diff plotdexseq.R @ 18:ffa256d657b2 draft default tip

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

--- a/plotdexseq.R	Tue Apr 04 08:25:36 2023 +0000
+++ b/plotdexseq.R	Fri Jan 31 18:00:29 2025 +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",
@@ -25,7 +25,9 @@
     "transcripts", "t", 1, "logical",
     "names", "a", 1, "logical",
     "normcounts", "n", 1, "logical",
-    "splicing", "s", 1, "logical"
+    "splicing", "s", 1, "logical",
+    "pl_width", "w", 2, "integer",
+    "pl_height", "h", 2, "integer"
 ), byrow = TRUE, ncol = 4)
 opt <- getopt(spec)
 
@@ -38,12 +40,18 @@
     genes <- opt$geneid
 }
 
-pdf("plot.pdf")
+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) {
-    plotDEXSeq(res, i, FDR = opt$fdr, fitExpToVar = opt$primaryfactor,
+    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)
+        color = NULL, color.samples = NULL, transcriptDb = NULL
+    )
 }
 dev.off()