Heat map feature complete.

svn path=/; revision=188

diff --git a/preecej/perl_singletons/pathway_gene_swapper.pl b/preecej/perl_singletons/pathway_gene_swapper.pl
index c8a8bb74bcf3ed034b6fa942aaca9da31f7cff8e..4b0a28808988b7830239b9ed300673d9396eb72b 100644 (file)
--- a/preecej/perl_singletons/pathway_gene_swapper.pl
+++ b/preecej/perl_singletons/pathway_gene_swapper.pl
@@ -22,8 +22,9 @@ that group will extend to any replacement genes. If no group
 existed previously, and multiple replacement gene boxes are required,
 a new group will be created.
 
-If an original gene had multiple instances displayed on the pathway
-diagram, each instance will be subjected to the replacement process.
+If an original gene had multiple instances (homologs) displayed on the pathway
+diagram, each instance will be subjected to the replacement process. There
+is a "heat-map" option avaliable to help highlight homolog sets. 
 
 There is also an option to read in an extra column of gene symbols, if the 
 user wishes to provide their own. Otherwise, the application will 
@@ -43,8 +44,6 @@ Add a comment containing the NCBI species id of the new homolog (for
 the purpose of multi-species pathway comparison or host-pathogen 
 interaction diagrams).
 
-Add a "heat-map" effect by making large paralog sets "hotter". 
-
 =head1 USAGE
 
 pathway_gene_swapper.pl -i INPUT_FILE -g GENE_FILE -c CONFIG_FILE -o OUTPUT_FILE -L -v -G -d
@@ -58,8 +57,8 @@ pathway_gene_swapper.pl -i INPUT_FILE -g GENE_FILE -c CONFIG_FILE -o OUTPUT_FILE
         (NOTE: if no path supplied for input files, 
         current working directory is assumed)
     -s  use provided gene symbols instead of config file's LabelPrefix
-    -h  apply a heat-map to any multi-mapped set of paralogs
-        (NOTE: precludes custom box-coloring for paralogs)
+    -h  apply a heat-map to any multi-mapped set of homologs
+        (NOTE: precludes custom box-coloring for homologs)
     -L  Remove literature references.
     -v  View verbose information
     -G  Display GPML input/output documents
@@ -149,6 +148,7 @@ my %swap_genes; # original and swapped genes
 my $gpml_doc; # imported GPML data for manipulation and output
 my %unmapped_genes; # original genes not mapped to homologs 
 my %gradient; # blue-red gradient used for opt. heat map box-coloring  
+my $max_homolog_count = 0; # count for heat map calibration 
 
 $Data::Dumper::Pad = "... "; 
 
@@ -302,41 +302,34 @@ sub init
 
 
 # ---------------------------------------------------------------------------
-=item B<void set_gradient()>
-Sets the blue-red gradient
+=item B<hash set_gradient(int $max_homolog_count)>
+Accepts: The maximum number of homologs for one gene in this data set  
+Creates a blue-red gradient and stores it in a hash.
+Returns: A hash of RRGGBB color values, keyed to the number set of 
+possible homologs (1..n).
 =cut
 # ---------------------------------------------------------------------------
 sub set_gradient($)
 {
     my @blue_red_array;
+
     for (my $i=0; $i<256; $i++) {
         push @blue_red_array, [$i, 0, (255-$i)];
     }
     
-    # print Dumper(@blue_red_array) . "\n\n";
-    
     register_gradient("blue_red",\@blue_red_array);
     
-    # print "[Available Gradients]";
-    # print Dumper(available_gradients()) . "\n\n";
-    # print Dumper(gradient("blue_red")) . "\n\n";
-    
     my %blue_red_gradient;
-    
     my $max_grad = $_[0];
     my $inc = sprintf("%.2f", 1/$max_grad);
     my $count = 1;
-    # print "Increment: $inc\n"; 
+
     for (my $i=$inc; $i<=0.99; $i=$i+$inc) {
-        #print "$i\n";
-        #print grad2rgb("blue_red",$i) . "\n";
         my $tmp_hex = grad2rgb("blue_red",$i);
-        $tmp_hex =~ s/\#//; 
+        $tmp_hex =~ s/\#//;
         $blue_red_gradient{$count} = $tmp_hex;
         $count++;
     }
-    # print "[My Gradient Hash]\n";
-    print Dumper(%blue_red_gradient) . "\n\n";
     
     return %blue_red_gradient;
 }
@@ -402,7 +395,6 @@ sub import_data
     
     # determine the original gene(s) with the highest # of homologs in the new 
     # gene set
-    my $max_homolog_count = 0; # count for heat map calibration 
     my @most_popular_genes; # identity of the gene(s) with the highest number of homologs 
     foreach my $orig_gene_key (keys %swap_genes)
     {
@@ -723,7 +715,9 @@ sub swap_genes
                 # makes sure each box is increasingly offset from the original
                 # (in all three dimensions)
                 my $offset_multiplier = 0;
-                my $gene_suffix_counter = 0; # used to affix numbers to multiple new gene symbols 
+                my $gene_suffix_counter = 0; # used to affix numbers to multiple new gene symbols
+                # used to track the application of the gradient in reverse
+                my $new_nodes_dec = scalar(@new_nodes_map) + 1;  
                 
                 # for new nodes ary
                 for (@new_nodes_map)
@@ -731,6 +725,7 @@ sub swap_genes
                     if (scalar(@new_nodes_map) > 1)
                     {
                         $gene_suffix_counter++;
+                        $new_nodes_dec--;
                     }
                     
                     my $curr_new_node = $$_[0];
@@ -779,18 +774,19 @@ sub swap_genes
                     # change box width and colors (<Graphics...Color="4488ff" ... />)
                     my $curr_graphics = ($curr_new_node->getElementsByTagName("Graphics"))[0];
                     $curr_graphics->setAttribute("Width",$configs{"BoxWidth"});
-                    if ($configs{"BoxBorder"}) {
-                        $curr_graphics->setAttribute("Color",$configs{"BoxBorder"}); }
 
-                    # add "heat" to genes with multiple paralogs
+                    # add "heat" to genes with multiple homologs
                     if ($apply_homolog_heat && ($gene_suffix_counter > 0))
                     {
-                        $curr_graphics->setAttribute("FillColor",$gradient{$gene_suffix_counter});
+                        $curr_graphics->setAttribute("FillColor", $gradient{$new_nodes_dec});
+                        $curr_graphics->setAttribute("Color","8888ff");
                     }
                     else
                     {
                         if ($configs{"BoxColor"}) {
                             $curr_graphics->setAttribute("FillColor",$configs{"BoxColor"}); }
+                        if ($configs{"BoxBorder"}) {
+                            $curr_graphics->setAttribute("Color",$configs{"BoxBorder"}); }
                     }
     
                     if ($is_first_homolog)