222 lines
9.2 KiB
R
222 lines
9.2 KiB
R
library("gsalib", lib.loc="/Users/depristo/Desktop/broadLocal/GATK/trunk/R/")
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require("ggplot2")
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require("gplots")
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# TODOs:
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# Assumes you have indels in your call set. If not you will get errors
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# Create pre/post calling sections
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# Allow conditional use of the preQCFile (where it's not available)
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args = commandArgs(TRUE)
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onCMDLine = ! is.na(args[1])
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LOAD_DATA = T
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# creates an array of c(sampleName1, ..., sampleNameN)
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parseHighlightSamples <- function(s) {
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return(unlist(strsplit(s, ",", fixed=T)))
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}
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if ( onCMDLine ) {
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ProjectName = args[1]
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VariantEvalRoot = args[2]
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preQCFile = args[3]
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outputPDF = args[4]
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if ( ! is.na(args[5]) )
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highlightSamples = parseHighlightSamples(args[5])
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else
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highlightSamples = c()
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} else {
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ProjectName = "InDevelopmentInR"
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preQCFile <- "~/Desktop/broadLocal/GATK/trunk/qcTestData/GoT2D_exomes_batch_005_per_sample_metrics.tsv"
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VariantEvalRoot <- "~/Desktop/broadLocal/GATK/trunk/qcTestData/GoT2D_exomes_batch_005.cleaned.snps_and_indels.filtered.annotated"
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outputPDF = "bar.pdf"
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highlightSamples = c() # parseHighlightSamples("29029,47243")
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}
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expandVEReport <- function(d) {
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d$TiTvVariantEvaluator$tiTvRatio = round(d$TiTvVariantEvaluator$tiTvRatio,2)
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d$CountVariants$deletionInsertionRatio = round(d$CountVariants$deletionInsertionRatio,2)
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d$CountVariants$nIndels = d$CountVariants$nInsertions + d$CountVariants$nDeletions
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return(d)
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}
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createMetricsBySites <- function(VariantEvalRoot, PreQCMetrics) {
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# Metrics by sites:
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# bySite -> counts of SNPs and Indels by novelty, with expectations
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# byAF -> snps and indels (known / novel)
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r = list( bySite = expandVEReport(gsa.read.gatkreport(paste(VariantEvalRoot, ".summary.eval", sep=""))),
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byAF = gsa.read.gatkreport(paste(VariantEvalRoot, ".byAF.eval", sep="")))
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r$byAF$CountVariants$nIndels = r$byAF$CountVariants$nInsertions + r$byAF$CountVariants$nDeletions
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nChrom = 1 / min(r$byAF$TiTvVariantEvaluator$AlleleFrequency[r$byAF$TiTvVariantEvaluator$AlleleFrequency > 0])
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r$byAF$TiTvVariantEvaluator$nSNPs = r$byAF$TiTvVariantEvaluator$nTi + r$byAF$TiTvVariantEvaluator$nTv
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r$byAF$CountVariants$AC = r$byAF$CountVariants$AlleleFrequency * nChrom
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r$byAF$TiTvVariantEvaluator$AC = r$byAF$TiTvVariantEvaluator$AlleleFrequency * nChrom
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return(r)
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}
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summaryTable <- function(metricsBySites, metricsBySample) {
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# SNP summary statistics
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merged = merge(metricsBySites$bySite$CountVariants, metricsBySites$bySite$TiTvVariantEvaluator)
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sub <- subset(merged, FunctionalClass=="all")
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raw = melt(sub, id.vars=c("Novelty"), measure.vars=c("nProcessedLoci", "nSNPs", "tiTvRatio", "nIndels", "deletionInsertionRatio"))
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table = cast(raw, Novelty ~ ...)
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# doesn't work with textplot
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colnames(table) <- c("Novelty", "Target size (bp)", "No. SNPs", "Ti/Tv", "No. Indels", "deletion/insertion ratio")
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return(table)
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}
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summaryPlots <- function(metricsBySites) {
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name = "SNP and Indel count by novelty and allele frequency"
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molten = melt(subset(metricsBySites$byAF$CountVariants, FunctionalClass == "all" & Novelty != "all" & AC > 0), id.vars=c("Novelty", "AC"), measure.vars=c(c("nSNPs", "nIndels")))
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p <- ggplot(data=molten, aes(x=AC, y=value+1, color=Novelty, fill=Novelty), group=variable)
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p <- p + opts(title = name)
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p <- p + scale_y_log10("Number of variants")
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p <- p + geom_area()
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p <- p + facet_grid(variable ~ ., scales="free")
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p <- p + scale_x_continuous("Allele count (AC)")
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print(p)
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p <- p + scale_x_log10("Allele count (AC)")
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print(p)
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# Counts vs. Allele frequency
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name = "Variant counts by allele count"
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for ( measure in c("nSNPs", "nIndels")) {
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molten = melt(subset(metricsBySites$byAF$CountVariants, FunctionalClass == "all" & AC > 0), id.vars=c("Novelty", "AC"), measure.vars=c(measure))
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p <- ggplot(data=molten, aes(x=AC, y=value+1, color=Novelty), group=variable)
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p <- p + opts(title = paste(name, ":", measure))
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p <- p + scale_y_log10("Number of variants")
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p <- p + scale_x_log10("Allele count (AC)")
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p <- p + geom_point(alpha=0.5, size=4)
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p <- p + geom_smooth(aes(weight=value), size=1, method="lm", formula = y ~ x)
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p <- p + facet_grid(Novelty ~ ., scales="free")
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print(p)
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}
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name = "Transition / transversion ratio by allele count"
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byAFNoAll = subset(metricsBySites$byAF$TiTvVariantEvaluator, Novelty != "all" & FunctionalClass == "all" & AC > 0)
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p <- ggplot(data=byAFNoAll, aes(x=AC, y=tiTvRatio, color=Novelty))
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p <- p + scale_y_continuous("Transition / transversion ratio", limits=c(0,4))
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p <- p + opts(title = name)
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p <- p + geom_smooth(size=2)
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p <- p + geom_point(aes(size=log10(nSNPs), weight=nSNPs), alpha=0.5)
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p <- p + scale_x_continuous("Allele count (AC)")
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print(p)
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p <- p + scale_x_log10("Allele count (AC)")
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print(p)
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# SNPs to indels ratio by allele frequency
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name = "SNPs to indels ratio by allele frequency"
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metricsBySites$byAF$CountVariants$SNP.Indel.Ratio = metricsBySites$byAF$CountVariants$nSNPs / metricsBySites$byAF$CountVariants$nIndels
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metricsBySites$byAF$CountVariants$SNP.Indel.Ratio[metricsBySites$byAF$CountVariants$nIndels == 0] = NaN
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p <- ggplot(data=subset(metricsBySites$byAF$CountVariants, FunctionalClass == "all" & Novelty == "all"), aes(x=AC, y=SNP.Indel.Ratio))
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p <- p + opts(title = name)
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p <- p + scale_y_continuous("SNP to indel ratio")
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#p <- p + scale_y_log10()
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p <- p + geom_point(alpha=0.5, aes(size=log10(nIndels)))
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p <- p + geom_smooth(size=2, aes(weight=nIndels))
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print(p)
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name = "SNP counts by functional class"
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molten = melt(subset(metricsBySites$bySite$CountVariants, Novelty != "all" & FunctionalClass != "all"), id.vars=c("Novelty", "FunctionalClass"), measure.vars=c(c("nSNPs")))
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p <- ggplot(data=molten, aes(x=FunctionalClass, y=value, fill=Novelty), group=FunctionalClass)
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p <- p + opts(title = name)
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p <- p + scale_y_log10("No. of SNPs")
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p <- p + geom_bar(position="dodge")
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print(p)
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}
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addSection <- function(name) {
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par("mar", c(5, 4, 4, 2))
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frame()
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title(name, cex=2)
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}
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createMetricsBySamples <- function(VariantEvalRoot) {
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byAFEval <- expandVEReport(gsa.read.gatkreport(paste(VariantEvalRoot, ".bySample.eval", sep="")))
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preQCMetrics <- read.table(preQCFile, header=T)
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r = merge(merge(byAFEval$TiTvVariantEvaluator, byAFEval$CountVariants), preQCMetrics)
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# order the samples by nSNPs -- it's the natural ordering.
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x = subset(r, Novelty=="all")
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r$Sample <- factor(x$Sample, levels=x$Sample[order(x$nSNPs)])
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# add highlight info
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r$highlight = r$Sample %in% highlightSamples
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#r = merge(merge(preQCMetrics, byAFEval$TiTvVariantEvaluator), byAFEval$CountVariants)
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return(subset(r, Sample != "all"))
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}
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# actually load the data.
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if ( onCMDLine || LOAD_DATA ) {
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metricsBySites <- createMetricsBySites(VariantEvalRoot)
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metricsBySamples <- createMetricsBySamples(VariantEvalRoot)
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}
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# -------------------------------------------------------
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# Per sample plots
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# -------------------------------------------------------
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perSamplePlots <- function(metricsBySamples) {
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metricsBySamples$highlightTextSizes = c(1,2)[metricsBySamples$highlight+1]
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sampleTextLabel <- geom_text(aes(label=Sample, size=highlightTextSizes))
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sampleTextLabelScale <- scale_size("Highlighted samples", to=c(3,5), breaks=c(1,2), labels=c("regular", "highlighted"))
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xAxis <- scale_x_discrete("Sample (ordered by nSNPs)", formatter=function(x) "")
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myRug <- geom_rug(position="jitter")
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#myRug <- geom_rug(aes(x = NULL))
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measures = c("nSNPs", "tiTvRatio", "nSingletons", "nIndels", "nInsertions", "nDeletions", "deletionInsertionRatio")
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# Counts vs. Allele frequency
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name = "Variant counts by allele count"
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for ( measure in measures ) {
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molten = melt(metricsBySamples, id.vars=c("Novelty", "Sample", "highlightTextSizes"), measure.vars=c(measure))
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p <- ggplot(data=molten, aes(x=Sample, y=value, group=Novelty, color=Novelty), y=value)
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p <- p + opts(title = paste(name, ":", measure))
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p <- p + geom_smooth(alpha=0.5, aes(group=Novelty))
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p <- p + sampleTextLabel + sampleTextLabelScale
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p <- p + myRug
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p <- p + facet_grid(Novelty ~ ., scales="free")
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# how do we remove the labels?
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p <- p + xAxis
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print(p)
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}
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for ( novelty in c("all", "known", "novel") ) {
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# TODO -- how can I color it as before?
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# TODO -- add marginal distributions?
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molten = melt(subset(metricsBySamples, Novelty==novelty), id.vars=c("Sample", "highlightTextSizes"), measure.vars=measures)
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p <- ggplot(data=molten, aes(x=Sample, y=value))
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p <- p + opts(title = paste(name, ":", novelty))
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# p <- p + scale_y_log10("Number of variants")
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# p <- p + geom_point(alpha=0.5, size=4)
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p <- p + sampleTextLabel + sampleTextLabelScale
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p <- p + myRug
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p <- p + facet_grid(variable ~ ., scales="free")
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# how do we remove the labels?
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p <- p + xAxis
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print(p)
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}
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}
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# -------------------------------------------------------
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# Actually invoke the above plotting functions
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# -------------------------------------------------------
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if ( ! is.na(outputPDF) ) {
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pdf(outputPDF, height=8.5, width=11)
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}
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# Table of overall counts and quality
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textplot(as.data.frame(summaryTable(metricsBySites)), show.rownames=F)
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title(paste("Overall summary metrics for project", ProjectName), cex=3)
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summaryPlots(metricsBySites)
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perSamplePlots(metricsBySamples)
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if ( ! is.na(outputPDF) ) {
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dev.off()
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}
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