Rをbatch modeで実行してFigureをたくさん描く

gistfile1.pl

#!/usr/bin/env perl

use strict;
use warnings;

use 5.16.0;

##
## This script makes figures that phosphorylation sites given specify output data by R batch mode.
## 

if ( scalar @ARGV != 1 ) {
    die "Usage:\n\tperl $0 <specify directory>\n\n";
}

my $path = shift;
opendir my $dir, $path || die "Cant load $path";
my @files;
foreach ( readdir $dir ) {
    next if /^\.{1,2}$/;
    my ($file) = split /\./, $_;
    push @files, $file;
}

for my $file ( @files ) {
    my $script = "/home/soh.i/genokai/R_plot/$file.R";
    open my $out, '>', "$script" || die $!;
    print $out <<EOF;
#Fig B
png("$file.B.png", width=800, height=500)
data<-read.table("$file.data", header=T)
labB<-c("B_PhosphoSerines", "B_ControlSerines")
bp<-as.matrix(data\$B_PhosphoSerines)
bc<-as.matrix(data\$B_ControlSerines)
C=cbind(bp, bc)
barplot(t(C), beside=T, legend=labB, names=data\$AA, col=c("red", "black"), ylab="Amino acid incidence(%)", xlab="Amino acid", main="$file")
dev.off()

#Fig C
png("$file.C.png", width=800, height=500)
labC<-c("C_PhosphoSerines", "C_ControlSerines")
cp<-as.matrix(data\$C_PhosphoSerines)
cc<-as.matrix(data\$C_ControlSerines)
C=cbind(bp, bc)
barplot(t(C), beside=T, legend=labC, names=data\$AA, col=c("red", "black"), ylab="Enrichment relative to overall AA abundance", xlab="Amino acid", main="$file")
dev.off()

#Fig D
png("$file.D.png", width=800, height=500)
ratio<-as.matrix(data\$cSer\.pSer)
C=cbind(ratio)
barplot(t(C-1), beside=T, names=data\$AA, col=c("red", "black"), ylab="Enrichment, pSer:Control Ser", xlab="Amino acid", main="$file")
dev.off()

EOF

close $out;
system("R --vanilla --slave < $script");

}