makeGraph.R

args <- commandArgs()

dataTable <-read.table(args[5], header=TRUE);

ratio<-data.frame(dataTable)
ploidy <- type.convert(args[4])

png(filename = paste(args[5],".png",sep = ""), width = 1180, height = 1180,
    units = "px", pointsize = 20, bg = "white", res = NA, type = 'cairo-png')
plot(1:10)
op <- par(mfrow = c(5,5))

maxLevelToPlot <- 3
for (i in c(1:length(ratio$Ratio))) {
	if (ratio$Ratio[i]>maxLevelToPlot) {
		ratio$Ratio[i]=maxLevelToPlot;
	}
}


for (i in c(1:22,'X','Y')) {
	tt <- which(ratio$Chromosome==i)
	if (length(tt)>0) {
	 plot(ratio$Start[tt],ratio$Ratio[tt]*ploidy,ylim = c(0,maxLevelToPlot*ploidy),xlab = paste ("position, chr",i),ylab = "normalized copy number profile",pch = ".",col = colors()[88])
	 tt <- which(ratio$Chromosome==i  & ratio$CopyNumber>ploidy )
	 points(ratio$Start[tt],ratio$Ratio[tt]*ploidy,pch = ".",col = colors()[136])
	
	tt <- which(ratio$Chromosome==i  & ratio$Ratio==maxLevelToPlot & ratio$CopyNumber>ploidy)	
	points(ratio$Start[tt],ratio$Ratio[tt]*ploidy,pch = ".",col = colors()[136],cex=4)
	 
	tt <- which(ratio$Chromosome==i  & ratio$CopyNumber<ploidy & ratio$CopyNumber!= -1)
	 points(ratio$Start[tt],ratio$Ratio[tt]*ploidy,pch = ".",col = colors()[461])
	 tt <- which(ratio$Chromosome==i)
	 #points(ratio$Start[tt],ratio$CopyNumber[tt], pch = ".", col = colors()[24],cex=4)
	}
	tt <- which(ratio$Chromosome==i)
	 #points(ratio$Start[tt],ratio$MedianRatio[tt]*ploidy, pch = ".", col = colors()[463],cex=4)
}

dev.off()

if (length(args)>5) {
	dataTable <-read.table(args[6], header=TRUE);
	BAF<-data.frame(dataTable)

	png(filename = paste(args[6],".png",sep = ""), width = 1180, height = 1180,
	    units = "px", pointsize = 20, bg = "white", res = NA, type = 'cairo-png')
	plot(1:10)
	op <- par(mfrow = c(5,5))

	for (i in c(1:22,'X','Y')) {
	    tt <- which(BAF$Chromosome==i)
	    if (length(tt)>0){
		lBAF <-BAF[tt,]
		plot(lBAF$Position,lBAF$BAF,ylim = c(-0.1,1.1),xlab = paste ("position, chr",i),ylab = "BAF",pch = ".",col = colors()[1])

		tt <- which(lBAF$A==0.5)		
		points(lBAF$Position[tt],lBAF$BAF[tt],pch = ".",col = colors()[92])
		tt <- which(lBAF$A!=0.5 & lBAF$A>=0)
		points(lBAF$Position[tt],lBAF$BAF[tt],pch = ".",col = colors()[62])
		tt <- 1
		pres <- 1

		if (length(lBAF$A)>4) {
			for (j in c(2:(length(lBAF$A)-pres-1))) {
				if (lBAF$A[j]==lBAF$A[j+pres]) {	
					tt[length(tt)+1] <- j 
				}
			}
			points(lBAF$Position[tt],lBAF$A[tt],pch = ".",col = colors()[24],cex=4)
			points(lBAF$Position[tt],lBAF$B[tt],pch = ".",col = colors()[24],cex=4)	
		}
	   }

	}
	dev.off()

}