--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cuffdiff_mds_plot.pl	Mon Feb 04 19:50:25 2013 -0500
@@ -0,0 +1,83 @@
+#!/usr/bin/perl -w
+
+###############################################################
+# cuffdiff_mds_plot.pl
+# John Garbe
+# Septmeber 2012
+#
+# Given a sample tracking file from cuffdiff2, convert it to 
+# the proper format for loading into R and generating an MDS plot
+#
+################################################################
+
+# check to make sure having correct files
+my $usage = "usage: cuffdiff_mds_plot.pl [TABULAR.in] [TABULAR.out] [PLOT.png]\n";
+die $usage unless @ARGV == 3;
+ 
+#get the input arguments
+my $inputFile = $ARGV[0];
+my $outputFile = $ARGV[1];
+my $plotFile = $ARGV[2];
+
+#Open files
+open (INPUT, "<", $inputFile) || die("Could not open file $inputFile \n");
+open (OUTPUT, ">", $outputFile) || die("Could not open file $outputFile \n");
+open (PLOT, ">", $plotFile) || die("Could not open file $plotFile \n");
+
+# header looks like this:
+# tracking_id condition replicate raw_frags internal_scaled_frags external_scaled_frags FPKM effective_length status
+my $header = <INPUT>;
+
+# read in the sample tracking file
+while (<INPUT>) {
+    chomp;
+    @line = split /\t/;
+    $tracking_id{$line[0]} = 1;
+    $sample = $line[1] . "-" . $line[2];
+    $fpkm{$sample}{$line[0]} = $line[6];
+}
+close(INPUT);
+
+@sorted_tracking_id = sort( keys(%tracking_id));
+
+# print out header
+foreach $tracking_id (@sorted_tracking_id) {
+    print OUTPUT "\t$tracking_id";
+}
+print OUTPUT "\n";
+
+# print out data
+foreach $sample (keys(%fpkm)) {
+    print OUTPUT "$sample";
+    
+    foreach $tracking_id (@sorted_tracking_id) {
+	print OUTPUT "\t$fpkm{$sample}{$tracking_id}";
+    }
+
+    print OUTPUT "\n";
+}
+close(OUTPUT);
+
+#variables to store the name of the R script file
+my $r_script = "cuffinks2mdf.r";
+
+open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n";
+print Rcmd "
+  datat <- read.table(\"$outputFile\"); 
+  cmd <- cmdscale(dist(datat)); 
+  png(filename=\"$plotFile\"); 
+  plot(cmd[,1], cmd[,2], type=\"n\", ann=FALSE); 
+  text(cmd[,1], cmd[,2], labels = rownames(datat)); 
+  title(main=\"Multidimensional Scaling Plot\"); 
+  title(xlab= \"Dimension 1\"); 
+  title(ylab= \"Dimension 2\"); 
+  dev.off();
+  #eof" . "\n";
+
+close Rcmd;
+
+
+system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
+#close the input and output files
+close(PLOT);
+