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#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 RSEM.isoforms.fpkm\n\n";
my $fpkm_file = $ARGV[0] or die $usage;
my $Rscript = "$fpkm_file.R";
open (my $ofh, ">$Rscript");
print $ofh "source(\"/usr/lib/trinityrnaseq/util/R/expression_analysis_lib.R\")\n";
print $ofh "pdf(\"$fpkm_file.genes_vs_minFPKM.pdf\")\n";
print $ofh "plot_expressed_gene_counts(\"$fpkm_file\", title=\"expressed transcripts vs. min FPKM\", fpkm_range=seq(0,5,0.01), outfile=\"$fpkm_file.genes_vs_minFPKM.dat\")\n";
print $ofh "dev.off()\n";
close $ofh;
&process_cmd("R --no-save --no-restore --no-site-file --no-init-file -q < $Rscript");
exit(0);
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
return;
}
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