--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_heatmap.R	Tue Nov 14 10:34:47 2017 -0500
@@ -0,0 +1,89 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library("optparse"))
+
+option_list <- list(
+    make_option(c("-i", "--input"), action="store", dest="input", help="IDEAS para file"),
+    make_option(c("-o", "--output"), action="store", dest="output", help="Output PDF file")
+)
+
+parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
+args <- parse_args(parser, positional_arguments=TRUE)
+opt <- args$options
+
+create_heatmap<-function(data_matrix, statecolor=NULL, markcolor=NULL, cols=c("white","dark blue")) {
+    k = dim(data_matrix)[2];
+    l = dim(data_matrix)[1];
+    p = (sqrt(9 + 8 * (k - 1)) - 3) / 2;
+    m = as.matrix(data_matrix[,1+1:p]/data_matrix[,1]);
+    marks = colnames(m);
+    rownames(m) = paste(1:l-1," (", round(data_matrix[,1] / sum(data_matrix[,1]) * 10000) / 100, "%)", sep="");
+    pdf(file=opt$output);
+    par(mar=c(6,1,1,6));
+    rg = range(m);
+    colors = 0:100/100*(rg[2]-rg[1])+rg[1];
+    my_palette = colorRampPalette(cols)(n=100);
+    defpalette = palette(my_palette);
+
+    plot(NA, NA, xlim=c(0,p+0.7), ylim=c(0,l), xaxt="n", yaxt="n", xlab=NA, ylab=NA, frame.plot=F);
+    axis(1, at=1:p-0.5, labels=colnames(m), las=2);
+    axis(4, at=1:l-0.5, labels=rownames(m), las=2);
+    rect(rep(1:p-1,l), rep(1:l-1,each=p), rep(1:p,l), rep(1:l,each=p), col=round((t(m)-rg[1])/(rg[2]-rg[1])*100));
+
+    if(length(statecolor)==0) {
+        if(length(markcolor)==0) {
+            markcolor=t(col2rgb(terrain.colors(ceiling(p))[1:p]));
+            for(i in 1:length(marks)) {
+                if(regexpr("h3k4me3",tolower(marks[i]))>0) {
+                    markcolor[i,]=c(255,0,0);
+                }
+                if(regexpr("h3k4me2",tolower(marks[i]))>0) {
+                    markcolor[i,]=c(250,100,0);
+                }
+                if(regexpr("h3k4me1",tolower(marks[i]))>0) {
+                    markcolor[i,]=c(250,250,0);
+                }
+                if(regexpr("h3k36me3",tolower(marks[i]))>0) {
+                    markcolor[i,]=c(0,150,0);
+                }
+                if(regexpr("h2a",tolower(marks[i]))>0) {
+                    markcolor[i,]=c(0,150,150);
+                }
+                if(regexpr("dnase",tolower(marks[i]))>0) {
+                    markcolor[i,]=c(0,200,200);
+                }
+                if(regexpr("h3k9ac",tolower(marks[i]))>0) {
+                    markcolor[i,]=c(250,0,200);
+                }
+                if(regexpr("h3k9me3",tolower(marks[i]))>0) {
+                    markcolor[i,]=c(100,100,100);
+                }
+                if(regexpr("h3k27ac",tolower(marks[i]))>0) {
+                    markcolor[i,]=c(250,150,0);
+                }
+                if(regexpr("h3k27me3",tolower(marks[i]))>0) {
+                    markcolor[i,]=c(0,0,200);
+                }
+                if(regexpr("h3k79me2",tolower(marks[i]))>0) {
+                    markcolor[i,]=c(200,0,200);
+                }
+                if(regexpr("h4k20me1",tolower(marks[i]))>0) {
+                    markcolor[i,]=c(50,200,50);
+                }
+                if(regexpr("ctcf",tolower(marks[i]))>0) {
+                    markcolor[i,]=c(200,0,250);
+                }
+            }
+        }
+        statecolor = stateColor(m, markcolor)[,2];
+    }
+    rect(rep(p+0.2,l), 1:l-0.8, rep(p+0.8,l), 1:l-0.2, col=statecolor);
+
+    palette(defpalette);
+    dev.off();
+    #return(statecolor);
+}
+
+# Read the input.
+data_matrix <- read.table(opt$input, header=T);
+create_heatmap(data_matrix);