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comparison 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
comparison
equal deleted inserted replaced
17:d104044e4257 18:ffa256d657b2
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",
24 "fdr", "c", 1, "double", 24 "fdr", "c", 1, "double",
25 "transcripts", "t", 1, "logical", 25 "transcripts", "t", 1, "logical",
26 "names", "a", 1, "logical", 26 "names", "a", 1, "logical",
27 "normcounts", "n", 1, "logical", 27 "normcounts", "n", 1, "logical",
28 "splicing", "s", 1, "logical" 28 "splicing", "s", 1, "logical",
29 "pl_width", "w", 2, "integer",
30 "pl_height", "h", 2, "integer"
29 ), byrow = TRUE, ncol = 4) 31 ), byrow = TRUE, ncol = 4)
30 opt <- getopt(spec) 32 opt <- getopt(spec)
31 33
32 res <- readRDS(opt$rdata) 34 res <- readRDS(opt$rdata)
33 35
36 genes <- genes[, 1] 38 genes <- genes[, 1]
37 } else { 39 } else {
38 genes <- opt$geneid 40 genes <- opt$geneid
39 } 41 }
40 42
41 pdf("plot.pdf") 43 pl_width <- pl_height <- 7
44 if (!is.null(opt$pl_width)) pl_width <- opt$pl_width
45 if (!is.null(opt$pl_height)) pl_height <- opt$pl_height
46 pdf("plot.pdf", width = pl_width, height = pl_height)
42 for (i in genes) { 47 for (i in genes) {
43 plotDEXSeq(res, i, FDR = opt$fdr, fitExpToVar = opt$primaryfactor, 48 par(oma = c(pl_height * 0.2, pl_width * 0.2, pl_height * 0.2, pl_width * 0.2))
49 plotDEXSeq(res, i,
50 FDR = opt$fdr, fitExpToVar = opt$primaryfactor,
44 norCounts = opt$normcounts, expression = TRUE, splicing = opt$splicing, 51 norCounts = opt$normcounts, expression = TRUE, splicing = opt$splicing,
45 displayTranscripts = opt$transcripts, names = opt$names, legend = TRUE, 52 displayTranscripts = opt$transcripts, names = opt$names, legend = TRUE,
46 color = NULL, color.samples = NULL, transcriptDb = NULL) 53 color = NULL, color.samples = NULL, transcriptDb = NULL
54 )
47 } 55 }
48 dev.off() 56 dev.off()
49 57
50 sessionInfo() 58 sessionInfo()