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