Mercurial > repos > iuc > dexseq

annotate plotdexseq.R @ 9:b47c006d90c5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit e3d05bd838e8a1d54bc45b38d74d9417d5ff21d5"
author iuc
date Tue, 03 May 2022 20:23:18 +0000
parents 62adf13b86ea
children df929f257179
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278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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1 ## Setup R error handling to go to stderr
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2 options(show.error.messages = F, error = function() {
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3 cat(geterrmessage(), file = stderr()); q("no", 1, F)
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4 })
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278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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5 # we need that to not crash galaxy with an UTF8 error on German LC settings.
278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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6 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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8 suppressPackageStartupMessages({
278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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9 library("DEXSeq")
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10 library("getopt")
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11 })
278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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13 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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14 args <- commandArgs(trailingOnly = TRUE)
278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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16 #get options, using the spec as defined by the enclosed list.
278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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17 #we read the options from the default: commandArgs(TRUE).
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18 spec <- matrix(c(
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19 "rdata", "r", 1, "character",
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20 "primaryfactor", "p", 1, "character",
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21 "geneid", "g", 1, "character",
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22 "genefile", "f", 1, "character",
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23 "fdr", "c", 1, "double",
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24 "transcripts", "t", 1, "logical",
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25 "names", "a", 1, "logical",
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26 "normcounts", "n", 1, "logical",
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27 "splicing", "s", 1, "logical"
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28 ), byrow = TRUE, ncol = 4);
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29 opt <- getopt(spec);
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278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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31 res <- readRDS(opt$rdata)
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33 if (!is.null(opt$genefile)) {
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34 genes <- read.delim(opt$genefile, header = FALSE)
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35 genes <- genes[, 1]
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36 } else {
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37 genes <- opt$geneid
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38 }
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278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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40 pdf("plot.pdf")
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41 for (i in genes) {
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42 plotDEXSeq(res, i, FDR = opt$fdr, fitExpToVar = opt$primaryfactor,
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43 norCounts = opt$normcounts, expression = TRUE, splicing = opt$splicing,
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44 displayTranscripts = opt$transcripts, names = opt$names, legend = TRUE,
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45 color = NULL, color.samples = NULL, transcriptDb = NULL)
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46 }
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47 dev.off()
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49 sessionInfo()