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|
#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling);
use File::Basename;
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use CanvasXpress::Heatmap;
use CGI;
use CGI::Carp qw(fatalsToBrowser);
my $usage = <<__EOUSAGE__;
###################################################################################
#
# -R <string> the filename for the stored RData (file.all.RData)
#
###################################################################################
__EOUSAGE__
;
my $help_flag = 0;
my $R_data_file;
&GetOptions ( 'h' => \$help_flag,
'R=s' => \$R_data_file,
);
if ($help_flag) {
die $usage;
}
unless ($R_data_file) {
die $usage;
}
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd $cmd died with ret $ret";
}
return;
}
main: {
unless (-s $R_data_file) {
die "Error, cannot find pre-existing R-session data as file: $R_data_file";
}
my $matrix_data = "$R_data_file.ordered_gene_matrix";
my $gene_tree = "$R_data_file.gene_nodist_tree";
my $gene_tree_text;
if (! (-s $matrix_data && -s $gene_tree)) {
# generate required files.
my $R_script = "__tmp_write_heatmap_html.R";
open (my $ofh, ">$R_script") or die "Error, cannot write to file $R_script";
print $ofh "source(\"/usr/lib/trinityrnaseq/Analysis/DifferentialExpression/R/get_cluster_info.R\")\n";
print $ofh "get_cluster_info(\"$R_data_file\")\n";
close $ofh;
&process_cmd("R --no-save --no-restore --no-site-file --no-init-file -q --slave < $R_script");
open (my $fh, $matrix_data) or die "Error, cannot open file $matrix_data";
my $header = <$fh>;
chomp $header;
my @gene_ids;
my $counter = 0;
while (<$fh>) {
chomp;
my ($gene_id, @expr_vals) = split(/\t/);
push (@gene_ids, $gene_id);
}
close $fh;
$gene_tree_text = `cat $gene_tree`;
$gene_tree_text =~ s/;\s+$//g;
$gene_tree_text = &convert_ids($gene_tree_text, \@gene_ids);
open ($ofh, ">$gene_tree.ids_converted") or die $!;
print $ofh $gene_tree_text;
close $ofh;
}
else {
$gene_tree_text = `cat $gene_tree.ids_converted`;
}
#############################################
## Generate HTML Heatmap ###################
#############################################
print "<html>\n";
my @sample_ids;
my @feature_matrix;
open (my $fh, $matrix_data) or die "Error, cannot open file $matrix_data";
my $header = <$fh>;
chomp $header;
@sample_ids = split(/\t/, $header);
my $counter = 0;
while (<$fh>) {
chomp;
my ($gene_id, @expr_vals) = split(/\t/);
push (@feature_matrix, [$gene_id, @expr_vals]);
$counter++;
# if ($counter > 10) { last; }
}
close $fh;
my %heatmap_inputs = ( samples => [@sample_ids],
value_matrix => [@feature_matrix],
feature_tree => $gene_tree_text,
);
print &CanvasXpress::Heatmap::draw(%heatmap_inputs);
#print "cx.clusterVariables();\n";
#print "cx.clusterSamples();\n";
print "</html>\n";
exit(0);
}
####
sub convert_ids {
my ($gene_tree_text, $gene_ids_aref) = @_;
my $counter = 0;
foreach my $gene_id (@$gene_ids_aref) {
$counter++;
$gene_tree_text =~ s/([\(,])$counter([\),])/$1$gene_id$2/ or die "Error, no replacement for identifier $counter, $gene_id";
}
return($gene_tree_text);
}
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