Mercurial > repos > iuc > dexseq
diff plotdexseq.R @ 11:9a7c5b6d8f1e draft default tip
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 |
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--- a/plotdexseq.R Tue Apr 04 08:25:51 2023 +0000 +++ b/plotdexseq.R Tue Apr 02 12:59:54 2024 +0000 @@ -14,8 +14,8 @@ options(stringAsfactors = FALSE, useFancyQuotes = FALSE) args <- commandArgs(trailingOnly = TRUE) -#get options, using the spec as defined by the enclosed list. -#we read the options from the default: commandArgs(TRUE). +# get options, using the spec as defined by the enclosed list. +# we read the options from the default: commandArgs(TRUE). spec <- matrix(c( "rdata", "r", 1, "character", "primaryfactor", "p", 1, "character", @@ -40,10 +40,12 @@ pdf("plot.pdf") for (i in genes) { - plotDEXSeq(res, i, FDR = opt$fdr, fitExpToVar = opt$primaryfactor, + plotDEXSeq(res, i, + FDR = opt$fdr, fitExpToVar = opt$primaryfactor, norCounts = opt$normcounts, expression = TRUE, splicing = opt$splicing, displayTranscripts = opt$transcripts, names = opt$names, legend = TRUE, - color = NULL, color.samples = NULL, transcriptDb = NULL) + color = NULL, color.samples = NULL, transcriptDb = NULL + ) } dev.off()