--- a/plotdexseq.R	Tue Feb 26 10:50:15 2019 -0500
+++ b/plotdexseq.R	Fri Mar 19 09:45:03 2021 +0000
@@ -1,11 +1,13 @@
 ## Setup R error handling to go to stderr
-options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+options(show.error.messages = F, error = function() {
+    cat(geterrmessage(), file = stderr()); q("no", 1, F)
+})
 # we need that to not crash galaxy with an UTF8 error on German LC settings.
 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
 
 suppressPackageStartupMessages({
     library("DEXSeq")
-    library('getopt')
+    library("getopt")
 })
 
 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
@@ -13,35 +15,35 @@
 
 #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);
+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)
 
 if (!is.null(opt$genefile)) {
-	genes <- read.delim(opt$genefile, header=FALSE)
-	genes <- genes[, 1]
+    genes <- read.delim(opt$genefile, header = FALSE)
+    genes <- genes[, 1]
 } else {
-	genes <- opt$geneid
+    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)
+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()
\ No newline at end of file
+sessionInfo()