comparison plotdexseq.R @ 11:9a7c5b6d8f1e draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0ccfadf8ac4bc6514836c4efe6f605973a08d1ed

10:df929f257179

})

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).
spec <- matrix(c(
    "rdata", "r", 1, "character",
    "primaryfactor", "p", 1, "character",
    "geneid", "g", 1, "character",
    "genefile", "f", 1, "character",

    genes <- opt$geneid
}

pdf("plot.pdf")
for (i in genes) {
    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)
}
dev.off()

sessionInfo()

11:9a7c5b6d8f1e

})

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).
spec <- matrix(c(
    "rdata", "r", 1, "character",
    "primaryfactor", "p", 1, "character",
    "geneid", "g", 1, "character",
    "genefile", "f", 1, "character",

    genes <- opt$geneid
}

pdf("plot.pdf")
for (i in genes) {
    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
    )
}
dev.off()

sessionInfo()