--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/population_structure.r	Mon Apr 09 12:03:06 2012 -0400
@@ -0,0 +1,19 @@
+library(RColorBrewer)
+
+args = commandArgs(trailingOnly=TRUE)
+q_file = args[[1]]
+output_file = args[[2]]
+populations = args[[3]]
+
+tbl <- read.table(q_file)
+
+if ( populations >= 3 && populations <= 12 ) {
+    colors = brewer.pal(populations, 'Paired')
+} else {
+    colors = rainbow(populations)
+}
+
+pdf(file=output_file, onefile=TRUE, width=7, height=3)
+barplot(t(as.matrix(tbl)), col=colors, xlab="Individual #", ylab="Ancestry", border=NA)
+
+dev.off()