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comparison plotdexseq.R @ 5:278b189248cd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
author iuc
date Mon, 14 Jan 2019 05:02:19 -0500
parents
children 62adf13b86ea
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4:251393b72616 5:278b189248cd
1 ## Setup R error handling to go to stderr
2 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
3 # we need that to not crash galaxy with an UTF8 error on German LC settings.
4 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
5
6 suppressPackageStartupMessages({
7 library("DEXSeq")
8 library('getopt')
9 })
10
11 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
12 args <- commandArgs(trailingOnly = TRUE)
13
14 #get options, using the spec as defined by the enclosed list.
15 #we read the options from the default: commandArgs(TRUE).
16 spec = matrix(c(
17 'rdata', 'r', 1, "character",
18 'primaryfactor', 'p', 1, "character",
19 'geneid', 'g', 1, "character",
20 'genefile', 'f', 1, "character",
21 'fdr', 'c', 1, "double",
22 'transcripts', 't', 1, "logical",
23 'names', 'a', 1, "logical",
24 'normcounts', 'n', 1, "logical",
25 'splicing', 's', 1, "logical"
26 ), byrow=TRUE, ncol=4);
27 opt = getopt(spec);
28
29 res <- readRDS(opt$rdata)
30
31 if (!is.null(opt$genefile)) {
32 genes <- read.delim(opt$genefile, header=FALSE)
33 genes <- genes[, 1]
34 } else {
35 genes <- opt$geneid
36 }
37
38 pdf("plot.pdf")
39 for (i in genes){
40 plotDEXSeq(res, i, FDR=opt$fdr, fitExpToVar=opt$primaryfactor,
41 norCounts=opt$normcounts, expression=TRUE, splicing=opt$splicing,
42 displayTranscripts=opt$transcripts, names=opt$names, legend=TRUE,
43 color=NULL, color.samples=NULL, transcriptDb=NULL)
44 }
45 dev.off()
46
47 sessionInfo()