Mercurial > repos > iuc > dexseq

comparison plotdexseq.R @ 7:62adf13b86ea draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 06f2c57b523aab7c997d82e1345fd23f178de598"
author iuc
date Fri, 19 Mar 2021 09:45:03 +0000
parents 278b189248cd
children df929f257179
comparison
equal deleted inserted replaced
6:9fd8b69e6e68 7:62adf13b86ea
1 ## Setup R error handling to go to stderr 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 ) } ) 2 options(show.error.messages = F, error = function() {
3 cat(geterrmessage(), file = stderr()); q("no", 1, F)
4 })
3 # we need that to not crash galaxy with an UTF8 error on German LC settings. 5 # we need that to not crash galaxy with an UTF8 error on German LC settings.
4 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") 6 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
5 7
6 suppressPackageStartupMessages({ 8 suppressPackageStartupMessages({
7 library("DEXSeq") 9 library("DEXSeq")
8 library('getopt') 10 library("getopt")
9 }) 11 })
10 12
11 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) 13 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
12 args <- commandArgs(trailingOnly = TRUE) 14 args <- commandArgs(trailingOnly = TRUE)
13 15
14 #get options, using the spec as defined by the enclosed list. 16 #get options, using the spec as defined by the enclosed list.
15 #we read the options from the default: commandArgs(TRUE). 17 #we read the options from the default: commandArgs(TRUE).
16 spec = matrix(c( 18 spec <- matrix(c(
17 'rdata', 'r', 1, "character", 19 "rdata", "r", 1, "character",
18 'primaryfactor', 'p', 1, "character", 20 "primaryfactor", "p", 1, "character",
19 'geneid', 'g', 1, "character", 21 "geneid", "g", 1, "character",
20 'genefile', 'f', 1, "character", 22 "genefile", "f", 1, "character",
21 'fdr', 'c', 1, "double", 23 "fdr", "c", 1, "double",
22 'transcripts', 't', 1, "logical", 24 "transcripts", "t", 1, "logical",
23 'names', 'a', 1, "logical", 25 "names", "a", 1, "logical",
24 'normcounts', 'n', 1, "logical", 26 "normcounts", "n", 1, "logical",
25 'splicing', 's', 1, "logical" 27 "splicing", "s", 1, "logical"
26 ), byrow=TRUE, ncol=4); 28 ), byrow = TRUE, ncol = 4);
27 opt = getopt(spec); 29 opt <- getopt(spec);
28 30
29 res <- readRDS(opt$rdata) 31 res <- readRDS(opt$rdata)
30 32
31 if (!is.null(opt$genefile)) { 33 if (!is.null(opt$genefile)) {
32 genes <- read.delim(opt$genefile, header=FALSE) 34 genes <- read.delim(opt$genefile, header = FALSE)
33 genes <- genes[, 1] 35 genes <- genes[, 1]
34 } else { 36 } else {
35 genes <- opt$geneid 37 genes <- opt$geneid
36 } 38 }
37 39
38 pdf("plot.pdf") 40 pdf("plot.pdf")
39 for (i in genes){ 41 for (i in genes) {
40 plotDEXSeq(res, i, FDR=opt$fdr, fitExpToVar=opt$primaryfactor, 42 plotDEXSeq(res, i, FDR = opt$fdr, fitExpToVar = opt$primaryfactor,
41 norCounts=opt$normcounts, expression=TRUE, splicing=opt$splicing, 43 norCounts = opt$normcounts, expression = TRUE, splicing = opt$splicing,
42 displayTranscripts=opt$transcripts, names=opt$names, legend=TRUE, 44 displayTranscripts = opt$transcripts, names = opt$names, legend = TRUE,
43 color=NULL, color.samples=NULL, transcriptDb=NULL) 45 color = NULL, color.samples = NULL, transcriptDb = NULL)
44 } 46 }
45 dev.off() 47 dev.off()
46 48
47 sessionInfo() 49 sessionInfo()