--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plotPrediction.R	Fri Oct 28 08:47:18 2016 -0400
@@ -0,0 +1,30 @@
+########################################################
+#
+# creation date : 07/06/16
+# last modification : 07/06/16
+# author : Dr Nicolas Beaume
+# owner : IRRI
+#
+########################################################
+
+library("miscTools")
+# scatterplot of the prediction vs target
+r2.plot <- function(true, predicted) {
+  # the scatterplot
+  plot(true, predicted, xlab="trait value", ylab="predicted value", main="", pch=16, 
+       ylim=c(min(min(true), min(predicted)), max(max(true), max(predicted))))
+  # add a red lines with ideal case
+  lines(true, true, col="red")
+}
+
+############################ main #############################
+# load argument
+cmd <- commandArgs(trailingOnly = T)
+source(cmd[1])
+# load prediction and target
+phenotype <- read.table(phenotype, sep="\t", h=T)[,1] 
+predicted <- read.table(predicted, sep = "\t", h=T)[,2]
+# plot in a pdf that will be available in galaxy history panel
+pdf(out)
+r2.plot(phenotype, predicted = predicted)
+dev.off()
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