--- a/ks_distribution.R	Fri Jun 23 15:00:42 2017 -0400
+++ b/ks_distribution.R	Mon Jun 26 07:51:11 2017 -0400
@@ -7,7 +7,7 @@
     make_option(c("-k", "--kaks_input"), action="store", dest="kaks_input", help="KaKs analysis input dataset"),
     make_option(c("-n", "--num_comp"), action="store", dest="num_comp", type="integer", help="Number of significant components in the Ks distribution"),
     make_option(c("-o", "--output"), action="store", dest="output", help="Output dataset"),
-    make_option(c("-r", "--colors"), action="store", default=NA, help="List of component colors")
+    make_option(c("-r", "--colors"), action="store", default=[], help="List of component colors")
 )
 
 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
@@ -82,7 +82,7 @@
     barplot(nc, space=0.25, offset=0, width=0.04, xlim=c(0, max_ks), ylim=c(0, ymax), col="lightpink1", border="lightpink3")
     # Add x-axis.
     axis(1)
-    if is.na(colors)
+    if (length(colors) == 0)
     {
         color <- c('red', 'yellow', 'green', 'black', 'blue', 'darkorange')
     }
@@ -96,27 +96,27 @@
             color <- c(color, item)
         }
         num_colors_specified = length(color)
-        if num_colors_specified < num_components:
+        if (num_colors_specified < num_components):
         {
             for (i in num_colors_specified:num_components)
             {
-                if !(any(color=='red')
+                if !(any(color=='red'))
                 {
                     color <- c(color, 'red')
                 }
-                else if !(any(color=='yellow')
+                else if !(any(color=='yellow'))
                 {
                     color <- c(color, 'yellow')
                 }
-                else if !(any(color=='green')
+                else if !(any(color=='green'))
                 {
                     color <- c(color, 'green')
                 }
-                else if !(any(color=='black')
+                else if !(any(color=='black'))
                 {
                     color <- c(color, 'black')
                 }
-                else if !(any(color=='blue')
+                else if !(any(color=='blue'))
                 {
                     color <- c(color, 'blue')
                 }