from the cat function with altered argument |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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108 # defaults) |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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109 cata <- function(..., file = opt$htmlPath, sep = "", fill = FALSE, labels = NULL, |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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110 append = TRUE) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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111 if (is.character(file)) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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112 if (file == "") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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113 file <- stdout() |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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114 else if (substring(file, 1L, 1L) == "|") { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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115 file <- pipe(substring(file, 2L), "w") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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116 on.exit(close(file)) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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117 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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118 else { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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119 file <- file(file, ifelse(append, "a", "w")) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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120 on.exit(close(file)) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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121 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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122 .Internal(cat(list(...), file, sep, fill, labels, append)) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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parents:
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123 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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124 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
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125 # Function to write code for html head and title |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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126 HtmlHead <- function(title) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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127 cata("<head>\n") |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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128 cata("<title>", title, "</title>\n") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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129 cata("</head>\n") |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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130 } |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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131 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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132 # Function to write code for html links |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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133 HtmlLink <- function(address, label=address) { |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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134 cata("<a href=\"", address, "\" target=\"_blank\">", label, "</a><br />\n") |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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135 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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136 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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137 # Function to write code for html images |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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138 HtmlImage <- function(source, label=source, height=500, width=500) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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139 cata("<img src=\"", source, "\" alt=\"", label, "\" height=\"", height) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
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140 cata("\" width=\"", width, "\"/>\n") |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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141 } |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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142 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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143 # Function to write code for html list items |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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144 ListItem <- function(...) { |
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38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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145 cata("<li>", ..., "</li>\n") |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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146 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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147 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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148 TableItem <- function(...) { |
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38aab66ae5cb
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149 cata("<td>", ..., "</td>\n") |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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150 } |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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151 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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152 TableHeadItem <- function(...) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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153 cata("<th>", ..., "</th>\n") |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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154 } |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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155 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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156 ################################################################################ |
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157 ### Input Processing |
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158 ################################################################################ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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159 |
3
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160 # Collect arguments from command line |
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161 args <- commandArgs(trailingOnly=TRUE) |
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162 |
3
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163 # Get options, using the spec as defined by the enclosed list. |
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164 # Read the options from the default: commandArgs(TRUE). |
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165 spec <- matrix(c( |
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166 "htmlPath", "R", 1, "character", |
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167 "outPath", "o", 1, "character", |
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168 "filesPath", "j", 2, "character", |
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169 "matrixPath", "m", 2, "character", |
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170 "factFile", "f", 2, "character", |
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171 "factInput", "i", 2, "character", |
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172 "annoPath", "a", 2, "character", |
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173 "contrastFile", "C", 1, "character", |
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174 "contrastInput", "D", 1, "character", |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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175 "cpmReq", "c", 1, "double", |
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176 "totReq", "y", 0, "logical", |
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177 "cntReq", "z", 1, "integer", |
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178 "sampleReq", "s", 1, "integer", |
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179 "filtCounts", "F", 0, "logical", |
3
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180 "normCounts", "x", 0, "logical", |
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181 "rdaOpt", "r", 0, "logical", |
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182 "lfcReq", "l", 1, "double", |
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183 "pValReq", "p", 1, "double", |
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184 "pAdjOpt", "d", 1, "character", |
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185 "normOpt", "n", 1, "character", |
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186 "robOpt", "b", 0, "logical", |
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187 "trend", "t", 1, "double", |
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188 "weightOpt", "w", 0, "logical", |
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189 "topgenes", "G", 1, "integer", |
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190 "treatOpt", "T", 0, "logical", |
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191 "plots", "P", 1, "character", |
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192 "libinfoOpt", "L", 0, "logical"), |
3
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193 byrow=TRUE, ncol=4) |
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194 opt <- getopt(spec) |
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195 |
1
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196 |
3
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197 if (is.null(opt$matrixPath) & is.null(opt$filesPath)) { |
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198 cat("A counts matrix (or a set of counts files) is required.\n") |
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199 q(status=1) |
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200 } |
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201 |
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202 if (is.null(opt$cpmReq)) { |
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203 filtCPM <- FALSE |
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204 } else { |
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205 filtCPM <- TRUE |
1
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206 } |
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207 |
3
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208 if (is.null(opt$cntReq) || is.null(opt$sampleReq)) { |
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209 filtSmpCount <- FALSE |
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210 } else { |
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211 filtSmpCount <- TRUE |
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212 } |
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213 |
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214 if (is.null(opt$totReq)) { |
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215 filtTotCount <- FALSE |
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216 } else { |
3
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217 filtTotCount <- TRUE |
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218 } |
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219 |
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220 if (is.null(opt$rdaOpt)) { |
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221 wantRda <- FALSE |
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222 } else { |
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223 wantRda <- TRUE |
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224 } |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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225 |
38aab66ae5cb
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226 if (is.null(opt$annoPath)) { |
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227 haveAnno <- FALSE |
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228 } else { |
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229 haveAnno <- TRUE |
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230 } |
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231 |
12
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232 if (is.null(opt$filtCounts)) { |
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233 wantFilt <- FALSE |
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234 } else { |
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235 wantFilt <- TRUE |
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236 } |
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237 |
3
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238 if (is.null(opt$normCounts)) { |
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239 wantNorm <- FALSE |
0
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iuc
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240 } else { |
3
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241 wantNorm <- TRUE |
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242 } |
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243 |
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244 if (is.null(opt$robOpt)) { |
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245 wantRobust <- FALSE |
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246 } else { |
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247 wantRobust <- TRUE |
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248 } |
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249 |
3
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250 if (is.null(opt$weightOpt)) { |
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251 wantWeight <- FALSE |
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252 } else { |
3
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253 wantWeight <- TRUE |
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254 } |
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255 |
3
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256 if (is.null(opt$trend)) { |
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257 wantTrend <- FALSE |
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258 deMethod <- "limma-voom" |
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259 } else { |
3
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260 wantTrend <- TRUE |
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261 deMethod <- "limma-trend" |
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262 priorCount <- opt$trend |
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263 } |
0
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264 |
6
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265 if (is.null(opt$treatOpt)) { |
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266 wantTreat <- FALSE |
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267 } else { |
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268 wantTreat <- TRUE |
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269 } |
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270 |
11
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271 if (is.null(opt$libinfoOpt)) { |
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272 wantLibinfo <- FALSE |
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273 } else { |
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274 wantLibinfo <- TRUE |
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275 } |
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276 |
0
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277 |
3
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278 if (!is.null(opt$filesPath)) { |
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279 # Process the separate count files (adapted from DESeq2 wrapper) |
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280 library("rjson") |
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281 parser <- newJSONParser() |
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282 parser$addData(opt$filesPath) |
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283 factorList <- parser$getObject() |
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284 factors <- sapply(factorList, function(x) x[[1]]) |
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285 filenamesIn <- unname(unlist(factorList[[1]][[2]])) |
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286 sampleTable <- data.frame(sample=basename(filenamesIn), |
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287 filename=filenamesIn, |
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288 row.names=filenamesIn, |
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289 stringsAsFactors=FALSE) |
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290 for (factor in factorList) { |
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291 factorName <- factor[[1]] |
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292 sampleTable[[factorName]] <- character(nrow(sampleTable)) |
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293 lvls <- sapply(factor[[2]], function(x) names(x)) |
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294 for (i in seq_along(factor[[2]])) { |
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295 files <- factor[[2]][[i]][[1]] |
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296 sampleTable[files,factorName] <- lvls[i] |
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297 } |
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298 sampleTable[[factorName]] <- factor(sampleTable[[factorName]], levels=lvls) |
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299 } |
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300 rownames(sampleTable) <- sampleTable$sample |
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301 rem <- c("sample","filename") |
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302 factors <- sampleTable[, !(names(sampleTable) %in% rem), drop=FALSE] |
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303 |
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304 #read in count files and create single table |
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305 countfiles <- lapply(sampleTable$filename, function(x){read.delim(x, row.names=1)}) |
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306 counts <- do.call("cbind", countfiles) |
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307 |
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308 } else { |
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309 # Process the single count matrix |
17
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310 counts <- read.table(opt$matrixPath, header=TRUE, sep="\t", strip.white=TRUE, stringsAsFactors=FALSE, check.names=FALSE) |
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311 row.names(counts) <- counts[, 1] |
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312 counts <- counts[ , -1] |
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313 countsRows <- nrow(counts) |
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314 |
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315 # Process factors |
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316 if (is.null(opt$factInput)) { |
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317 factorData <- read.table(opt$factFile, header=TRUE, sep="\t", strip.white=TRUE) |
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318 if(!setequal(factorData[, 1], colnames(counts))) |
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319 stop("Sample IDs in counts and factors files don't match") |
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320 # order samples as in counts matrix |
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321 factorData <- factorData[match(colnames(counts), factorData[, 1]), ] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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322 factors <- factorData[, -1, drop=FALSE] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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323 } else { |
17
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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324 factors <- unlist(strsplit(opt$factInput, "|", fixed=TRUE)) |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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325 factorData <- list() |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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326 for (fact in factors) { |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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327 newFact <- unlist(strsplit(fact, split="::")) |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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328 factorData <- rbind(factorData, newFact) |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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329 } # Factors have the form: FACT_NAME::LEVEL,LEVEL,LEVEL,LEVEL,... The first factor is the Primary Factor. |
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330 |
17
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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331 # Set the row names to be the name of the factor and delete first row |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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332 row.names(factorData) <- factorData[, 1] |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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333 factorData <- factorData[, -1] |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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334 factorData <- sapply(factorData, sanitiseGroups) |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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335 factorData <- sapply(factorData, strsplit, split=",") |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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336 # Transform factor data into data frame of R factor objects |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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337 factors <- data.frame(factorData) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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338 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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339 } |
17
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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340 # check there are the same number of samples in counts and factors |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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341 if(nrow(factors) != ncol(counts)) { |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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342 stop("There are a different number of samples in the counts files and factors") |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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343 } |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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344 # make groups valid R names, required for makeContrasts |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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345 factors <- sapply(factors, make.names) |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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346 factors <- data.frame(factors) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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347 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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348 # if annotation file provided |
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349 if (haveAnno) { |
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350 geneanno <- read.table(opt$annoPath, header=TRUE, sep="\t", quote= "", strip.white=TRUE, stringsAsFactors=FALSE) |
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351 } |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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352 |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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353 #Create output directory |
3
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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354 dir.create(opt$outPath, showWarnings=FALSE) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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355 |
19
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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356 # Process contrasts |
c9c6427edfe9
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357 if (is.null(opt$contrastInput)) { |
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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358 contrastData <- read.table(opt$contrastFile, header=TRUE, sep="\t", quote= "", strip.white=TRUE, stringsAsFactors=FALSE) |
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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359 contrastData <- contrastData[, 1, drop=TRUE] |
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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360 } else { |
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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361 # Split up contrasts seperated by comma into a vector then sanitise |
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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362 contrastData <- unlist(strsplit(opt$contrastInput, split=",")) |
c9c6427edfe9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
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363 } |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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364 contrastData <- sanitiseEquation(contrastData) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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365 contrastData <- gsub(" ", ".", contrastData, fixed=TRUE) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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366 |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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367 # in case input groups start with numbers make the names valid R names, required for makeContrasts |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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368 cons <- NULL |
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369 cons_d <- NULL |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
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370 for (i in contrastData) { |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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371 |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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372 # if the contrast is a difference of differences e.g. (A-B)-(X-Y) |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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373 if (grepl("\\)-\\(", i)) { |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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374 i <- unlist(strsplit(i, split="\\)-\\(")) |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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375 i <- gsub("\\(|\\)","", i) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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376 for (j in i) { |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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377 j <- sanitiseContrast(j) |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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378 j <- paste0("(", j, ")") |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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379 cons_d <- append(cons_d, unlist(j)) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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380 } |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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381 cons_d <- paste(cons_d, collapse = '-') |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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382 cons <- append(cons, unlist(cons_d)) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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383 } else { |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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384 i <- sanitiseContrast(i) |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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385 cons <- append(cons, unlist(i)) |
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
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386 } |
17
86b3df7db58b
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iuc
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387 } |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
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388 |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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389 plots <- character() |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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390 if (!is.null(opt$plots)) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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391 plots <- unlist(strsplit(opt$plots, split=",")) |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
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392 } |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
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393 |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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394 denOutPng <- makeOut("densityplots.png") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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395 denOutPdf <- makeOut("densityplots.pdf") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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396 cpmOutPdf <- makeOut("cpmplots.pdf") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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397 boxOutPng <- makeOut("boxplots.png") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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398 boxOutPdf <- makeOut("boxplots.pdf") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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399 mdsscreeOutPng <- makeOut("mdsscree.png") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
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400 mdsscreeOutPdf <- makeOut("mdsscree.pdf") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
401 mdsxOutPdf <- makeOut("mdsplot_extra.pdf") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
402 mdsxOutPng <- makeOut("mdsplot_extra.png") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
403 mdsamOutPdf <- makeOut("mdplots_samples.pdf") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
404 mdOutPdf <- character() # Initialise character vector |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
405 volOutPdf <- character() |
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
406 heatOutPdf <- character() |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
407 stripOutPdf <- character() |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
408 mdvolOutPng <- character() |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
409 topOut <- character() |
9
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
410 glimmaOut <- character() |
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
411 for (i in 1:length(cons)) { |
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
412 con <- cons[i] |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
413 con <- gsub("\\(|\\)", "", con) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
414 mdOutPdf[i] <- makeOut(paste0("mdplot_", con, ".pdf")) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
415 volOutPdf[i] <- makeOut(paste0("volplot_", con, ".pdf")) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
416 heatOutPdf[i] <- makeOut(paste0("heatmap_", con, ".pdf")) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
417 stripOutPdf[i] <- makeOut(paste0("stripcharts_", con, ".pdf")) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
418 mdvolOutPng[i] <- makeOut(paste0("mdvolplot_", con, ".png")) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
419 topOut[i] <- makeOut(paste0(deMethod, "_", con, ".tsv")) |
9
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
420 glimmaOut[i] <- makeOut(paste0("glimma_", con, "/MD-Plot.html")) |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
421 } |
13
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
422 filtOut <- makeOut(paste0(deMethod, "_", "filtcounts")) |
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
423 normOut <- makeOut(paste0(deMethod, "_", "normcounts")) |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
424 rdaOut <- makeOut(paste0(deMethod, "_analysis.RData")) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
425 sessionOut <- makeOut("session_info.txt") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
426 |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
427 # Initialise data for html links and images, data frame with columns Label and |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
428 # Link |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
429 linkData <- data.frame(Label=character(), Link=character(), |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
430 stringsAsFactors=FALSE) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
431 imageData <- data.frame(Label=character(), Link=character(), |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
432 stringsAsFactors=FALSE) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
433 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
434 # Initialise vectors for storage of up/down/neutral regulated counts |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
435 upCount <- numeric() |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
436 downCount <- numeric() |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
437 flatCount <- numeric() |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
438 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
439 ################################################################################ |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
440 ### Data Processing |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
441 ################################################################################ |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
442 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
443 # Extract counts and annotation data |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
444 print("Extracting counts") |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
445 data <- list() |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
446 data$counts <- counts |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
447 if (haveAnno) { |
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
448 # order annotation by genes in counts (assumes gene ids are in 1st column of geneanno) |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
449 annoord <- geneanno[match(row.names(counts), geneanno[,1]), ] |
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
450 data$genes <- annoord |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
451 } else { |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
452 data$genes <- data.frame(GeneID=row.names(counts)) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
453 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
454 |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
455 # Creating naming data |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
456 samplenames <- colnames(data$counts) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
457 sampleanno <- data.frame("sampleID"=samplenames, factors) |
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
458 row.names(factors) <- samplenames # for "Summary of experimental data" table |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
459 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
460 # Creating colours for the groups |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
461 cols <- as.numeric(factors[, 1]) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
462 col.group <- palette()[cols] |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
463 |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
464 # If filter crieteria set, filter out genes that do not have a required cpm/counts in a required number of |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
465 # samples. Default is no filtering |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
466 preFilterCount <- nrow(data$counts) |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
467 nsamples <- ncol(data$counts) |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
468 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
469 if (filtCPM || filtSmpCount || filtTotCount) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
470 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
471 if (filtTotCount) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
472 keep <- rowSums(data$counts) >= opt$cntReq |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
473 } else if (filtSmpCount) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
474 keep <- rowSums(data$counts >= opt$cntReq) >= opt$sampleReq |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
475 } else if (filtCPM) { |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
476 myCPM <- cpm(data$counts) |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
477 thresh <- myCPM >= opt$cpmReq |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
478 keep <- rowSums(thresh) >= opt$sampleReq |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
479 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
480 if ("c" %in% plots) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
481 # Plot CPM vs raw counts (to check threshold) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
482 pdf(cpmOutPdf, width=6.5, height=10) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
483 par(mfrow=c(3, 2)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
484 for (i in 1:nsamples) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
485 plot(data$counts[, i], myCPM[, i], xlim=c(0,50), ylim=c(0,3), main=samplenames[i], xlab="Raw counts", ylab="CPM") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
486 abline(v=10, col="red", lty=2, lwd=2) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
487 abline(h=opt$cpmReq, col=4) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
488 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
489 linkName <- "CpmPlots.pdf" |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
490 linkAddr <- "cpmplots.pdf" |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
491 linkData <- rbind(linkData, data.frame(Label=linkName, Link=linkAddr, stringsAsFactors=FALSE)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
492 invisible(dev.off()) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
493 } |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
494 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
495 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
496 data$counts <- data$counts[keep, ] |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
497 data$genes <- data$genes[keep, , drop=FALSE] |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
498 |
12
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
499 if (wantFilt) { |
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
500 print("Outputting filtered counts") |
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
501 filt_counts <- data.frame(data$genes, data$counts, check.names=FALSE) |
12
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
502 write.table(filt_counts, file=filtOut, row.names=FALSE, sep="\t", quote=FALSE) |
13
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
503 linkData <- rbind(linkData, data.frame(Label=paste0(deMethod, "_", "filtcounts.tsv"), Link=paste0(deMethod, "_", "filtcounts"), stringsAsFactors=FALSE)) |
12
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
504 } |
81796eb60bd0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 33651907e4d5d6672537b80142c022d2b4951e8c
iuc
parents:
11
diff
changeset
|
505 |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
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diff
changeset
|
506 # Plot Density |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
507 if ("d" %in% plots) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
508 # PNG |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
509 png(denOutPng, width=1000, height=500) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
510 par(mfrow=c(1,2), cex.axis=0.8) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
511 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
512 # before filtering |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
513 lcpm1 <- cpm(counts, log=TRUE) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
514 plot(density(lcpm1[, 1]), col=col.group[1], lwd=2, las=2, main="", xlab="") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
515 title(main="Density Plot: Raw counts", xlab="Log-cpm") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
516 for (i in 2:nsamples){ |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
517 den <- density(lcpm1[, i]) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
518 lines(den$x, den$y, col=col.group[i], lwd=2) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
519 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
520 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
521 # after filtering |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
522 lcpm2 <- cpm(data$counts, log=TRUE) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
523 plot(density(lcpm2[,1]), col=col.group[1], lwd=2, las=2, main="", xlab="") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
524 title(main="Density Plot: Filtered counts", xlab="Log-cpm") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
525 for (i in 2:nsamples){ |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
526 den <- density(lcpm2[, i]) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
527 lines(den$x, den$y, col=col.group[i], lwd=2) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
528 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
529 legend("topright", samplenames, text.col=col.group, bty="n") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
530 imgName <- "Densityplots.png" |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
531 imgAddr <- "densityplots.png" |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
532 imageData <- rbind(imageData, data.frame(Label=imgName, Link=imgAddr, stringsAsFactors=FALSE)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
533 invisible(dev.off()) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
534 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
535 # PDF |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
536 pdf(denOutPdf, width=14) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
537 par(mfrow=c(1,2), cex.axis=0.8) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
538 plot(density(lcpm1[, 1]), col=col.group[1], lwd=2, las=2, main="", xlab="") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
539 title(main="Density Plot: Raw counts", xlab="Log-cpm") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
540 for (i in 2:nsamples){ |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
541 den <- density(lcpm1[, i]) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
542 lines(den$x, den$y, col=col.group[i], lwd=2) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
543 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
544 plot(density(lcpm2[, 1]), col=col.group[1], lwd=2, las=2, main="", xlab="") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
545 title(main="Density Plot: Filtered counts", xlab="Log-cpm") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
546 for (i in 2:nsamples){ |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
547 den <- density(lcpm2[, i]) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
548 lines(den$x, den$y, col=col.group[i], lwd=2) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
549 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
550 legend("topright", samplenames, text.col=col.group, bty="n") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
551 linkName <- "DensityPlots.pdf" |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
552 linkAddr <- "densityplots.pdf" |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
553 linkData <- rbind(linkData, data.frame(Label=linkName, Link=linkAddr, stringsAsFactors=FALSE)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
554 invisible(dev.off()) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
555 } |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
556 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
557 |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
558 postFilterCount <- nrow(data$counts) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
559 filteredCount <- preFilterCount-postFilterCount |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
560 |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
561 # Generating the DGEList object "y" |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
562 print("Generating DGEList object") |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
563 data$samples <- sampleanno |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
564 data$samples$lib.size <- colSums(data$counts) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
565 data$samples$norm.factors <- 1 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
566 row.names(data$samples) <- colnames(data$counts) |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
567 y <- new("DGEList", data) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
568 |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
569 print("Generating Design") |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
570 factorList <- sapply(names(factors), pasteListName) |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
571 formula <- "~0" |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
572 for (i in 1:length(factorList)) { |
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
573 formula <- paste(formula,factorList[i], sep="+") |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
574 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
575 formula <- formula(formula) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
576 design <- model.matrix(formula) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
577 for (i in 1:length(factorList)) { |
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
578 colnames(design) <- gsub(factorList[i], "", colnames(design), fixed=TRUE) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
579 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
580 |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
581 # Calculating normalising factors |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
582 print("Calculating Normalisation Factors") |
11
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
583 logcounts <- y #store for plots |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
584 y <- calcNormFactors(y, method=opt$normOpt) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
585 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
586 # Generate contrasts information |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
587 print("Generating Contrasts") |
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
588 contrasts <- makeContrasts(contrasts=cons, levels=design) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
589 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
590 ################################################################################ |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
591 ### Data Output |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
592 ################################################################################ |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
593 |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
594 # Plot Box plots (before and after normalisation) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
595 if (opt$normOpt != "none" & "b" %in% plots) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
596 png(boxOutPng, width=1000, height=500) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
597 par(mfrow=c(1,2), mar=c(6,4,2,2)+0.1) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
598 labels <- colnames(counts) |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
599 |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
600 lcpm1 <- cpm(y$counts, log=TRUE) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
601 boxplot(lcpm1, las=2, col=col.group, xaxt="n", xlab="") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
602 axis(1, at=seq_along(labels), labels = FALSE) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
603 abline(h=median(lcpm1), col=4) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
604 text(x=seq_along(labels), y=par("usr")[3]-1, srt=45, adj=1, labels=labels, xpd=TRUE) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
605 title(main="Box Plot: Unnormalised counts", ylab="Log-cpm") |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
606 |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
607 lcpm2 <- cpm(y, log=TRUE) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
608 boxplot(lcpm2, las=2, col=col.group, xaxt="n", xlab="") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
609 axis(1, at=seq_along(labels), labels = FALSE) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
610 text(x=seq_along(labels), y=par("usr")[3]-1, srt=45, adj=1, labels=labels, xpd=TRUE) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
611 abline(h=median(lcpm2), col=4) |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
612 title(main="Box Plot: Normalised counts", ylab="Log-cpm") |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
613 |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
614 imgName <- "Boxplots.png" |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
615 imgAddr <- "boxplots.png" |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
616 imageData <- rbind(imageData, data.frame(Label=imgName, Link=imgAddr, stringsAsFactors=FALSE)) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
617 invisible(dev.off()) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
618 |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
619 pdf(boxOutPdf, width=14) |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
620 par(mfrow=c(1,2), mar=c(6,4,2,2)+0.1) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
621 boxplot(lcpm1, las=2, col=col.group, xaxt="n", xlab="") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
622 axis(1, at=seq_along(labels), labels = FALSE) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
623 abline(h=median(lcpm1), col=4) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
624 text(x=seq_along(labels), y=par("usr")[3]-1, srt=45, adj=1, labels=labels, xpd=TRUE) |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
625 title(main="Box Plot: Unnormalised counts", ylab="Log-cpm") |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
626 boxplot(lcpm2, las=2, col=col.group, xaxt="n", xlab="") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
627 axis(1, at=seq_along(labels), labels = FALSE) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
628 text(x=seq_along(labels), y=par("usr")[3]-1, srt=45, adj=1, labels=labels, xpd=TRUE) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
629 abline(h=median(lcpm2), col=4) |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
630 title(main="Box Plot: Normalised counts", ylab="Log-cpm") |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
631 linkName <- "BoxPlots.pdf" |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
632 linkAddr <- "boxplots.pdf" |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
633 linkData <- rbind(linkData, data.frame(Label=linkName, Link=linkAddr, stringsAsFactors=FALSE)) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
634 invisible(dev.off()) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
635 } |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
636 |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
637 # Plot MDS |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
638 print("Generating MDS plot") |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
639 labels <- names(counts) |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
640 |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
641 # Scree plot (Variance Explained) code copied from Glimma |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
642 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
643 # get column of matrix |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
644 getCols <- function(x, inds) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
645 x[, inds, drop=FALSE] |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
646 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
647 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
648 x <- cpm(y, log=TRUE) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
649 ndim <- nsamples - 1 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
650 nprobes <- nrow(x) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
651 top <- 500 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
652 top <- min(top, nprobes) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
653 cn <- colnames(x) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
654 bad <- rowSums(is.finite(x)) < nsamples |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
655 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
656 if (any(bad)) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
657 warning("Rows containing infinite values have been removed") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
658 x <- x[!bad, , drop=FALSE] |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
659 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
660 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
661 dd <- matrix(0, nrow=nsamples, ncol=nsamples, dimnames=list(cn, cn)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
662 topindex <- nprobes - top + 1L |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
663 for (i in 2L:(nsamples)) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
664 for (j in 1L:(i - 1L)) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
665 dists <- (getCols(x, i) - getCols(x, j))^2 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
666 dists <- sort.int(dists, partial = topindex ) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
667 topdist <- dists[topindex:nprobes] |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
668 dd[i, j] <- sqrt(mean(topdist)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
669 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
670 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
671 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
672 a1 <- suppressWarnings(cmdscale(as.dist(dd), k=min(ndim, 8), eig=TRUE)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
673 eigen <- data.frame(name = 1:min(ndim, 8), eigen = round(a1$eig[1:min(ndim, 8)]/sum(a1$eig), 2)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
674 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
675 png(mdsscreeOutPng, width=1000, height=500) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
676 par(mfrow=c(1, 2)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
677 plotMDS(y, labels=samplenames, col=as.numeric(factors[, 1]), main="MDS Plot: Dims 1 and 2") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
678 barplot(eigen$eigen, names.arg=eigen$name, main = "Scree Plot: Variance Explained", xlab = "Dimension", ylab = "Proportion", las=1) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
679 imgName <- paste0("MDSPlot_", names(factors)[1], ".png") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
680 imgAddr <- "mdsscree.png" |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
681 imageData <- rbind(imageData, data.frame(Label=imgName, Link=imgAddr, stringsAsFactors=FALSE)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
682 invisible(dev.off()) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
683 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
684 pdf(mdsscreeOutPdf, width=14) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
685 par(mfrow=c(1, 2)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
686 plotMDS(y, labels=samplenames, col=as.numeric(factors[, 1]), main="MDS Plot: Dims 1 and 2") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
687 barplot(eigen$eigen, names.arg=eigen$name, main = "Scree Plot: Variance Explained", xlab = "Dimension", ylab = "Proportion", las=1) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
688 linkName <- paste0("MDSPlot_", names(factors)[1], ".pdf") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
689 linkAddr <- "mdsscree.pdf" |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
690 linkData <- rbind(linkData, data.frame(Label=linkName, Link=linkAddr, stringsAsFactors=FALSE)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
691 invisible(dev.off()) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
692 |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
693 # generate Glimma interactive MDS Plot |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
694 if ("i" %in% plots) { |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
695 Glimma::glMDSPlot(y, labels=samplenames, groups=factors[, 1], |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
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696 folder="glimma_MDS", launch=FALSE) |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
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697 linkName <- "Glimma_MDSPlot.html" |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
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698 linkAddr <- "glimma_MDS/MDS-Plot.html" |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
699 linkData <- rbind(linkData, c(linkName, linkAddr)) |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
700 } |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
701 |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
702 if ("x" %in% plots) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
703 png(mdsxOutPng, width=1000, height=500) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
704 par(mfrow=c(1, 2)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
705 for (i in 2:3) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
706 dim1 <- i |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
707 dim2 <- i + 1 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
708 plotMDS(y, dim=c(dim1, dim2), labels=samplenames, col=as.numeric(factors[, 1]), main=paste("MDS Plot: Dims", dim1, "and", dim2)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
709 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
710 imgName <- paste0("MDSPlot_extra.png") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
711 imgAddr <- paste0("mdsplot_extra.png") |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
712 imageData <- rbind(imageData, data.frame(Label=imgName, Link=imgAddr, stringsAsFactors=FALSE)) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
713 invisible(dev.off()) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
714 |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
715 pdf(mdsxOutPdf, width=14) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
716 par(mfrow=c(1, 2)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
717 for (i in 2:3) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
718 dim1 <- i |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
719 dim2 <- i + 1 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
720 plotMDS(y, dim=c(dim1, dim2), labels=samplenames, col=as.numeric(factors[, 1]), main=paste("MDS Plot: Dims", dim1, "and", dim2)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
721 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
722 linkName <- "MDSPlot_extra.pdf" |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
723 linkAddr <- "mdsplot_extra.pdf" |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
724 linkData <- rbind(linkData, data.frame(Label=linkName, Link=linkAddr, stringsAsFactors=FALSE)) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
725 invisible(dev.off()) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
726 } |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
727 |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
728 if ("m" %in% plots) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
729 # Plot MD plots for individual samples |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
730 print("Generating MD plots for samples") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
731 pdf(mdsamOutPdf, width=6.5, height=10) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
732 par(mfrow=c(3, 2)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
733 for (i in 1:nsamples) { |
11
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
734 if (opt$normOpt != "none") { |
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
735 plotMD(logcounts, column=i, main=paste(colnames(logcounts)[i], "(before)")) |
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
736 abline(h=0, col="red", lty=2, lwd=2) |
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
737 } |
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
738 plotMD(y, column=i) |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
739 abline(h=0, col="red", lty=2, lwd=2) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
740 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
741 linkName <- "MDPlots_Samples.pdf" |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
742 linkAddr <- "mdplots_samples.pdf" |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
743 linkData <- rbind(linkData, c(linkName, linkAddr)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
744 invisible(dev.off()) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
745 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
746 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
747 |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
748 if (wantTrend) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
749 # limma-trend approach |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
750 logCPM <- cpm(y, log=TRUE, prior.count=opt$trend) |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
751 fit <- lmFit(logCPM, design) |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
752 fit$genes <- y$genes |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
753 fit <- contrasts.fit(fit, contrasts) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
754 if (wantRobust) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
755 fit <- eBayes(fit, trend=TRUE, robust=TRUE) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
756 } else { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
757 fit <- eBayes(fit, trend=TRUE, robust=FALSE) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
758 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
759 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
760 plotData <- logCPM |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
761 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
762 # Save normalised counts (log2cpm) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
763 if (wantNorm) { |
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
764 write.table(logCPM, file=normOut, row.names=TRUE, sep="\t", quote=FALSE) |
13
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
765 linkData <- rbind(linkData, c((paste0(deMethod, "_", "normcounts.tsv")), (paste0(deMethod, "_", "normcounts")))) |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
766 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
767 } else { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
768 # limma-voom approach |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
769 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
770 if (wantWeight) { |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
771 voomWtsOutPdf <- makeOut("voomwtsplot.pdf") |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
772 voomWtsOutPng <- makeOut("voomwtsplot.png") |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
773 # Creating voom data object and plot |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
774 png(voomWtsOutPng, width=1000, height=500) |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
775 vData <- voomWithQualityWeights(y, design=design, plot=TRUE) |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
776 imgName <- "VoomWithQualityWeightsPlot.png" |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
777 imgAddr <- "voomwtsplot.png" |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
778 imageData <- rbind(imageData, c(imgName, imgAddr)) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
779 invisible(dev.off()) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
780 |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
781 pdf(voomWtsOutPdf, width=14) |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
782 vData <- voomWithQualityWeights(y, design=design, plot=TRUE) |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
783 linkName <- "VoomWithQualityWeightsPlot.pdf" |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
784 linkAddr <- "voomwtsplot.pdf" |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
785 linkData <- rbind(linkData, c(linkName, linkAddr)) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
786 invisible(dev.off()) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
787 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
788 # Generating fit data and top table with weights |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
789 wts <- vData$weights |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
790 voomFit <- lmFit(vData, design, weights=wts) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
791 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
792 } else { |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
793 voomOutPdf <- makeOut("voomplot.pdf") |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
794 voomOutPng <- makeOut("voomplot.png") |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
795 # Creating voom data object and plot |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
796 png(voomOutPng, width=500, height=500) |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
797 vData <- voom(y, design=design, plot=TRUE) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
798 imgName <- "VoomPlot" |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
799 imgAddr <- "voomplot.png" |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
800 imageData <- rbind(imageData, c(imgName, imgAddr)) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
801 invisible(dev.off()) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
802 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
803 pdf(voomOutPdf) |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
804 vData <- voom(y, design=design, plot=TRUE) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
805 linkName <- "VoomPlot.pdf" |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
806 linkAddr <- "voomplot.pdf" |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
807 linkData <- rbind(linkData, c(linkName, linkAddr)) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
808 invisible(dev.off()) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
809 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
810 # Generate voom fit |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
811 voomFit <- lmFit(vData, design) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
812 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
813 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
814 # Save normalised counts (log2cpm) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
815 if (wantNorm) { |
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
816 norm_counts <- data.frame(vData$genes, vData$E, check.names=FALSE) |
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
817 write.table(norm_counts, file=normOut, row.names=FALSE, sep="\t", quote=FALSE) |
13
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
818 linkData <- rbind(linkData, c((paste0(deMethod, "_", "normcounts.tsv")), (paste0(deMethod, "_", "normcounts")))) |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
819 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
820 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
821 # Fit linear model and estimate dispersion with eBayes |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
822 voomFit <- contrasts.fit(voomFit, contrasts) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
823 if (wantRobust) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
824 fit <- eBayes(voomFit, robust=TRUE) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
825 } else { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
826 fit <- eBayes(voomFit, robust=FALSE) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
827 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
828 plotData <- vData |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
829 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
830 |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
831 # plot final model mean-variance trend with plotSA |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
832 saOutPng <- makeOut("saplot.png") |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
833 saOutPdf <- makeOut("saplot.pdf") |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
834 |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
835 png(saOutPng, width=500, height=500) |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
836 plotSA(fit, main="Final model: Mean-variance trend (SA Plot)") |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
837 imgName <- "SAPlot.png" |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
838 imgAddr <- "saplot.png" |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
839 imageData <- rbind(imageData, c(imgName, imgAddr)) |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
840 invisible(dev.off()) |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
841 |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
842 pdf(saOutPdf) |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
843 plotSA(fit, main="Final model: Mean-variance trend (SA Plot)") |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
844 linkName <- "SAPlot.pdf" |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
845 linkAddr <- "saplot.pdf" |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
846 linkData <- rbind(linkData, c(linkName, linkAddr)) |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
847 invisible(dev.off()) |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
848 |
11
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
849 # Save library size info |
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
850 if (wantLibinfo) { |
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
851 efflibsize <- round(y$samples$lib.size * y$samples$norm.factors) |
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
852 libsizeinfo <- cbind(y$samples, EffectiveLibrarySize=efflibsize) |
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
853 libsizeinfo$lib.size <- round(libsizeinfo$lib.size) |
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
854 names(libsizeinfo)[names(libsizeinfo)=="sampleID"] <- "SampleID" |
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
855 names(libsizeinfo)[names(libsizeinfo)=="lib.size"] <- "LibrarySize" |
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
856 names(libsizeinfo)[names(libsizeinfo)=="norm.factors"] <- "NormalisationFactor" |
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
857 write.table(libsizeinfo, file="libsizeinfo", row.names=FALSE, sep="\t", quote=FALSE) |
7e8af58c8052
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4bcbd83574ecf7194f3370aa883a9573563afdbc
iuc
parents:
10
diff
changeset
|
858 } |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
859 |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
860 print("Generating DE results") |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
861 |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
862 if (wantTreat) { |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
863 print("Applying TREAT method") |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
864 if (wantRobust) { |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
865 fit <- treat(fit, lfc=opt$lfcReq, robust=TRUE) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
866 } else { |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
867 fit <- treat(fit, lfc=opt$lfcReq, robust=FALSE) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
868 } |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
869 } |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
870 |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
871 status = decideTests(fit, adjust.method=opt$pAdjOpt, p.value=opt$pValReq, |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
872 lfc=opt$lfcReq) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
873 sumStatus <- summary(status) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
874 |
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
875 for (i in 1:length(cons)) { |
20
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
parents:
19
diff
changeset
|
876 con_name <- cons[i] |
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
877 con <- cons[i] |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
878 con <- gsub("\\(|\\)", "", con) |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
879 # Collect counts for differential expression |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
880 upCount[i] <- sumStatus["Up", i] |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
881 downCount[i] <- sumStatus["Down", i] |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
882 flatCount[i] <- sumStatus["NotSig", i] |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
883 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
884 # Write top expressions table |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
885 if (wantTreat) { |
16
5d903d528193
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 349e35a66009449851b21e2810bc5aaa58225fca
iuc
parents:
14
diff
changeset
|
886 top <- topTreat(fit, coef=i, adjust.method=opt$pAdjOpt, number=Inf, sort.by="P") |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
887 } else{ |
16
5d903d528193
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 349e35a66009449851b21e2810bc5aaa58225fca
iuc
parents:
14
diff
changeset
|
888 top <- topTable(fit, coef=i, adjust.method=opt$pAdjOpt, number=Inf, sort.by="P") |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
889 } |
4
a61a6e62e91f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 6a458881c0819b75e55e64b3f494679d43bb9ee8
iuc
parents:
3
diff
changeset
|
890 write.table(top, file=topOut[i], row.names=FALSE, sep="\t", quote=FALSE) |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
891 linkName <- paste0(deMethod, "_", con, ".tsv") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
892 linkAddr <- paste0(deMethod, "_", con, ".tsv") |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
893 linkData <- rbind(linkData, c(linkName, linkAddr)) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
894 |
5
d8a55b5f0de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents:
4
diff
changeset
|
895 # Plot MD (log ratios vs mean average) using limma package on weighted |
d8a55b5f0de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents:
4
diff
changeset
|
896 pdf(mdOutPdf[i]) |
d8a55b5f0de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents:
4
diff
changeset
|
897 limma::plotMD(fit, status=status[, i], coef=i, |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
898 main=paste("MD Plot:", unmake.names(con)), |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
899 hl.col=alpha(c("firebrick", "blue"), 0.4), values=c(1, -1), |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
900 xlab="Average Expression", ylab="logFC") |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
901 abline(h=0, col="grey", lty=2) |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
902 linkName <- paste0("MDPlot_", con, ".pdf") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
903 linkAddr <- paste0("mdplot_", con, ".pdf") |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
904 linkData <- rbind(linkData, c(linkName, linkAddr)) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
905 invisible(dev.off()) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
906 |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
907 # Generate Glimma interactive Volcano, MD plot and tables, requires annotation file (assumes gene labels/symbols in 2nd column) |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
908 if ("i" %in% plots & haveAnno) { |
10
e26047c4562d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3
iuc
parents:
9
diff
changeset
|
909 # make gene labels unique to handle NAs |
e26047c4562d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3
iuc
parents:
9
diff
changeset
|
910 geneanno <- y$genes |
e26047c4562d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c31767d02eeeda7346bb33ba71ebde9189d7e4a3
iuc
parents:
9
diff
changeset
|
911 geneanno[, 2] <- make.unique(geneanno[, 2]) |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
912 |
18
97e06a4c7c75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666
iuc
parents:
17
diff
changeset
|
913 # use the logCPMS for the counts |
97e06a4c7c75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666
iuc
parents:
17
diff
changeset
|
914 if (wantTrend) { |
97e06a4c7c75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666
iuc
parents:
17
diff
changeset
|
915 cnts <- logCPM |
97e06a4c7c75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666
iuc
parents:
17
diff
changeset
|
916 } else{ |
97e06a4c7c75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666
iuc
parents:
17
diff
changeset
|
917 cnts <- vData$E |
97e06a4c7c75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666
iuc
parents:
17
diff
changeset
|
918 } |
97e06a4c7c75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666
iuc
parents:
17
diff
changeset
|
919 |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
920 # MD plot |
18
97e06a4c7c75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666
iuc
parents:
17
diff
changeset
|
921 Glimma::glMDPlot(fit, coef=i, counts=cnts, anno=geneanno, groups=factors[, 1], |
9
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
922 status=status[, i], sample.cols=col.group, |
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
923 main=paste("MD Plot:", unmake.names(con)), side.main=colnames(y$genes)[2], |
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
924 folder=paste0("glimma_", unmake.names(con)), launch=FALSE) |
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
925 linkName <- paste0("Glimma_MDPlot_", con, ".html") |
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
926 linkAddr <- paste0("glimma_", con, "/MD-Plot.html") |
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
927 linkData <- rbind(linkData, c(linkName, linkAddr)) |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
928 |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
929 # Volcano plot |
18
97e06a4c7c75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666
iuc
parents:
17
diff
changeset
|
930 Glimma::glXYPlot(x=fit$coefficients[, i], y=-log10(fit$p.value[, i]), counts=cnts, anno=geneanno, groups=factors[, 1], |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
931 status=status[, i], sample.cols=col.group, |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
932 main=paste("Volcano Plot:", unmake.names(con)), side.main=colnames(y$genes)[2], |
18
97e06a4c7c75
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f5e2ad38bf004b33fc5da5d9d4e75cf1130f666
iuc
parents:
17
diff
changeset
|
933 xlab="logFC", ylab="-log10(P-value)", |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
934 folder=paste0("glimma_volcano_", unmake.names(con)), launch=FALSE) |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
935 linkName <- paste0("Glimma_VolcanoPlot_", con, ".html") |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
936 linkAddr <- paste0("glimma_volcano_", con, "/XY-Plot.html") |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
937 linkData <- rbind(linkData, c(linkName, linkAddr)) |
9
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
938 } |
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
939 |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
940 # Plot Volcano |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
941 pdf(volOutPdf[i]) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
942 if (haveAnno) { |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
943 # labels must be in second column currently |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
944 labels <- fit$genes[, 2] |
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
945 } else { |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
946 labels <- fit$genes$GeneID |
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
947 } |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
948 limma::volcanoplot(fit, coef=i, |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
949 main=paste("Volcano Plot:", unmake.names(con)), |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
950 highlight=opt$topgenes, |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
951 names=labels) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
952 linkName <- paste0("VolcanoPlot_", con, ".pdf") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
953 linkAddr <- paste0("volplot_", con, ".pdf") |
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
954 linkData <- rbind(linkData, c(linkName, linkAddr)) |
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
955 invisible(dev.off()) |
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
956 |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
957 # PNG of MD and Volcano |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
958 png(mdvolOutPng[i], width=1000, height=500) |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
959 par(mfrow=c(1, 2), mar=c(5,4,2,2)+0.1, oma=c(0,0,3,0)) |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
960 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
961 # MD plot |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
962 limma::plotMD(fit, status=status[, i], coef=i, main="MD Plot", |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
963 hl.col=alpha(c("firebrick", "blue"), 0.4), values=c(1, -1), |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
964 xlab="Average Expression", ylab="logFC") |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
965 abline(h=0, col="grey", lty=2) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
966 |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
967 # Volcano |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
968 if (haveAnno) { |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
969 # labels must be in second column currently |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
970 limma::volcanoplot(fit, coef=i, main="Volcano Plot", |
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
971 highlight=opt$topgenes, |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
972 names=fit$genes[, 2]) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
973 } else { |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
974 limma::volcanoplot(fit, coef=i, main="Volcano Plot", |
7
e6a4ff41af6b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
6
diff
changeset
|
975 highlight=opt$topgenes, |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
976 names=fit$genes$GeneID) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
977 } |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
978 |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
979 imgName <- paste0("MDVolPlot_", con) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
980 imgAddr <- paste0("mdvolplot_", con, ".png") |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
981 imageData <- rbind(imageData, c(imgName, imgAddr)) |
20
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
parents:
19
diff
changeset
|
982 title(paste0("Contrast: ", con_name), outer=TRUE, cex.main=1.5) |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
983 invisible(dev.off()) |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
984 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
985 if ("h" %in% plots) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
986 # Plot Heatmap |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
987 topgenes <- rownames(top[1:opt$topgenes, ]) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
988 if (wantTrend) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
989 topexp <- plotData[topgenes, ] |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
990 } else { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
991 topexp <- plotData$E[topgenes, ] |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
992 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
993 pdf(heatOutPdf[i]) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
994 mycol <- colorpanel(1000,"blue","white","red") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
995 if (haveAnno) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
996 # labels must be in second column currently |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
997 labels <- top[topgenes, 2] |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
998 } else { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
999 labels <- rownames(topexp) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1000 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1001 heatmap.2(topexp, scale="row", Colv=FALSE, Rowv=FALSE, dendrogram="none", |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1002 main=paste("Contrast:", unmake.names(con), "\nTop", opt$topgenes, "genes by adj.P.Val"), |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1003 trace="none", density.info="none", lhei=c(2,10), margin=c(8, 6), labRow=labels, cexRow=0.7, srtCol=45, |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1004 col=mycol, ColSideColors=col.group) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1005 linkName <- paste0("Heatmap_", con, ".pdf") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1006 linkAddr <- paste0("heatmap_", con, ".pdf") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1007 linkData <- rbind(linkData, c(linkName, linkAddr)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1008 invisible(dev.off()) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1009 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1010 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1011 if ("s" %in% plots) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1012 # Plot Stripcharts of top genes |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1013 pdf(stripOutPdf[i], title=paste("Contrast:", unmake.names(con))) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1014 par(mfrow = c(3,2), cex.main=0.8, cex.axis=0.8) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1015 cols <- unique(col.group) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1016 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1017 for (j in 1:length(topgenes)) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1018 lfc <- round(top[topgenes[j], "logFC"], 2) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1019 pval <- round(top[topgenes[j], "adj.P.Val"], 5) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1020 if (wantTrend) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1021 stripchart(plotData[topgenes[j], ] ~ factors[, 1], vertical=TRUE, las=2, pch=16, cex=0.8, cex.lab=0.8, col=cols, |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1022 method="jitter", ylab="Normalised log2 expression", main=paste0(labels[j], "\nlogFC=", lfc, ", adj.P.Val=", pval)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1023 } else { |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
1024 stripchart(plotData$E[topgenes[j], ] ~ factors[, 1], vertical=TRUE, las=2, pch=16, cex=0.8, cex.lab=0.8, col=cols, |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1025 method="jitter", ylab="Normalised log2 expression", main=paste0(labels[j], "\nlogFC=", lfc, ", adj.P.Val=", pval)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1026 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1027 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1028 linkName <- paste0("Stripcharts_", con, ".pdf") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1029 linkAddr <- paste0("stripcharts_", con, ".pdf") |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1030 linkData <- rbind(linkData, c(linkName, linkAddr)) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1031 invisible(dev.off()) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1032 } |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1033 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1034 sigDiff <- data.frame(Up=upCount, Flat=flatCount, Down=downCount) |
17
86b3df7db58b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 42b1160a549a85c87ed5226a83b55c4e44648597
iuc
parents:
16
diff
changeset
|
1035 row.names(sigDiff) <- cons |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1036 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1037 # Save relevant items as rda object |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1038 if (wantRda) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1039 print("Saving RData") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1040 if (wantWeight) { |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1041 save(counts, data, y, status, plotData, labels, factors, wts, fit, top, contrastData, contrasts, design, |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1042 file=rdaOut, ascii=TRUE) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1043 } else { |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1044 save(counts, data, y, status, plotData, labels, factors, fit, top, contrastData, contrasts, design, |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1045 file=rdaOut, ascii=TRUE) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1046 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1047 linkData <- rbind(linkData, c((paste0(deMethod, "_analysis.RData")), (paste0(deMethod, "_analysis.RData")))) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1048 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1049 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1050 # Record session info |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1051 writeLines(capture.output(sessionInfo()), sessionOut) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1052 linkData <- rbind(linkData, c("Session Info", "session_info.txt")) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1053 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1054 # Record ending time and calculate total run time |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1055 timeEnd <- as.character(Sys.time()) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1056 timeTaken <- capture.output(round(difftime(timeEnd,timeStart), digits=3)) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1057 timeTaken <- gsub("Time difference of ", "", timeTaken, fixed=TRUE) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1058 ################################################################################ |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1059 ### HTML Generation |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1060 ################################################################################ |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1061 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1062 # Clear file |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1063 cat("", file=opt$htmlPath) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1064 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1065 cata("<html>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1066 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1067 cata("<body>\n") |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1068 cata("<h3>Limma Analysis Output:</h3>\n") |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1069 cata("Links to PDF copies of plots are in 'Plots' section below <br />\n") |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1070 |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1071 for (i in 1:nrow(imageData)) { |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
1072 if (grepl("density|box|mds|mdvol|wts", imageData$Link[i])) { |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1073 HtmlImage(imageData$Link[i], imageData$Label[i], width=1000) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1074 } else { |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1075 HtmlImage(imageData$Link[i], imageData$Label[i]) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1076 } |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1077 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1078 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1079 cata("<h4>Differential Expression Counts:</h4>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1080 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1081 cata("<table border=\"1\" cellpadding=\"4\">\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1082 cata("<tr>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1083 TableItem() |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1084 for (i in colnames(sigDiff)) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1085 TableHeadItem(i) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1086 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1087 cata("</tr>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1088 for (i in 1:nrow(sigDiff)) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1089 cata("<tr>\n") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1090 TableHeadItem(unmake.names(row.names(sigDiff)[i])) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1091 for (j in 1:ncol(sigDiff)) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1092 TableItem(as.character(sigDiff[i, j])) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1093 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1094 cata("</tr>\n") |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1095 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1096 cata("</table>") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1097 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1098 cata("<h4>Plots:</h4>\n") |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1099 #PDFs |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1100 for (i in 1:nrow(linkData)) { |
20
0921444c832d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 0cc16fe170b5c8d3b9441177bf2749aa7bddca7b
iuc
parents:
19
diff
changeset
|
1101 if (grepl(".pdf", linkData$Link[i]) & grepl("density|cpm|boxplot|mds|mdplots|voom|saplot", linkData$Link[i])) { |
8
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1102 HtmlLink(linkData$Link[i], linkData$Label[i]) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1103 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1104 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1105 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1106 for (i in 1:nrow(linkData)) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1107 if (grepl("mdplot_", linkData$Link[i])) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1108 HtmlLink(linkData$Link[i], linkData$Label[i]) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1109 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1110 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1111 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1112 for (i in 1:nrow(linkData)) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1113 if (grepl("volplot", linkData$Link[i])) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1114 HtmlLink(linkData$Link[i], linkData$Label[i]) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1115 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1116 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1117 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1118 for (i in 1:nrow(linkData)) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1119 if (grepl("heatmap", linkData$Link[i])) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1120 HtmlLink(linkData$Link[i], linkData$Label[i]) |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1121 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1122 } |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1123 |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1124 for (i in 1:nrow(linkData)) { |
00a42b66e522
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 48125e8638453668f889a67791421f14d3ebe623
iuc
parents:
7
diff
changeset
|
1125 if (grepl("stripcharts", linkData$Link[i])) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1126 HtmlLink(linkData$Link[i], linkData$Label[i]) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1127 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1128 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1129 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1130 cata("<h4>Tables:</h4>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1131 for (i in 1:nrow(linkData)) { |
13
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
1132 if (grepl("counts$", linkData$Link[i])) { |
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
1133 HtmlLink(linkData$Link[i], linkData$Label[i]) |
d5a940112511
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 8560b34a261fde200bd77dc2e817d55d386ac811
iuc
parents:
12
diff
changeset
|
1134 } else if (grepl(".tsv", linkData$Link[i])) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1135 HtmlLink(linkData$Link[i], linkData$Label[i]) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1136 } |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1137 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1138 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1139 if (wantRda) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1140 cata("<h4>R Data Object:</h4>\n") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1141 for (i in 1:nrow(linkData)) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1142 if (grepl(".RData", linkData$Link[i])) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1143 HtmlLink(linkData$Link[i], linkData$Label[i]) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1144 } |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1145 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1146 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1147 |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
1148 if ("i" %in% plots) { |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
1149 cata("<h4>Glimma Interactive Results:</h4>\n") |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
1150 for (i in 1:nrow(linkData)) { |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
1151 if (grepl("glimma", linkData$Link[i])) { |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
1152 HtmlLink(linkData$Link[i], linkData$Label[i]) |
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
1153 } |
9
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
1154 } |
14
3133e833b3ce
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit c915bd7e68cb3a2944397aaf184c2b1db97cb3a5
iuc
parents:
13
diff
changeset
|
1155 } |
9
4255881bebb1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f8052ab47b789da5ea47feb48e1b8e08b5fc1e0
iuc
parents:
8
diff
changeset
|
1156 |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1157 cata("<p>Alt-click links to download file.</p>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1158 cata("<p>Click floppy disc icon associated history item to download ") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1159 cata("all files.</p>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1160 cata("<p>.tsv files can be viewed in Excel or any spreadsheet program.</p>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1161 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1162 cata("<h4>Additional Information</h4>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1163 cata("<ul>\n") |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1164 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1165 if (filtCPM || filtSmpCount || filtTotCount) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1166 if (filtCPM) { |
5
d8a55b5f0de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents:
4
diff
changeset
|
1167 tempStr <- paste("Genes without more than", opt$cpmReq, |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1168 "CPM in at least", opt$sampleReq, "samples are insignificant", |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1169 "and filtered out.") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1170 } else if (filtSmpCount) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1171 tempStr <- paste("Genes without more than", opt$cntReq, |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1172 "counts in at least", opt$sampleReq, "samples are insignificant", |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1173 "and filtered out.") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1174 } else if (filtTotCount) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1175 tempStr <- paste("Genes without more than", opt$cntReq, |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1176 "counts, after summing counts for all samples, are insignificant", |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1177 "and filtered out.") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1178 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1179 |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1180 ListItem(tempStr) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1181 filterProp <- round(filteredCount/preFilterCount*100, digits=2) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1182 tempStr <- paste0(filteredCount, " of ", preFilterCount," (", filterProp, |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1183 "%) genes were filtered out for low expression.") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1184 ListItem(tempStr) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1185 } |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1186 ListItem(opt$normOpt, " was the method used to normalise library sizes.") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1187 if (wantTrend) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1188 ListItem("The limma-trend method was used.") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1189 } else { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1190 ListItem("The limma-voom method was used.") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1191 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1192 if (wantWeight) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1193 ListItem("Weights were applied to samples.") |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1194 } else { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1195 ListItem("Weights were not applied to samples.") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1196 } |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1197 if (wantTreat) { |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1198 ListItem(paste("Testing significance relative to a fold-change threshold (TREAT) was performed using a threshold of log2 =", opt$lfcReq, "at FDR of", opt$pValReq, ".")) |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1199 } |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1200 if (wantRobust) { |
6
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1201 if (wantTreat) { |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1202 ListItem("TREAT was used with robust settings (robust=TRUE).") |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1203 } else { |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1204 ListItem("eBayes was used with robust settings (robust=TRUE).") |
39fa12a6d885
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 60cae222b10f43f830936c19298bd723ac47e43d
iuc
parents:
5
diff
changeset
|
1205 } |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1206 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1207 if (opt$pAdjOpt!="none") { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1208 if (opt$pAdjOpt=="BH" || opt$pAdjOpt=="BY") { |
5
d8a55b5f0de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents:
4
diff
changeset
|
1209 tempStr <- paste0("MD Plot highlighted genes are significant at FDR ", |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1210 "of ", opt$pValReq," and exhibit log2-fold-change of at ", |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1211 "least ", opt$lfcReq, ".") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1212 ListItem(tempStr) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1213 } else if (opt$pAdjOpt=="holm") { |
5
d8a55b5f0de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents:
4
diff
changeset
|
1214 tempStr <- paste0("MD Plot highlighted genes are significant at adjusted ", |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1215 "p-value of ", opt$pValReq," by the Holm(1979) ", |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1216 "method, and exhibit log2-fold-change of at least ", |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1217 opt$lfcReq, ".") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1218 ListItem(tempStr) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1219 } |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1220 } else { |
5
d8a55b5f0de0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 5f0db9544002b02d3ccffb8c983b5c8baef6bacd
iuc
parents:
4
diff
changeset
|
1221 tempStr <- paste0("MD Plot highlighted genes are significant at p-value ", |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1222 "of ", opt$pValReq," and exhibit log2-fold-change of at ", |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1223 "least ", opt$lfcReq, ".") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1224 ListItem(tempStr) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1225 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1226 cata("</ul>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1227 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1228 cata("<h4>Summary of experimental data:</h4>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1229 |
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
1230 cata("<p>*CHECK THAT SAMPLES ARE ASSOCIATED WITH CORRECT GROUP(S)*</p>\n") |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1231 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1232 cata("<table border=\"1\" cellpadding=\"3\">\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1233 cata("<tr>\n") |
1
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
1234 TableHeadItem("SampleID") |
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
1235 TableHeadItem(names(factors)[1]," (Primary Factor)") |
76d01fe0ec36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 58c05c0ce9334f8b9c800283cfd1f40573546edd
iuc
parents:
0
diff
changeset
|
1236 |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1237 if (ncol(factors) > 1) { |
2
a330ddf43861
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa
iuc
parents:
1
diff
changeset
|
1238 for (i in names(factors)[2:length(names(factors))]) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1239 TableHeadItem(i) |
2
a330ddf43861
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa
iuc
parents:
1
diff
changeset
|
1240 } |
a330ddf43861
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa
iuc
parents:
1
diff
changeset
|
1241 cata("</tr>\n") |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1242 } |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1243 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1244 for (i in 1:nrow(factors)) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1245 cata("<tr>\n") |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1246 TableHeadItem(row.names(factors)[i]) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1247 for (j in 1:ncol(factors)) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1248 TableItem(as.character(unmake.names(factors[i, j]))) |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1249 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1250 cata("</tr>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1251 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1252 cata("</table>") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1253 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1254 cit <- character() |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1255 link <- character() |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1256 link[1] <- paste0("<a href=\"", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1257 "http://www.bioconductor.org/packages/release/bioc/", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1258 "vignettes/limma/inst/doc/usersguide.pdf", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1259 "\">", "limma User's Guide", "</a>.") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1260 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1261 link[2] <- paste0("<a href=\"", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1262 "http://www.bioconductor.org/packages/release/bioc/", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1263 "vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1264 "\">", "edgeR User's Guide", "</a>") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1265 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1266 cit[1] <- paste("Please cite the following paper for this tool:") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1267 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1268 cit[2] <- paste("Liu R, Holik AZ, Su S, Jansz N, Chen K, Leong HS, Blewitt ME,", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1269 "Asselin-Labat ML, Smyth GK, Ritchie ME (2015). Why weight? ", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1270 "Modelling sample and observational level variability improves power ", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1271 "in RNA-seq analyses. Nucleic Acids Research, 43(15), e97.") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1272 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1273 cit[3] <- paste("Please cite the paper below for the limma software itself.", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1274 "Please also try to cite the appropriate methodology articles", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1275 "that describe the statistical methods implemented in limma,", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1276 "depending on which limma functions you are using. The", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1277 "methodology articles are listed in Section 2.1 of the", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1278 link[1], |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1279 "Cite no. 3 only if sample weights were used.") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1280 cit[4] <- paste("Smyth GK (2005). Limma: linear models for microarray data.", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1281 "In: 'Bioinformatics and Computational Biology Solutions using", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1282 "R and Bioconductor'. R. Gentleman, V. Carey, S. doit,.", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1283 "Irizarry, W. Huber (eds), Springer, New York, pages 397-420.") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1284 cit[5] <- paste("Please cite the first paper for the software itself and the", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1285 "other papers for the various original statistical methods", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1286 "implemented in edgeR. See Section 1.2 in the", link[2], |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1287 "for more detail.") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1288 cit[6] <- paste("Robinson MD, McCarthy DJ and Smyth GK (2010). edgeR: a", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1289 "Bioconductor package for differential expression analysis", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1290 "of digital gene expression data. Bioinformatics 26, 139-140") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1291 cit[7] <- paste("Robinson MD and Smyth GK (2007). Moderated statistical tests", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1292 "for assessing differences in tag abundance. Bioinformatics", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1293 "23, 2881-2887") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1294 cit[8] <- paste("Robinson MD and Smyth GK (2008). Small-sample estimation of", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1295 "negative binomial dispersion, with applications to SAGE data.", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1296 "Biostatistics, 9, 321-332") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1297 cit[9] <- paste("McCarthy DJ, Chen Y and Smyth GK (2012). Differential", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1298 "expression analysis of multifactor RNA-Seq experiments with", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1299 "respect to biological variation. Nucleic Acids Research 40,", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1300 "4288-4297") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1301 cit[10] <- paste("Law CW, Chen Y, Shi W, and Smyth GK (2014). Voom:", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1302 "precision weights unlock linear model analysis tools for", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1303 "RNA-seq read counts. Genome Biology 15, R29.") |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1304 cit[11] <- paste("Ritchie ME, Diyagama D, Neilson J, van Laar R,", |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1305 "Dobrovic A, Holloway A and Smyth GK (2006).", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1306 "Empirical array quality weights for microarray data.", |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1307 "BMC Bioinformatics 7, Article 261.") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1308 cata("<h3>Citations</h3>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1309 cata(cit[1], "\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1310 cata("<br>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1311 cata(cit[2], "\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1312 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1313 cata("<h4>limma</h4>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1314 cata(cit[3], "\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1315 cata("<ol>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1316 ListItem(cit[4]) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1317 ListItem(cit[10]) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1318 ListItem(cit[11]) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1319 cata("</ol>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1320 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1321 cata("<h4>edgeR</h4>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1322 cata(cit[5], "\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1323 cata("<ol>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1324 ListItem(cit[6]) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1325 ListItem(cit[7]) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1326 ListItem(cit[8]) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1327 ListItem(cit[9]) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1328 cata("</ol>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1329 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1330 cata("<p>Please report problems or suggestions to: su.s@wehi.edu.au</p>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1331 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1332 for (i in 1:nrow(linkData)) { |
3
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1333 if (grepl("session_info", linkData$Link[i])) { |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1334 HtmlLink(linkData$Link[i], linkData$Label[i]) |
38aab66ae5cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 1640914b9812b0482a3cf684f05465f8d9cfdc65
iuc
parents:
2
diff
changeset
|
1335 } |
0
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1336 } |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1337 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1338 cata("<table border=\"0\">\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1339 cata("<tr>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1340 TableItem("Task started at:"); TableItem(timeStart) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1341 cata("</tr>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1342 cata("<tr>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1343 TableItem("Task ended at:"); TableItem(timeEnd) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1344 cata("</tr>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1345 cata("<tr>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1346 TableItem("Task run time:"); TableItem(timeTaken) |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1347 cata("<tr>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1348 cata("</table>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1349 |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1350 cata("</body>\n") |
bdebdea5f6a7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 2f34a215c35f08c3666f314a87d235437baa1d21
iuc
parents:
diff
changeset
|
1351 cata("</html>") |