restore old makeGraph_Chromosome.R

Author: valeu

scripts/makeGraph_Chromosome.R

@@ -1,121 +1,48 @@
-<<<<<<< HEAD
-path = "/data/tmp/cgurjao/Graphical_outputs/R\ scripts/FREEC_7.4/Single-end"
-setwd(path)
-
-args = c()
-args[8] = 0
-args[7] = 0
-args[6] = "ratios_0.txt"
-args[5] = 2
-args[4] = 1
-
-dataTable <-read.table(args[6], header=T, na.strings="NA");
-print(paste (args[6],"read"))
-=======
-#!/usr/bin/env Rscript
-
 args <- commandArgs()
 
 dataTable <-read.table(args[6], header=TRUE);
 print( paste (args[6],"read"))
->>>>>>> 76030ffbfebd715b07a1c240056a37cb02bbb1ff
 ratio<-data.frame(dataTable)
 chr <- type.convert(args[4])
-ploidy <- type.convert(args[5])
-CN_subc = ratio$Subclones
-
-max_value = 10#max(ratio$CopyNumber)
+#chr <- 'X'
+ploidy <- type.convert(args[5])
 
-plot(1:10)
-even_odd = 0
-even_odd2 = 0
-par(mfrow = c(2,1))
-for (i in c(1:11))
-{
-  png(filename = paste(path, "/Results/","chr", i,".png",sep = ""), width = 1180, height = 1180,
-    units = "px", pointsize = 20, bg = "white", res = NA)
-	tt <- which(ratio$Chromosome==i)
-	if (length(tt)>0) {
-	   tt <- which(ratio$Chromosome==i  & ratio$CopyNumber==ploidy )
-		 plot(ratio$Start[tt],ratio$Ratio[tt]*ploidy,ylim = c(0,max_value),xlab = paste ("position, chr",i),ylab = "normalized copy number profile",pch = ".",col = rgb(0,1,0, alpha = 0.2),cex=8)
-		 tt <- which(ratio$Chromosome==i  & ratio$CopyNumber>ploidy )
-		 points(ratio$Start[tt],ratio$Ratio[tt]*ploidy,pch = ".",col = rgb(1,0,0, alpha = 0.2),cex=8)
-		 tt <- which(ratio$Chromosome==i  & ratio$CopyNumber<ploidy )
-		 points(ratio$Start[tt],ratio$Ratio[tt]*ploidy,pch = ".",col = rgb(0,0,1, alpha = 0.2),cex=8)
-		 tt <- which(ratio$Chromosome==i)
-		 points(ratio$Start[tt],ratio$CopyNumber[tt], pch = ".", col = colors()[24],cex=8)
-		 tt <- which(ratio$Chromosome==i)
-		 for (k in c(1:length(levels(CN_subc))))
-		 {
-		   if (levels(CN_subc)[k] != "0/0" && length(CN_subc) > 0)
-		   {
-		     ttt <- which(ratio$Subclones == levels(CN_subc)[k] &  ratio$Chromosome==i)
-         if (length(ttt)>0)
-		        {
-		     j = 1
-		     CN = ''
-         pop = ''
-		     while (substr(as.character(ratio$Subclones[ttt]),j,j)[1] != "/")
-		     { 
-		       CN = paste(CN,substr(as.character(ratio$Subclones[ttt]),j,j))
-		       j = j+1
-		     }
-         j = 9
-		     while (substr(as.character(ratio$Subclones[ttt]),j,j)[1] != "/" )
-		     { 
-		        pop[j] = paste(pop,substr(as.character(ratio$Subclones[ttt]),j,j))
-            j = j-1
-		     }
+maxLevelToPlot <- 3
+for (i in c(1:length(ratio$Ratio))) {
+	if (ratio$Ratio[i]>maxLevelToPlot) {
+		ratio$Ratio[i]=maxLevelToPlot;
+	}
+}
 
-         x = NA
-         y = NA
-         if (round(length(ttt)/2) > 0 && (-ratio$Start[ttt[1]] + ratio$Start[ttt[length(ttt)-1]]) > 10000000 )
-           {
-           if (even_odd %% 2 == 0) #(ratio$CopyNumber[ttt][round(length(ttt)/2)] > as.numeric(gsub(" ", "",CN[1])))
-		        {
-             points(ratio$Start[ttt],CN, pch = ".", col = colors()[99],cex=8)
-             if (even_odd2 %% 2 == 0)
-                {x = as.numeric(ratio$Start[ttt][round(length(ttt)/3)])
-                y = as.numeric(CN[1]) - 0.25
-                even_odd2 = even_odd2 + 1}
-             else
-                {x = as.numeric(ratio$Start[ttt][round(length(ttt)/3)])
-                 y = as.numeric(CN[1]) + 0.25
-                 even_odd2 = even_odd2 + 1}
-            even_odd = even_odd +1   
-            }
-           else 
-            {
-              points(ratio$Start[ttt],CN, pch = ".", col = colors()[96],cex=8)
-              if (even_odd2 %% 2 != 0)
-                {
-                x = as.numeric(ratio$Start[ttt][round(length(ttt)/3)])
-                y = as.numeric(CN[1]) + 0.25
-                even_odd2 = even_odd2 + 1}
-              else
-                {x = as.numeric(ratio$Start[ttt][round(length(ttt)/3)])
-                y = as.numeric(CN[1]) - 0.25
-                even_odd2 = even_odd2 + 1}
-            even_odd = even_odd +1  
-            } 
-          }
-         pop = as.numeric(gsub("NA", "",gsub(",","",gsub(' ',"", toString(pop))))) * 100;
-         pop = paste(as.character(as.integer(pop)),"%")
-         text(x, y, as.character(pop), cex = 0.8, col = 'black')
-        }
-      }
-		 }
-   }             
-             
-  if (args[7] != 0) {
-  dataTable <-read.table(args[7], header=TRUE);
+png(filename = paste(args[6],".png",sep = ""), width = 1180, height = 1180,
+    units = "px", pointsize = 20, bg = "white", res = NA)
+plot(1:10)
+op <- par(mfrow = c(2,1))
+i <- chr
+	tt <- which(ratio$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],cex=2)
+		 tt <- which(ratio$Chromosome==i  & ratio$CopyNumber>ploidy )
+		 points(ratio$Start[tt],ratio$Ratio[tt]*ploidy,pch = ".",col = colors()[136],cex=2)
+		 tt <- which(ratio$Chromosome==i  & ratio$Ratio==maxLevelToPlot)
+		 points(ratio$Start[tt],ratio$Ratio[tt]*ploidy,pch = ".",col = colors()[136],cex=4)
+		 tt <- which(ratio$Chromosome==i  & ratio$CopyNumber<ploidy )
+		 points(ratio$Start[tt],ratio$Ratio[tt]*ploidy,pch = ".",col = colors()[461],cex=2)
+		 tt <- which(ratio$Chromosome==i)
+		 points(ratio$Start[tt],ratio$CopyNumber[tt], pch = ".", col = colors()[24],cex=2)
+		 points(ratio$Start[tt],ratio$MedianRatio[tt]*ploidy, pch = ".", col = colors()[98],cex=4)
+	}
+if (length(args)>=7) {
+	dataTable <-read.table(args[7], header=TRUE);
 	BAF<-data.frame(dataTable)
 	tt <- which(BAF$Chromosome==i)
-	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])
+	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$BAF[tt],pch = ".",col = colors()[450])
+	tt <- which(lBAF$B==1)
 	points(lBAF$Position[tt],lBAF$BAF[tt],pch = ".",col = colors()[62])
 	tt <- 1
 	pres <- 1
@@ -129,4 +56,4 @@ for (i in c(1:11))
 	print( paste (args[7],"read"))
 }
 dev.off()
-}
+