From 81ffb8243db19f9c014d38a732e92c339b420b81 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 8 Mar 2010 21:42:51 +0000
Subject: [PATCH] Waypoint commit of plotting R script for Depth Of
 Coverage/Coverage Statistics

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2958 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/PlotDepthOfCoverage.R | 84 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 84 insertions(+)
 create mode 100644 R/PlotDepthOfCoverage.R

diff --git a/R/PlotDepthOfCoverage.R b/R/PlotDepthOfCoverage.R
new file mode 100644
index 000000000..7df0ccf2f
--- /dev/null
+++ b/R/PlotDepthOfCoverage.R
@@ -0,0 +1,84 @@
+#!/broad/tools/apps/R-2.6.0/bin/Rscript
+
+args <- commandArgs(TRUE)
+docBase <- args[1]
+locusStats <- cat(docBase,".sample_locus_statistics")
+targetStats <- cat(docBase,".sample_interval_statistics")
+sampleSum <- cat(docBase,".sample_summary_statistics")
+sampleStats <- cat(docBase,".sample_statistics")
+targetSum <- cat(docBase(".sample_interval_summary"))
+
+PlotDepths <- function(X) {
+	Y <- as.matrix(X)
+	colors <- rainbow(nrow(Y),gamma=0.8)
+	plot(Y[1,],col=colors[1],type="b",xlab="",xaxt="n",ylab="Number of Loci")
+	axis(1,labels=FALSE)
+	labels <- colnames(X)
+	text(1:ncol(Y),par("usr")[3]-0.25,srt=45,adj=1,labels=labels,xpd=TRUE)
+	for ( jj in 2:nrow(Y) ) {
+		points(Y[jj,],col=colors[jj],type="b")
+	}
+	ymax = par("usr")[4]
+	xmax = par("usr")[2]
+	legend(y=0.95*ymax,x=0.8*xmax,col=colors,rownames(X),lty=c(1))
+}
+
+PlotLocusQuantiles <- function(X) {
+	Y <- as.matrix(X)
+	Y <- Y/sum(Y[1,])
+	Z <- matrix(nrow=nrow(Y),ncol=ncol(Y))
+	for ( ii in 1:nrow(Y) ) {
+		for ( jj in 1:ncol(Y) ) {
+		# see how much density is in the remaining columns
+			Z[ii,jj] = sum(Y[ii,jj:ncol(Y)])
+		}	
+	}
+	
+	medians = matrix(nrow=1,ncol=ncol(Z))
+	quan90 = matrix(nrow=1,ncol=ncol(Z))
+	for ( cc in 1:ncol(Z) ) {
+		medians[cc] = median(Z[,cc])
+		quan90[cc] = quantile(Z[,cc],0.9)
+	}
+	
+	plot(t(medians),xlab="",xaxt="n",ylab="Proportion of loci with >X coverage",type="b",col="blue")
+	axis(1,labels=FALSE)
+	parseColNames <- function(K) {
+		M = matrix(nrow=1,ncol=length(labels))
+		number = 0
+		for ( lab in K ) {
+			number = 1 + number
+			M[1,number] = unlist(strsplit(lab,split="_"))[2]
+		}
+		
+		return(M)
+	}
+	labels <- parseColNames(colnames(X))
+	text(1:length(labels),par("usr")[3]-0.05,srt=90,adj=1,labels=labels,xpd=TRUE)
+	points(t(quan90),type="b",col="red")
+	legend(x=floor(0.6*length(labels)),y=1,c("50% of samples","90% of samples"),col=c("red","blue"),lty=c(1,1))
+}
+
+HistogramMedians <- function(X) {
+	hist(as.numeric(as.matrix(unlist(X[1:nrow(X)-1,5]))),floor(nrow(X)/2),xlab="Median Coverage",ylab="Number of Samples", main="Median coverage acrosss samples",col="grey")
+}
+
+HeatmapLocusTable <- function(X) {
+	Y <- as.matrix(X)
+	heatmap(Y,Rowv=NA,Colv=NA)
+}
+
+PlotMeanMeadianQuartiles <- function(X) {
+	colors <- rainbow(4,start=0.6,end=0.9,gamma=1)
+	means = as.numeric(as.matrix(unlist(X[1:nrow(X)-1,3])))
+	medians = as.numeric(as.matrix(unlist(X[1:nrow(X)-1,5])))
+	thirdQ = as.numeric(as.matrix(unlist(X[1:nrow(X)-1,4])))
+	firstQ = as.numeric(as.matrix(unlist(X[1:nrow(X)-1,6])))
+	plot(means,xlab="",ylab="Depth of Coverage",xaxt="n",col=colors[1],pch=3,type="b")
+	points(firstQ,col=colors[2],pch=2,type="b")
+	points(medians,col=colors[3],pch=1,type="b")
+	points(thirdQ,col=colors[4],pch=2,type="b")
+	axis(1,labels=FALSE)
+	labels <- X[1:nrow(X)-1,1]
+	text(1:nrow(X)-1,par("usr")[3]-0.25,srt=45,adj=1,labels=labels,xpd=TRUE)
+}
\ No newline at end of file