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#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use POSIX qw (floor ceil);
my $usage = <<__EOUSAGE__;
########################################################################
#
# --matrix <string> matrix file
#
#
########################################################################
#
# Dimensions:
#
# --width_per_plot <float> default: 2.5
# --height_per_plot <float> default: 2.5
#
# Layout:
#
# --plots_per_row <int> default: 2
# --plots_per_col <int> default: 3
#
# Misc:
#
# --barplot
# --log2
#
########################################################################
__EOUSAGE__
;
my $width_per_plot = 2.5;
my $height_per_plot = 2.5;
my $matrix;
my $plots_per_row = 2;
my $plots_per_col = 3;
my $help_flag;
my $barplot_flag = 0;
my $log2_flag = 0;
&GetOptions( 'h' => \$help_flag,
'matrix=s' => \$matrix,
'width_per_plot=f' => \$width_per_plot,
'height_per_plot=f' => \$height_per_plot,
'plots_per_row=i' => \$plots_per_row,
'plots_per_col=i' => \$plots_per_col,
'barplot' => \$barplot_flag,
'log2_flag' => \$log2_flag,
);
if ($help_flag) {
die $usage;
}
unless ($matrix) {
die $usage;
}
main: {
my $R_script = "__tmp_plot_clusters.R";
open (my $ofh, ">$R_script") or die "Error, cannot write to $R_script";
#print $ofh "postscript(file=\"my_cluster_plots.eps\", horizontal=FALSE, width=$width, height=$height, paper=\"special\")\n";
print $ofh "pdf(file=\"$matrix.per_gene_plots.pdf\")\n";
print $ofh "par(mfrow=c($plots_per_col, $plots_per_row))\n";
#print $ofh "# png(file=\"my_cluster_plots.png\");\n";
print $ofh "all_data = read.table(file=\"$matrix\", header=T, com=\'\', row.names=1)\n";
print $ofh "gene_names = rownames(all_data)\n";
if ($log2_flag) {
print $ofh "all_data = log2(all_data+1);\n";
}
print $ofh "for (i in 1:length(all_data[,1])) {\n";
print $ofh " data = all_data[i,]\n";
print $ofh " ymin = min(data); ymax = max(data);\n";
if ($barplot_flag) {
print $ofh " barplot(as.numeric(data), cex.names=0.75, names.arg=colnames(data), las=2, main=gene_names[i])\n";
}
else {
print $ofh " plot(as.numeric(data), type='l', ylim=c(ymin,ymax), main=gene_names[i], col='blue', xaxt='n', xlab='', ylab='')\n";
print $ofh " axis(side=1, at=1:length(data), labels=colnames(all_data), las=2)\n";
}
print $ofh "}\n";
print $ofh "dev.off()\n";
close $ofh;
&process_cmd("R --no-save --no-restore --no-site-file --no-init-file -q < $R_script");
exit(0);
}
####
sub process_cmd {
my ($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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