--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/create_heatmaps.R	Mon Feb 12 09:52:26 2018 -0500
@@ -0,0 +1,35 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library("optparse"))
+
+option_list <- list(
+    make_option(c("--input_dir"), action="store", dest="input_dir", help="IDEAS para files directory"),
+    make_option(c("--output_dir"), action="store", dest="output_dir", help="PDF output directory"),
+    make_option(c("--script_dir"), action="store", dest="script_dir", help="R script source directory"),
+    make_option(c("--in_training_mode"), action="store_true", dest="in_training_mode", default=FALSE, help="Flag for training mode")
+)
+
+parser <- OptionParser(usage="%prog [options] file", option_list=option_list);
+args <- parse_args(parser, positional_arguments=TRUE);
+opt <- args$options;
+
+heatmap_path = paste(opt$script_dir, "create_heatmap.R", sep="/");
+source(heatmap_path);
+
+if (opt$in_training_mode) {
+    ext = ".para0";
+    pattern = "\\.para0$";
+} else {
+    ext = ".para";
+    pattern = "\\.para$"
+}
+para_files = list.files(path=opt$input_dir, pattern=pattern, full.names=TRUE);
+for (i in 1:length(para_files)) {
+    para_file = para_files[i];
+    para_file_base_name = strsplit(para_file, split="/")[[1]][2];
+    output_file_base_name = gsub(ext, "", para_file_base_name);
+    output_file_name = paste(output_file_base_name, "state", i, "pdf", sep=".");
+    output_file_path = paste(opt$output_dir, output_file_name, sep="/");
+    data_frame = read.table(para_file, comment="!", header=T);
+    create_heatmap(data_frame, output_file_path);
+}