--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/regVariation/draw_stacked_barplots.pl	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,78 @@
+#!/usr/bin/perl -w
+
+# This program draws, in a pdf file, a stacked bars plot for different categories of data and for 
+# different criteria. For each criterion a stacked bar is drawn, such that the height of each stacked 
+# sub-bar represents the number of elements in each category satisfying that criterion.
+# The input consists of a TABULAR format file, where the left column represents the names of categories 
+# and the other columns are headed by the names of criteria, such that each data value in the file 
+# represents the number of elements in a certain category satisfying a certain criterion.
+# The output is a PDF file containing a stacked bars plot representing the number of elements in each 
+# category satisfying each criterion. The drawing is done using R code.  
+
+  
+use strict;
+use warnings;
+
+my $criterion;
+my @criteriaArray = ();
+my $criteriaNumber = 0;
+my $lineCounter = 0;
+
+#variable to store the names of R script file
+my $r_script;
+
+# check to make sure having correct files
+my $usage = "usage: draw_stacked_bar_plot.pl [TABULAR.in] [PDF.out] \n";
+die $usage unless @ARGV == 2;
+
+my $categoriesInputFile = $ARGV[0];
+
+my $categories_criteria_bars_plot_outputFile = $ARGV[1];
+
+#open the input file
+open (INPUT, "<", $categoriesInputFile) || die("Could not open file $categoriesInputFile \n"); 
+open (OUTPUT, ">", $categories_criteria_bars_plot_outputFile) || die("Could not open file $categories_criteria_bars_plot_outputFile \n");
+
+# R script to implement the drawing of a stacked bar plot representing thes significant motifs in each category of motifs 	
+#construct an R script file 
+$r_script = "motif_significance_bar_plot.r";
+open(Rcmd,">", $r_script) or die "Cannot open $r_script \n\n";
+print Rcmd "
+			#store the table content of the first file into a matrix
+			categoriesTable <- read.table(\"$categoriesInputFile\", header = TRUE);
+			categoriesMatrix <- as.matrix(categoriesTable); 
+			
+			
+			#compute the sum of elements in the column with the maximum sum in each matrix
+			columnSumsVector <- colSums(categoriesMatrix);
+			maxColumn <- max (columnSumsVector);
+			
+			if (maxColumn %% 10 != 0){
+				maxColumn <- maxColumn + 10;
+			}
+			
+			plotHeight = maxColumn/8;
+			criteriaVector <- names(categoriesTable);
+			
+			pdf(file = \"$categories_criteria_bars_plot_outputFile\", width = length(criteriaVector), height = plotHeight, family = \"Times\", pointsize = 12, onefile = TRUE);
+			
+			
+			
+			#draw the first barplot
+			barplot(categoriesMatrix, ylab = \"No. of elements in each category\", xlab = \"Criteria\", ylim = range(0, maxColumn), col = \"black\", density = c(10, 20, 30, 40, 50, 60, 70, 80), angle = c(45, 90, 135), names.arg = criteriaVector);
+			
+			#draw the legend
+			legendX = 0.2;
+			legendY = maxColumn;
+			
+			legend (legendX, legendY, legend = rownames(categoriesMatrix), density = c(10, 20, 30, 40, 50, 60, 70, 80), angle = c(45, 90, 135));
+   			
+   			dev.off();
+			
+			#eof\n";
+close Rcmd;	
+system("R --no-restore --no-save --no-readline < $r_script > $r_script.out");
+
+#close the input files
+close(OUTPUT);
+close(INPUT);