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Merge pull request #869 from broadinstitute/gg_fix_vqsr_plots_GSA-860 

Switched VQSR tranches plot ordering rule
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Geraldine Van der Auwera 2015-03-13 10:46:55 -04:00
parent 3276a964f4 aa4084d42f
commit 7681e89454
1 changed files with 1 additions and 1 deletions
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public/gatk-tools-public/src/main/resources/org/broadinstitute/gatk/tools/walkers/variantrecalibration/plot_Tranches.R
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@ -41,7 +41,7 @@ leftShift <- function(x, leftValue = 0) {
# Tranches plot # Tranches plot
# ----------------------------------------------------------------------------------------------- # -----------------------------------------------------------------------------------------------
data2 = read.table(tranchesFile,sep=",",head=T) data2 = read.table(tranchesFile,sep=",",head=T)
data2 = data2[order(data2$novelTiTv, decreasing=F),] data2 = data2[order(data2$targetTruthSensitivity, decreasing=T),]
#data2 = data2[order(data2$FDRtranche, decreasing=T),] #data2 = data2[order(data2$FDRtranche, decreasing=T),]
cols = c("cornflowerblue", "cornflowerblue", "darkorange", "darkorange") cols = c("cornflowerblue", "cornflowerblue", "darkorange", "darkorange")
density=c(20, -1, -1, 20) density=c(20, -1, -1, 20)