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annotate plotdexseq.R @ 11:9a7c5b6d8f1e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0ccfadf8ac4bc6514836c4efe6f605973a08d1ed
author iuc
date Tue, 02 Apr 2024 12:59:54 +0000
parents df929f257179
children
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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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df929f257179 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
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2 options(show.error.messages = FALSE, error = function() {
df929f257179 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
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3 cat(geterrmessage(), file = stderr())
df929f257179 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
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4 q("no", 1, FALSE)
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5 })
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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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6 # 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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7 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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9 suppressPackageStartupMessages({
278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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10 library("DEXSeq")
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11 library("getopt")
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12 })
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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14 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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15 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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17 # get options, using the spec as defined by the enclosed list.
9a7c5b6d8f1e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0ccfadf8ac4bc6514836c4efe6f605973a08d1ed
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18 # we read the options from the default: commandArgs(TRUE).
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19 spec <- matrix(c(
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20 "rdata", "r", 1, "character",
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21 "primaryfactor", "p", 1, "character",
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22 "geneid", "g", 1, "character",
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23 "genefile", "f", 1, "character",
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24 "fdr", "c", 1, "double",
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25 "transcripts", "t", 1, "logical",
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26 "names", "a", 1, "logical",
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27 "normcounts", "n", 1, "logical",
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28 "splicing", "s", 1, "logical"
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29 ), byrow = TRUE, ncol = 4)
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30 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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32 res <- readRDS(opt$rdata)
278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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278b189248cd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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34 if (!is.null(opt$genefile)) {
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35 genes <- read.delim(opt$genefile, header = FALSE)
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36 genes <- genes[, 1]
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37 } else {
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38 genes <- opt$geneid
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39 }
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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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41 pdf("plot.pdf")
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42 for (i in genes) {
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43 plotDEXSeq(res, i,
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44 FDR = opt$fdr, fitExpToVar = opt$primaryfactor,
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45 norCounts = opt$normcounts, expression = TRUE, splicing = opt$splicing,
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46 displayTranscripts = opt$transcripts, names = opt$names, legend = TRUE,
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47 color = NULL, color.samples = NULL, transcriptDb = NULL
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48 )
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49 }
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50 dev.off()
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52 sessionInfo()