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comparison plotPrediction.R @ 36:d961f726b619 draft

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author nicolas
date Tue, 25 Oct 2016 14:41:04 -0400
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35:2e66da6efc41 36:d961f726b619
1 ########################################################
2 #
3 # creation date : 07/06/16
4 # last modification : 07/06/16
5 # author : Dr Nicolas Beaume
6 # owner : IRRI
7 #
8 ########################################################
9
10 library("miscTools")
11 # scatterplot of the prediction vs target
12 r2.plot <- function(true, predicted) {
13 # the scatterplot
14 plot(true, predicted, xlab="trait value", ylab="predicted value", main="", pch=16,
15 ylim=c(min(min(true), min(predicted)), max(max(true), max(predicted))))
16 # add a red lines with ideal case
17 lines(true, true, col="red")
18 }
19
20 ############################ main #############################
21 # load argument
22 cmd <- commandArgs(trailingOnly = T)
23 source(cmd[1])
24 # load prediction and target
25 phenotype <- read.table(phenotype, sep="\t", h=T)[,1]
26 predicted <- read.table(predicted, sep = "\t", h=T)[,2]
27 # plot in a pdf that will be available in galaxy history panel
28 pdf(out)
29 r2.plot(phenotype, predicted = predicted)
30 dev.off()