makeGraph_each_chr.R~

args <- commandArgs()

dataTable <-read.table(args[4], header=TRUE);

ratio<-data.frame(dataTable)

#png(filename = paste(args[5],".png",sep = ""), width = 1180, height = 1180,
 #   units = "px", pointsize = 20, bg = "white", res = NA)
#plot(1:10)
#op <- par(mfrow = c(5,5))
for (i in c(1:22,'X','Y')) {
        png(filename = paste(args[5],".", i, ".png",sep = ""), width = 1180, height = 1180, units = "px", pointsize = 20, bg = "white", res = NA)
	tt <- which(ratio$Chromosome==i)
	if (length(tt)>0) {
         plot(ratio$Position[tt],ratio$LogRatio[tt],ylim = c(-2,2),xlab = paste ("position, chr",i),ylab = "log2-ratios",pch = ".",col = colors()[88], cex=4)
	 tt <- which(ratio$Chromosome==i  & ratio$Summary > 0.2 )
	 points(ratio$Position[tt],ratio$LogRatio[tt],pch = ".",col = colors()[136], cex=4)
	 tt <- which(ratio$Chromosome==i  & ratio$Summary < -0.2)
	 points(ratio$Position[tt],ratio$LogRatio[tt],pch = ".",col = colors()[461], cex=4)
	 #tt <- which(ratio$Chromosome==i)
	 #points(ratio$Position[tt],ratio$CopyNumber[tt], pch = ".", col = colors()[24],cex=4)
	}
}

dev.off()