comparison plotdexseq.R @ 18:ffa256d657b2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit ed4091f895ae0f46323534ca42da290c6e103598

17:d104044e4257

})

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",
    "fdr", "c", 1, "double",
    "transcripts", "t", 1, "logical",
    "names", "a", 1, "logical",
    "normcounts", "n", 1, "logical",
    "splicing", "s", 1, "logical"
), byrow = TRUE, ncol = 4)
opt <- getopt(spec)

res <- readRDS(opt$rdata)

    genes <- genes[, 1]
} else {
    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()

18:ffa256d657b2

})

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",
    "fdr", "c", 1, "double",
    "transcripts", "t", 1, "logical",
    "names", "a", 1, "logical",
    "normcounts", "n", 1, "logical",
    "splicing", "s", 1, "logical",
    "pl_width", "w", 2, "integer",
    "pl_height", "h", 2, "integer"
), byrow = TRUE, ncol = 4)
opt <- getopt(spec)

res <- readRDS(opt$rdata)

    genes <- genes[, 1]
} else {
    genes <- opt$geneid
}

pl_width <- pl_height <- 7
if (!is.null(opt$pl_width)) pl_width <- opt$pl_width
if (!is.null(opt$pl_height)) pl_height <- opt$pl_height
pdf("plot.pdf", width = pl_width, height = pl_height)
for (i in genes) {
    par(oma = c(pl_height * 0.2, pl_width * 0.2, pl_height * 0.2, pl_width * 0.2))
    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()