--- a/create_heatmap.R	Fri Dec 15 16:48:18 2017 -0500
+++ b/create_heatmap.R	Fri Dec 15 16:48:53 2017 -0500
@@ -3,8 +3,8 @@
 suppressPackageStartupMessages(library("optparse"))
 
 option_list <- list(
-    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")
+            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)
@@ -19,9 +19,9 @@
     num_rows = dim(data_frame)[1];
     p = (sqrt(9 + 8 * (num_columns - 1)) - 3) / 2;
     data_matrix = as.matrix(data_frame[,1+1:p] / data_frame[,1]);
-    column_names(data_matrix) = column_names(data_frame)[1+1:p];
-    marks = column_names(data_matrix);
-    row_names(data_matrix) = paste(1:num_rows, " (", round(data_frame[,1]/sum(data_frame[,1])*10000)/100, "%)", sep="");
+    colnames(data_matrix) = colnames(data_frame)[1+1:p];
+    marks = colnames(data_matrix);
+    rownames(data_matrix) = paste(1:num_rows, " (", round(data_frame[,1]/sum(data_frame[,1])*10000)/100, "%)", sep="");
 
     # Open the output PDF file.
     pdf(file=output_file_name);
@@ -35,9 +35,9 @@
     my_palette = colorRampPalette(c("white", "dark blue"))(n=100);
     defpalette = palette(my_palette);
     # Plot the heatmap for the current .para / .state combination.
-    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=column_names(data_matrix), las=2);
-    axis(4, at=1:num_rows-0.5, labels=row_names(data_matrix), las=2);
+    plot(NA, NA, xlim=c(0, p+0.7), ylim=c(0, num_rows), xaxt="n", yaxt="n", xlab=NA, ylab=NA, frame.plot=F);
+    axis(1, at=1:p-0.5, labels=colnames(data_matrix), las=2);
+    axis(4, at=1:num_rows-0.5, labels=rownames(data_matrix), las=2);
     rect(rep(1:p-1, num_rows), rep(1:num_rows, each=p), rep(1:p, num_rows), rep(1:num_rows, each=p),
             col=round((t(data_matrix)-min_max_vector[1])/(min_max_vector[2]-min_max_vector[1])*100));
     markcolor = t(col2rgb(terrain.colors(ceiling(p))[1:p]));