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) 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$CopyNumber5) { dataTable <-read.table(args[6], header=TRUE); BAF<-data.frame(dataTable) png(filename = paste(args[6],".png",sep = ""), width = 1180, height = 1180, units = "px", pointsize = 20, bg = "white", res = NA) plot(1:10) op <- par(mfrow = c(5,5)) for (i in c(1:22,'X','Y')) { tt <- which(BAF$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$B[tt],pch = ".",col = colors()[24],cex=4) } tt <- 1 pres <- 1 if (length(lBAF$FittedA)>4) { for (j in c(2:(length(lBAF$FittedA)-pres-1))) { if (lBAF$FittedA[j]==lBAF$FittedA[j+pres]) { tt[length(tt)+1] <- j } } points(lBAF$Position[tt],lBAF$FittedA[tt],pch = ".",col = colors()[463],cex=4) points(lBAF$Position[tt],lBAF$FittedB[tt],pch = ".",col = colors()[463],cex=4) } } } dev.off() }