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annotate plotdexseq.R @ 18:ffa256d657b2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598
author iuc
date Fri, 31 Jan 2025 18:00:29 +0000
parents d104044e4257
children
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577d1c8baab4 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 = FALSE, error = function() {
d104044e4257 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())
d104044e4257 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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6 # we need that to not crash galaxy with an UTF8 error on German LC settings.
577d1c8baab4 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")
577d1c8baab4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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577d1c8baab4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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9 suppressPackageStartupMessages({
577d1c8baab4 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 })
577d1c8baab4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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577d1c8baab4 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)
577d1c8baab4 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)
577d1c8baab4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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ffa256d657b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598
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17 # get options, using the spec as defined by the enclosed list.
ffa256d657b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598
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18 # we read the options from the default: commandArgs(TRUE).
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19 spec <- matrix(c(
3762d6644ec4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
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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",
ffa256d657b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598
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29 "pl_width", "w", 2, "integer",
ffa256d657b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598
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30 "pl_height", "h", 2, "integer"
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31 ), byrow = TRUE, ncol = 4)
d104044e4257 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140
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32 opt <- getopt(spec)
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34 res <- readRDS(opt$rdata)
577d1c8baab4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
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36 if (!is.null(opt$genefile)) {
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37 genes <- read.delim(opt$genefile, header = FALSE)
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38 genes <- genes[, 1]
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39 } else {
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40 genes <- opt$geneid
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41 }
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43 pl_width <- pl_height <- 7
ffa256d657b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598
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44 if (!is.null(opt$pl_width)) pl_width <- opt$pl_width
ffa256d657b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598
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45 if (!is.null(opt$pl_height)) pl_height <- opt$pl_height
ffa256d657b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598
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46 pdf("plot.pdf", width = pl_width, height = pl_height)
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47 for (i in genes) {
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48 par(oma = c(pl_height * 0.2, pl_width * 0.2, pl_height * 0.2, pl_width * 0.2))
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49 plotDEXSeq(res, i,
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50 FDR = opt$fdr, fitExpToVar = opt$primaryfactor,
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51 norCounts = opt$normcounts, expression = TRUE, splicing = opt$splicing,
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52 displayTranscripts = opt$transcripts, names = opt$names, legend = TRUE,
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53 color = NULL, color.samples = NULL, transcriptDb = NULL
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54 )
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55 }
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56 dev.off()
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58 sessionInfo()