--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GALAXY_FILES/tools/EMBER/Make_Logo_Galaxy.pl	Thu Mar 22 13:49:52 2012 -0400
@@ -0,0 +1,254 @@
+#!/usr/bin/perl
+# make a logo-ish gnu-plottable representation of a score matrix
+
+use Getopt::Long;
+
+#
+# command line arguments
+#
+$options = "Usage: ./Make_Logo.pl <OPTIONS>
+	-m  .model file from EMBER (required)
+	-c  comparison list (used to make labels for the x-axis)
+	-o  output (required)
+	-a  include comparisons not used by EMBER (preceded by # in the .model file: y or n, default n)
+	-f  image file format (default 1)
+	     1 - eps
+	     2 - cgm
+	-k  key on/off (y or n, default y)
+	-lx x labels on/off (y or n, default y)
+	-ly y labels on/off (y or n, default y)
+	-yr set yrange manually (enter <min>,<max>, e.g. -1.5,3.5; default chosen automatically)
+\n";
+
+$m = "";
+$c = "";
+$o = "";
+$a = "n";
+$f = 1;
+$k = "y";
+$lx= "y";
+$ly= "y";
+$yr= "zzzzzzzzzzz";
+
+GetOptions('m=s' => \$m,
+	   'c=s' => \$c,
+	   'o=s' => \$o,
+	   'a=s' => \$a,
+	   'f=i' => \$f,
+	   'k=s' => \$k,
+	   'lx=s'=> \$lx,
+	   'ly=s'=> \$ly,
+	   'yr=s'=> \$yr
+) || die "\n$options";
+
+if( $m eq "" ){
+	print "Error: set a value for -m\n\n$options";
+	exit;
+}
+if( $o eq "" ){
+	print "Error: set a value for -o\n\n$options";
+	exit;
+}
+if( $f != 1 && $f != 2 ){
+	print "Error: set -f to be 1 or 2\n\n$options";
+	exit;
+}
+if( $a ne "y" && $a ne "n" ){
+	print "Error: set -a to be y or n\n\n$options";
+	exit;
+}
+if( $k ne "y" && $k ne "n" ){
+	print "Error: set -k to be y or n\n\n$options";
+	exit;
+}
+if( $lx ne "y" && $lx ne "n" ){
+	print "Error: set -lx to be y or n\n\n$options";
+	exit;
+}
+if( $ly ne "y" && $ly ne "n" ){
+	print "Error: set -ly to be y or n\n\n$options";
+	exit;
+}
+if( $yr ne "zzzzzzzzzzz" && $yr !~ /,/ ){
+	print "Error: if setting -yr, choose a range delimited by a comma\n\n$options";
+	exit;
+}
+
+@parts = split('\.',$m);
+$name = $o;
+#for($i=1; $i< $#parts; $i++){
+#	$name = sprintf("%s.%s", $name, $parts[$i]);
+#}
+
+#
+# read in matrix
+#
+open(IN,"$m") || die "Error: can't open file $m\n";
+@re = ();
+@mat = ();
+
+# burn 2 lines
+$line = <IN>;
+$line = <IN>;
+
+@coloffs = ();
+while($line = <IN>){
+	chomp($line);
+	@parts = split(' ',$line);
+	if( ($a eq "n" && $parts[0] !~ /#/) || $a eq "y" ){
+		push(@coloffs, 1 );
+		($ind, $reval) = split(',', $parts[0]);
+		if( $reval eq "nan" ){$reval = 0.0;}
+		push(@re, $reval);
+		@tmp = ();
+		for($i=1; $i<= $#parts; $i++){
+			if( $parts[$i] eq "NA" ){
+				$parts[$i] = 0.0;
+			}
+			push(@tmp, $parts[$i]);
+		}
+		push(@mat, [@tmp] );
+	}
+	else{
+		push(@coloffs, 0);
+	}
+}
+close(IN);
+
+#
+# rescale matrix so it's between 0 and 1, then multiply by re
+#
+for($i=0; $i<= $#mat; $i++){
+	$min = $mat[$i][0];
+	$max = $mat[$i][0];
+	for($j=1; $j< 5; $j++){
+		if( $min > $mat[$i][$j] ){ $min = $mat[$i][$j]; }
+		if( $max < $mat[$i][$j] ){ $max = $mat[$i][$j]; }
+	}
+	for($j=0; $j< 5; $j++){
+		if( $max != $min ){
+			$mat[$i][$j] = $re[$i]*(($mat[$i][$j]-$min)/($max-$min));
+		}
+		else{
+			$mat[$i][$j] = 0;
+		}
+	}
+}
+	
+
+#
+# print out in stacked format
+#
+open(OUT,">$name.logo");
+for($i=0; $i<= $#mat; $i++){
+	$posn = ($mat[$i][0] + $mat[$i][1] + 0.5*$mat[$i][2]);
+	printf OUT ("%f ", -0.5*$mat[$i][2]);
+	printf OUT ("%f ", -$mat[$i][3]);
+	printf OUT ("%f ", -$mat[$i][4]);
+	printf OUT ("%f ", 0.5*$mat[$i][2]);
+	printf OUT ("%f ", $mat[$i][1]);
+	printf OUT ("%f ", $mat[$i][0]);
+	printf OUT ("0 0 0 0 0\n");
+}
+close(OUT);
+
+#
+# make gnu-plotable file
+#
+
+# possibly read in conditions to define xtics
+$tics = "";
+if( $c ne "" ){
+	open(IN,"$c") || die "Error: can't open file $c\n";
+	@comps = ();
+	$i = 0;
+	while($line = <IN>){
+		chomp($line);
+		@parts = split(' ',$line);
+		if( $#parts != 1 ){
+			print "Error: comparisons list does not have 2 columns\n";
+			exit;
+		}
+		if( $coloffs[$i] == 1 ){
+			$val = sprintf("%s vs %s", $parts[0], $parts[1]);
+			push(@comps, $val);
+		}
+		$i++;
+	}
+	$tics = "set xtics(\"$comps[0]\" 0";
+	for($i=1; $i<= $#comps; $i++){
+		$tics = sprintf("%s, \"%s\" %i", $tics, $comps[$i], $i);
+	}
+	$tics = sprintf("%s)\nset xtics rotate by -45", $tics);
+}
+
+# choose format
+if( $f == 1 ){
+	$format = "postscript eps color 24";
+	$suff = "eps";
+}
+if( $f == 2 ){
+	$format = "cgm \"Helvetica\" 14";
+	$suff = "cgm";
+}
+
+# set xrange min and max
+$min = -0.5;
+$max = $#mat+0.5;
+
+# possibly turn off key, xlabel, ylabel
+$keytoggle = "";
+$xtoggle = "";
+$ytoggle = "";
+if( $k eq "n" ){
+	$keytoggle = "unset key";
+}
+if( $lx eq "n" ){
+	$xtoggle = "unset xtics";
+}
+if( $ly eq "n" ){
+	$ytoggle = "unset ylabel";
+}
+
+# possibly set yrange
+$yrange = "";
+if( $yr ne "zzzzzzzzzzz" ){
+	@parts = split(',',$yr);
+	if( $#parts != 1 ){
+		print "Error: more than two fields in your -yr value\n";
+		exit;
+	}
+	$yrange = sprintf("set yrange [%f:%f]", $parts[0], $parts[1]);
+}
+
+@lines = (  "#!/bin/sh",
+            "gnuplot << EOF",
+            "reset",
+            "set style fill solid 1.00 noborder",
+            "set style histogram rowstacked",
+            "set style data histograms",
+            "set ylabel \"Bits x direction of regulation\"",
+            "set key outside",
+            "set xrange [$min: $max]",
+            "$tics",
+            "$keytoggle",
+            "$xtoggle",
+            "$ytoggle",
+            "$yrange",
+            "set terminal $format",
+            "set output \'$o\'",
+            "plot \'$name.logo\' u 1 notitle lc rgbcolor \"#000000\", \'\' u 2 notitle lc rgbcolor \"#008800\", \'\' u 3 notitle lc rgbcolor \"#00FF00\", \'\' u 7 t \"++\" lc rgbcolor \"#FF0000\", \'\' u 8 t \"+\" lc rgbcolor \"#880000\", \'\' u 9 t \"0\" lc rgbcolor \"#000000\", \'\' u 10 t \"-\" lc rgbcolor \"#008800\", \'\' u 11 t \"--\" lc rgbcolor \"#00FF00\", \'\' u 4 notitle lc rgbcolor \"#000000\", \'\' u 5 notitle lc rgbcolor \"#880000\", \'\' u 6 notitle lc rgbcolor \"#FF0000\"",
+            "EOF"
+	 );
+
+$command = sprintf("%s\n", $lines[0]);
+for($i=1; $i<= $#lines; $i++){
+	$command = sprintf("%s%s\n", $command, $lines[$i]);
+}
+
+system("$command");
+
+
+
+
+