From 1d421ad2a39f40f9144955330d41dbc8e5724603 Mon Sep 17 00:00:00 2001
From: preecej <preecej@localhost>
Date: Sat, 7 Jan 2012 02:11:07 +0000
Subject: [PATCH] Fixed white-box paralogy bug (caused to even-numbered max
 paralogs); cleanly separated heat-map f(x) from custom BoxColor; spread
 heat-map increments more evenly across the gradient via fixed outer bounds

svn path=/; revision=255
---
 .../perl_singletons/pathway_gene_swapper.pl   | 35 ++++++++++++++-----
 1 file changed, 26 insertions(+), 9 deletions(-)

diff --git a/Personnel/preecej/perl_singletons/pathway_gene_swapper.pl b/Personnel/preecej/perl_singletons/pathway_gene_swapper.pl
index 490959f..5734596 100644
--- a/Personnel/preecej/perl_singletons/pathway_gene_swapper.pl
+++ b/Personnel/preecej/perl_singletons/pathway_gene_swapper.pl
@@ -6,7 +6,7 @@ Pathway Gene Swapper
 
 =head1 VERSION
 
-0.2
+0.3
 
 =head1 DESCRIPTION
 
@@ -36,7 +36,8 @@ replacement genes.
 
 Any new gene boxes may be painted with a custom color and border, and
 will be stacked and offset for ease of visualization (much like a deck
-of cards).
+of cards). If the heat-map option is invoked, the custom box color will
+be ignored and a red-blue gradient will be applied to all mapped boxes.
 
 =head1 FUTURE CHANGES
 
@@ -68,7 +69,12 @@ pathway_gene_swapper.pl -i INPUT_FILE -g GENE_MAPPING_FILE -c CONFIG_FILE -o OUT
 
 =head1 DEPENDENCIES and PREREQUISITES
 
-    - Non-standard Perl modules: Switch, Data::Dumper, XML::DOM
+    - Non-standard Perl modules:
+        Switch
+        Data::Dumper
+        XML::DOM
+        Graphics::ColorUtils
+        
     - The input file must be a valid GPML file
     - The CSV file must have a single-line column header.
         
@@ -323,14 +329,23 @@ sub set_gradient($)
     
     my %blue_red_gradient;
     my $max_grad = $_[0];
-    my $inc = sprintf("%.2f", 1/$max_grad);
-    my $count = 1;
+    my $inc = sprintf("%.2f", 0.98/($max_grad-1));
+
+    # set the fixed outer bounds
+    my $lower_bound = grad2rgb("blue_red",0.01);
+    $lower_bound =~ s/\#//;
+    $blue_red_gradient{1} = $lower_bound;
+
+    my $upper_bound = grad2rgb("blue_red",0.99);
+    $upper_bound =~ s/\#//;
+    $blue_red_gradient{$max_grad} = $upper_bound;
 
-    for (my $i=$inc; $i<=0.99; $i=$i+$inc) {
-        my $tmp_hex = grad2rgb("blue_red",$i);
+    # set the inner increments    
+    for (my $count = 2; $count<$max_grad; $count++) {
+        my $tmp_hex = grad2rgb("blue_red",($inc+0.01));
         $tmp_hex =~ s/\#//;
         $blue_red_gradient{$count} = $tmp_hex;
-        $count++;
+        $inc += $inc;
     }
     
     return %blue_red_gradient;
@@ -439,6 +454,8 @@ sub import_data
     if ($apply_homolog_heat)
     {
         %gradient = set_gradient($max_homolog_count);
+        if ($debug) { print "...<DEBUG: \%gradient>\n"
+            . Dumper(%gradient) . "\n\n"; }
     }
     
     print "Opening GPML pathway file and reading data...\n\n";
@@ -775,7 +792,7 @@ sub swap_genes
                     $curr_graphics->setAttribute("Width",$configs{"BoxWidth"});
 
                     # add "heat" to genes with multiple homologs
-                    if ($apply_homolog_heat && ($gene_suffix_counter > 0))
+                    if ($apply_homolog_heat)
                     {
                         $curr_graphics->setAttribute("FillColor", $gradient{scalar(@new_nodes_map)});
                         $curr_graphics->setAttribute("Color","8888ff");
-- 
2.34.1