From ede87a03c278d1ece93f7a995b1c048b010c257c Mon Sep 17 00:00:00 2001 From: depristo Date: Tue, 17 Aug 2010 19:20:58 +0000 Subject: [PATCH] Nicer plotting routine for tranches. Add a third arg to suppress the legend. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4049 348d0f76-0448-11de-a6fe-93d51630548a --- R/plot_Tranches.R | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/R/plot_Tranches.R b/R/plot_Tranches.R index e83d10075..343d48e28 100755 --- a/R/plot_Tranches.R +++ b/R/plot_Tranches.R @@ -5,6 +5,7 @@ verbose = TRUE input = args[1] targetTITV = as.numeric(args[2]) +suppressLegend = ! is.na(args[3]) # ----------------------------------------------------------------------------------------------- # Useful general routines @@ -40,7 +41,7 @@ data2 = read.table(paste(input,".tranches",sep=""),sep=",",head=T) cols = c("cornflowerblue", "cornflowerblue", "darkorange", "darkorange") density=c(20, -1, -1, 20) outfile = paste(input, ".FDRtranches.pdf", sep="") -pdf(outfile, height=7, width=8) +pdf(outfile, height=5, width=8) alpha = 1 - titvFPEstV(targetTITV, data2$novelTITV) #print(alpha) @@ -56,12 +57,16 @@ numNewBad = numBad - numPrevBad d=matrix(c(numPrevGood,numNewGood, numNewBad, numPrevBad),4,byrow=TRUE) #print(d) -barplot(d/1000,horiz=TRUE,col=cols,space=0.2,xlab="Number of Novel Variants (1000s)",ylab="Novel Ti/Tv --> FDR (%)", density=density) # , xlim=c(250000,350000)) +barplot(d/1000,horiz=TRUE,col=cols,space=0.2,xlab="Number of Novel Variants (1000s)", density=density, cex.axis=1.25, cex.lab=1.25) # , xlim=c(250000,350000)) #abline(v= d[2,dim(d)[2]], lty=2) #abline(v= d[1,3], lty=2) -legend(10000/1000, 2.25, c('Cumulative TPs','Tranch-specific TPs', 'Tranch-specific FPs', 'Cumulative FPs' ), fill=cols, density=density, bg='white', cex=1.25) -axis(2,line=-1,at=0.7+(0:(length(data2$FDRtranche)-1))*1.2,tick=FALSE,labels=data2$FDRtranche) -axis(2,line=0.4,at=0.7+(0:(length(data2$FDRtranche)-1))*1.2,tick=FALSE,labels=data2$novelTITV) +if ( ! suppressLegend ) + legend(5, 2.25, c('Cumulative TPs','Tranch-specific TPs', 'Tranch-specific FPs', 'Cumulative FPs' ), fill=cols, density=density, bg='white', cex=1.25) + +mtext("Ti/Tv",2,line=2.25,at=length(data2$FDRtranche)*1.2,las=1, cex=1) +mtext("FDR",2,line=0,at=length(data2$FDRtranche)*1.2,las=1, cex=1) +axis(2,line=-1,at=0.7+(0:(length(data2$FDRtranche)-1))*1.2,tick=FALSE,labels=data2$FDRtranche, las=1, cex.axis=1.25) +axis(2,line=1,at=0.7+(0:(length(data2$FDRtranche)-1))*1.2,tick=FALSE,labels=data2$novelTITV, las=1, cex.axis=1.25) dev.off()