--- a/create_heatmap.R	Fri Nov 17 13:13:27 2017 -0500
+++ b/create_heatmap.R	Fri Nov 17 13:13:37 2017 -0500
@@ -3,8 +3,8 @@
 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")
+    make_option(c("-i", "--input_dir"), action="store", dest="input_dir", help="IDEAS para files directory"),
+    make_option(c("-o", "--output_dir"), action="store", dest="output_dir", help="PDF output directory")
 )
 
 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
@@ -38,7 +38,7 @@
     return(rt);
 }
 
-create_heatmap<-function(data_frame, statecolor=NULL, markcolor=NULL, cols=c("white","dark blue")) {
+create_heatmap<-function(data_frame, output_file_name, statecolor=NULL, markcolor=NULL, cols=c("white","dark blue")) {
     k = dim(data_frame)[2];
     l = dim(data_frame)[1];
     p = (sqrt(9 + 8 * (k - 1)) - 3) / 2;
@@ -46,10 +46,10 @@
     colnames(data_matrix) = colnames(data_frame)[1+1:p];
     marks = colnames(data_matrix);
     rownames(data_matrix) = paste(1:l," (", round(data_frame[,1] / sum(data_frame[,1]) * 10000) / 100, "%)", sep="");
-    pdf(file=opt$output);
-    par(mar=c(6,1,1,6));
+    pdf(file=output_file_name);
+    par(mar=c(6, 1, 1, 6));
     rg = range(data_matrix);
-    colors = 0:100/100*(rg[2]-rg[1])+rg[1];
+    colors = 0:100 / 100 * (rg[2] - rg[1]) + rg[1];
     my_palette = colorRampPalette(cols)(n=100);
     defpalette = palette(my_palette);
 
@@ -110,6 +110,12 @@
     dev.off();
 }
 
-# Read the input.
-data_frame <- read.table(opt$input, comment="!", header=T);
-create_heatmap(data_frame);
+# Read the inputs.
+para_files <- list.files(path=input_dir, pattern="*.para", full.names=TRUE);
+for (i in 1:length(para_files) {
+    para_file <- para_files[i];
+    para_file_base_name <- strsplit(para_file, ".para", fixed=TRUE)[1];
+    output_file_name <- paste(opt$output_dir, "/", para_file_base_name, ".pdf", sep="");
+    data_frame <- read.table(para_file, comment="!", header=T);
+    create_heatmap(data_frame, output_file_name);
+}