From a837a49328d58a5d27f5ddfb70c5b75cf0f54534 Mon Sep 17 00:00:00 2001 From: depristo Date: Mon, 13 Jun 2011 20:50:34 +0000 Subject: [PATCH] Minor fixes git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5988 348d0f76-0448-11de-a6fe-93d51630548a --- R/exomePostQC.R | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/R/exomePostQC.R b/R/exomePostQC.R index d840adf9d..7fb27cad8 100644 --- a/R/exomePostQC.R +++ b/R/exomePostQC.R @@ -1,8 +1,8 @@ library("gsalib", lib.loc="/Users/depristo/Desktop/broadLocal/GATK/trunk/R/") require("ggplot2") +require("gplots") -args = commandArgs(TRUE); - +args = commandArgs(TRUE) onCMDLine = ! is.na(args[1]) LOAD_DATA = F @@ -21,7 +21,7 @@ if ( onCMDLine ) { highlightSamples = c() } else { 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" outputPDF = "bar.pdf" highlightSamples = c() # parseHighlightSamples("29029,47243") @@ -128,8 +128,8 @@ addSection <- function(name) { createMetricsBySamples <- function(VariantEvalRoot) { byAFEval <- expandVEReport(gsa.read.gatkreport(paste(VariantEvalRoot, ".bySample.eval", sep=""))) - #preQCMetrics <- read.table(preQCFile, header=T) - r = merge(byAFEval$TiTvVariantEvaluator, byAFEval$CountVariants) + preQCMetrics <- read.table(preQCFile, header=T) + r = merge(merge(byAFEval$TiTvVariantEvaluator, byAFEval$CountVariants), preQCMetrics) # order the samples by nSNPs -- it's the natural ordering. x = subset(r, Novelty=="all") @@ -188,7 +188,7 @@ perSamplePlots <- function(metricsBySamples) { p <- p + facet_grid(variable ~ ., scales="free") # how do we remove the labels? p <- p + xAxis -print(p) + print(p) } }