From dab25afc88e268d1f69867768bfef8762b0b5078 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 25 Apr 2012 12:22:32 -0400 Subject: [PATCH] Add warning message about ratios in variantQCreport, give ratio for MAF > 10% --- .../sting/utils/R/gsalib/R/gsa.variantqc.utils.R | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) diff --git a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R b/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R index 88fc48e2a..19567e7e6 100644 --- a/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R +++ b/public/R/src/org/broadinstitute/sting/utils/R/gsalib/R/gsa.variantqc.utils.R @@ -169,7 +169,8 @@ compute.ratio.on.LogLinear.AC.intervals <- function(ACs, num, denom, scaleFactor plotVariantQC <- function(metrics, measures, requestedStrat = "Sample", fixHistogramX=F, anotherStrat = NULL, nObsField = "n_indels", - onSamePage=F, facetVariableOnXPerSample = F, facetVariableOnXForDist = T, moreTitle="") { + onSamePage=F, facetVariableOnXPerSample = F, facetVariableOnXForDist = T, + moreTitle="", note = NULL) { metrics$strat = metrics[[requestedStrat]] otherFacet = "." @@ -184,7 +185,14 @@ plotVariantQC <- function(metrics, measures, requestedStrat = "Sample", molten <- melt(metrics, id.vars=id.vars, measure.vars=c(measures)) perSampleGraph <- ggplot(data=molten, aes(x=strat, y=value, group=variable, color=variable, fill=variable)) - title <- opts(title=paste(paste(paste(measures, collapse=", "), "by", requestedStrat), moreTitle)) + + # create the title + titleText=paste(paste(paste(measures, collapse=", "), "by", requestedStrat), moreTitle) + if ( !is.null(note) ) { + titleText=paste(titleText, note, sep="\n") + } + paste(titleText) + title <- opts(title=titleText) determineFacet <- function(onX) { if ( onX ) { @@ -200,7 +208,7 @@ plotVariantQC <- function(metrics, measures, requestedStrat = "Sample", if ( requestedStrat == "Sample" ) { perSampleGraph <- perSampleGraph + geom_text(aes(label=strat), size=1.5) + geom_blank() # don't display a scale perSampleGraph <- perSampleGraph + scale_x_discrete("Sample (ordered by nSNPs)", formatter=function(x) "") - } else { + } else { # by AlleleCount perSampleGraph <- perSampleGraph + geom_point(aes(size=log10(nobs))) #+ geom_smooth(aes(weight=log10(nobs))) perSampleGraph <- perSampleGraph + scale_x_log10("AlleleCount") }