35 lines
1.5 KiB
R
Executable File
35 lines
1.5 KiB
R
Executable File
#!/broad/tools/apps/R-2.6.0/bin/Rscript
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args <- commandArgs(TRUE)
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verbose = TRUE
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input = args[1]
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targetTITV = as.numeric(args[2])
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data = read.table(input,sep=",",head=T)
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maxVars = max(data$numKnown, data$numNovel)
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maxTITV = max(data$knownTITV[is.finite(data$knownTITV) & data$numKnown>2000], data$novelTITV[is.finite(data$novelTITV) & data$numNovel > 2000], targetTITV)
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maxTITV = min(maxTITV, targetTITV + 1)
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minTITV = min(data$knownTITV[length(data$knownTITV)], data$novelTITV[length(data$novelTITV)], targetTITV)
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maxPCut = max(data$pCut[data$numKnown>0 | data$numNovel>0])
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outfile = paste(input, ".optimizationCurve.pdf", sep="")
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pdf(outfile, height=7, width=8)
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par(mar=c(4,4,1,4),cex=1.3)
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plot(data$pCut, data$knownTITV, axes=F,xlab="Keep variants with QUAL >= X",ylab="",ylim=c(minTITV,maxTITV),xlim=c(0,maxPCut),col="Blue",pch=20)
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points(data$pCut, data$novelTITV,,col="DarkBlue",pch=20)
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abline(h=targetTITV,lty=3,col="Blue")
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axis(side=2,col="DarkBlue")
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axis(side=1)
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mtext("Ti/Tv Ratio", side=2, line=2, col="blue",cex=1.4)
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legend("left", c("Known Ti/Tv","Novel Ti/Tv"), col=c("Blue","DarkBlue"), pch=c(20,20),cex=0.7)
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par(new=T)
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plot(data$pCut, data$numKnown, axes=F,xlab="",ylab="",ylim=c(0,maxVars),xlim=c(0,maxPCut),col="Green",pch=20)
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points(data$pCut, data$numNovel,col="DarkGreen",pch=20)
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axis(side=4,col="DarkGreen")
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mtext("Number of Variants", side=4, line=2, col="DarkGreen",cex=1.4)
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legend("topright", c("Known","Novel"), col=c("Green","DarkGreen"), pch=c(20,20),cex=0.7)
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dev.off() |