Mercurial > repos > iuc > dexseq

comparison 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
comparison
equal deleted inserted replaced
10:df929f257179 11:9a7c5b6d8f1e
12 }) 12 })
13 13
14 options(stringAsfactors = FALSE, useFancyQuotes = FALSE) 14 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
15 args <- commandArgs(trailingOnly = TRUE) 15 args <- commandArgs(trailingOnly = TRUE)
16 16
17 #get options, using the spec as defined by the enclosed list. 17 # get options, using the spec as defined by the enclosed list.
18 #we read the options from the default: commandArgs(TRUE). 18 # we read the options from the default: commandArgs(TRUE).
19 spec <- matrix(c( 19 spec <- matrix(c(
20 "rdata", "r", 1, "character", 20 "rdata", "r", 1, "character",
21 "primaryfactor", "p", 1, "character", 21 "primaryfactor", "p", 1, "character",
22 "geneid", "g", 1, "character", 22 "geneid", "g", 1, "character",
23 "genefile", "f", 1, "character", 23 "genefile", "f", 1, "character",
38 genes <- opt$geneid 38 genes <- opt$geneid
39 } 39 }
40 40
41 pdf("plot.pdf") 41 pdf("plot.pdf")
42 for (i in genes) { 42 for (i in genes) {
43 plotDEXSeq(res, i, FDR = opt$fdr, fitExpToVar = opt$primaryfactor, 43 plotDEXSeq(res, i,
44 FDR = opt$fdr, fitExpToVar = opt$primaryfactor,
44 norCounts = opt$normcounts, expression = TRUE, splicing = opt$splicing, 45 norCounts = opt$normcounts, expression = TRUE, splicing = opt$splicing,
45 displayTranscripts = opt$transcripts, names = opt$names, legend = TRUE, 46 displayTranscripts = opt$transcripts, names = opt$names, legend = TRUE,
46 color = NULL, color.samples = NULL, transcriptDb = NULL) 47 color = NULL, color.samples = NULL, transcriptDb = NULL
48 )
47 } 49 }
48 dev.off() 50 dev.off()
49 51
50 sessionInfo() 52 sessionInfo()