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gatk-3.8
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Minor fixes 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5988 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-06-13 20:50:34 +00:00
parent e0ed30681e
commit a837a49328
1 changed files with 6 additions and 6 deletions
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12
R/exomePostQC.R
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@ -1,8 +1,8 @@
library("gsalib", lib.loc="/Users/depristo/Desktop/broadLocal/GATK/trunk/R/") library("gsalib", lib.loc="/Users/depristo/Desktop/broadLocal/GATK/trunk/R/")
require("ggplot2") require("ggplot2")
require("gplots")
args = commandArgs(TRUE); args = commandArgs(TRUE)
onCMDLine = ! is.na(args[1]) onCMDLine = ! is.na(args[1])
LOAD_DATA = F LOAD_DATA = F
@ -21,7 +21,7 @@ if ( onCMDLine ) {
highlightSamples = c() highlightSamples = c()
} else { } else {
ProjectName = "InDevelopmentInR" ProjectName = "InDevelopmentInR"
preQCFile <- "~/Desktop/broadLocal/GATK/trunk/qcTestData/GoT2D_exomes_batch_005.cleaned.snps_and_indels.filtered.annotated.preQC.tsv" preQCFile <- "~/Desktop/broadLocal/GATK/trunk/qcTestData/GoT2D_exomes_batch_005_per_sample_metrics.tsv"
VariantEvalRoot <- "~/Desktop/broadLocal/GATK/trunk/qcTestData/GoT2D_exomes_batch_005.cleaned.snps_and_indels.filtered.annotated" VariantEvalRoot <- "~/Desktop/broadLocal/GATK/trunk/qcTestData/GoT2D_exomes_batch_005.cleaned.snps_and_indels.filtered.annotated"
outputPDF = "bar.pdf" outputPDF = "bar.pdf"
highlightSamples = c() # parseHighlightSamples("29029,47243") highlightSamples = c() # parseHighlightSamples("29029,47243")
@ -128,8 +128,8 @@ addSection <- function(name) {
createMetricsBySamples <- function(VariantEvalRoot) { createMetricsBySamples <- function(VariantEvalRoot) {
byAFEval <- expandVEReport(gsa.read.gatkreport(paste(VariantEvalRoot, ".bySample.eval", sep=""))) byAFEval <- expandVEReport(gsa.read.gatkreport(paste(VariantEvalRoot, ".bySample.eval", sep="")))
#preQCMetrics <- read.table(preQCFile, header=T) preQCMetrics <- read.table(preQCFile, header=T)
r = merge(byAFEval$TiTvVariantEvaluator, byAFEval$CountVariants) r = merge(merge(byAFEval$TiTvVariantEvaluator, byAFEval$CountVariants), preQCMetrics)
# order the samples by nSNPs -- it's the natural ordering. # order the samples by nSNPs -- it's the natural ordering.
x = subset(r, Novelty=="all") x = subset(r, Novelty=="all")
@ -188,7 +188,7 @@ perSamplePlots <- function(metricsBySamples) {
p <- p + facet_grid(variable ~ ., scales="free") p <- p + facet_grid(variable ~ ., scales="free")
# how do we remove the labels? # how do we remove the labels?
p <- p + xAxis p <- p + xAxis
print(p) print(p)
} }
} }