Mercurial > repos > iuc > dexseq
comparison plotdexseq.R @ 5:278b189248cd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit c027cb925607cda29bb1e78fe76716af49a276ca
author | iuc |
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date | Mon, 14 Jan 2019 05:02:19 -0500 |
parents | |
children | 62adf13b86ea |
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4:251393b72616 | 5:278b189248cd |
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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() |