--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pattern_plots.r	Mon Aug 22 07:00:23 2016 -0400
@@ -0,0 +1,17 @@
+library(ggplot2)
+library(reshape2)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+input.file = args[1] #the data that's get turned into the "SHM overview" table in the html report "data_sum.txt"
+plot1.file = args[2] 
+plot2.file = args[3]
+plot3.file = args[4]
+
+dat = read.table(input.file, header=F, sep=",", quote="", stringsAsFactors=F, fill=T)
+
+classes = c("ca", "ca1", "ca2", "cg", "cg1", "cg2", "cg3", "cg4", "cm")
+xyz = c("x", "y", "z")
+
+names(dat) = c("info", paste(rep(classes, each=3), xyz, sep="."), paste("un", xyz, sep="."), paste("all", xyz, sep="."))
+