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BoevaLab · Jun 7, 2017 · d4c2a9f · d4c2a9f
1 parent c376126
commit d4c2a9f
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diff --git a/scripts/_makeGraph_Chromosome.R b/scripts/_makeGraph_Chromosome.R
@@ -0,0 +1,59 @@
+args <- commandArgs()
+
+dataTable <-read.table(args[6], header=TRUE);
+print( paste (args[6],"read"))
+ratio<-data.frame(dataTable)
+chr <- type.convert(args[4])
+#chr <- 'X'
+ploidy <- type.convert(args[5])
+
+maxLevelToPlot <- 3
+for (i in c(1:length(ratio$Ratio))) {
+	if (ratio$Ratio[i]>maxLevelToPlot) {
+		ratio$Ratio[i]=maxLevelToPlot;
+	}
+}
+
+png(filename = paste(args[6],".png",sep = ""), width = 1180, height = 1180,
+    units = "px", pointsize = 20, bg = "white", res = NA)
+plot(1:10)
+op <- par(mfrow = c(2,1))
+i <- chr
+	tt <- which(ratio$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])
+	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
+	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)
+	print( paste (args[7],"read"))
+}
+dev.off()
+
diff --git a/scripts/makeGraph.R b/scripts/makeGraph.R
@@ -5,6 +5,38 @@ dataTable <-read.table(args[5], header=TRUE);
 ratio<-data.frame(dataTable)
 ploidy <- type.convert(args[4])
 
+
+png(filename = paste(args[5],".log2.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(ratio$Chromosome==i)
+	if (length(tt)>0) {
+	 plot(ratio$Start[tt],log2(ratio$Ratio[tt]),xlab = paste ("position, chr",i),ylab = "normalized copy number profile (log2)",pch = ".",col = colors()[88])
+	 tt <- which(ratio$Chromosome==i  & ratio$CopyNumber>ploidy )
+	 points(ratio$Start[tt],log2(ratio$Ratio[tt]),pch = ".",col = colors()[136])
+
+
+	tt <- which(ratio$Chromosome==i  & ratio$CopyNumber<ploidy & ratio$CopyNumber!= -1)
+	 points(ratio$Start[tt],log2(ratio$Ratio[tt]),pch = ".",col = colors()[461])
+	 tt <- which(ratio$Chromosome==i)
+
+	 #UNCOMMENT HERE TO SEE THE PREDICTED COPY NUMBER LEVEL:
+	 #points(ratio$Start[tt],log2(ratio$CopyNumber[tt]/ploidy), pch = ".", col = colors()[24],cex=4)
+
+	}
+	tt <- which(ratio$Chromosome==i)
+
+	#UNCOMMENT HERE TO SEE THE EVALUATED MEDIAN LEVEL PER SEGMENT:
+	#points(ratio$Start[tt],log2(ratio$MedianRatio[tt]), pch = ".", col = colors()[463],cex=4)
+
+}
+
+dev.off()
+
+
 png(filename = paste(args[5],".png",sep = ""), width = 1180, height = 1180,
     units = "px", pointsize = 20, bg = "white", res = NA)
 plot(1:10)
@@ -45,6 +77,9 @@ for (i in c(1:22,'X','Y')) {
 
 dev.off()
 
+
+
+
 if (length(args)>5) {
 	dataTable <-read.table(args[6], header=TRUE);
 	BAF<-data.frame(dataTable)

diff --git a/scripts/makeGraph.R~ b/scripts/makeGraph.R~
@@ -0,0 +1,134 @@
+args <- commandArgs()
+
+dataTable <-read.table(args[5], header=TRUE);
+
+ratio<-data.frame(dataTable)
+ploidy <- type.convert(args[4])
+
+
+png(filename = paste(args[5],".log2.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(ratio$Chromosome==i)
+	if (length(tt)>0) {
+	 plot(ratio$Start[tt],log2(ratio$Ratio[tt]),xlab = paste ("position, chr",i),ylab = "normalized copy number profile (log2)",pch = ".",col = colors()[88])
+	 tt <- which(ratio$Chromosome==i  & ratio$CopyNumber>ploidy )
+	 points(ratio$Start[tt],log2(ratio$Ratio[tt]),pch = ".",col = colors()[136])
+
+	tt <- which(ratio$Chromosome==i  & ratio$Ratio==maxLevelToPlot & ratio$CopyNumber>ploidy)	
+	points(ratio$Start[tt],log2(ratio$Ratio[tt]),pch = ".",col = colors()[136],cex=4)
+
+	tt <- which(ratio$Chromosome==i  & ratio$CopyNumber<ploidy & ratio$CopyNumber!= -1)
+	 points(ratio$Start[tt],log2(ratio$Ratio[tt]),pch = ".",col = colors()[461])
+	 tt <- which(ratio$Chromosome==i)
+
+	 #UNCOMMENT HERE TO SEE THE PREDICTED COPY NUMBER LEVEL:
+	 #points(ratio$Start[tt],log2(ratio$CopyNumber[tt]/ploidy), pch = ".", col = colors()[24],cex=4)
+
+	}
+	tt <- which(ratio$Chromosome==i)
+
+	#UNCOMMENT HERE TO SEE THE EVALUATED MEDIAN LEVEL PER SEGMENT:
+	#points(ratio$Start[tt],log2(ratio$MedianRatio[tt]), pch = ".", col = colors()[463],cex=4)
+
+}
+
+dev.off()
+
+
+png(filename = paste(args[5],".png",sep = ""), width = 1180, height = 1180,
+    units = "px", pointsize = 20, bg = "white", res = NA)
+plot(1:10)
+op <- par(mfrow = c(5,5))
+
+maxLevelToPlot <- 3
+for (i in c(1:length(ratio$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$Chromosome==i  & ratio$CopyNumber<ploidy & ratio$CopyNumber!= -1)
+	 points(ratio$Start[tt],ratio$Ratio[tt]*ploidy,pch = ".",col = colors()[461])
+	 tt <- which(ratio$Chromosome==i)
+
+	 #UNCOMMENT HERE TO SEE THE PREDICTED COPY NUMBER LEVEL:
+	 #points(ratio$Start[tt],ratio$CopyNumber[tt], pch = ".", col = colors()[24],cex=4)
+
+	}
+	tt <- which(ratio$Chromosome==i)
+
+	#UNCOMMENT HERE TO SEE THE EVALUATED MEDIAN LEVEL PER SEGMENT:
+	#points(ratio$Start[tt],ratio$MedianRatio[tt]*ploidy, pch = ".", col = colors()[463],cex=4)
+
+}
+
+dev.off()
+
+
+
+
+if (length(args)>5) {
+	dataTable <-read.table(args[6], header=TRUE);
+	BAF<-data.frame(dataTable)
+
+	png(filename = paste(args[6],".png",sep = ""), width = 1180, height = 1180,
+	    units = "px", pointsize = 20, bg = "white", res = NA)
+	plot(1:10)
+	op <- par(mfrow = c(5,5))
+
+	for (i in c(1:22,'X','Y')) {
+	    tt <- which(BAF$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$FittedB[tt],pch = ".",col = colors()[463],cex=4)	
+		}
+
+	   }
+
+	}
+	dev.off()
+
+}
diff --git a/scripts/makeGraph_Chromosome.R b/scripts/makeGraph_Chromosome.R
@@ -1,48 +1,112 @@
-args <- commandArgs()
-
-dataTable <-read.table(args[6], header=TRUE);
-print( paste (args[6],"read"))
+path = "/data/tmp/cgurjao/Graphical_outputs/R\ scripts/FREEC_7.4/Single-end"
+setwd(path)
+
+args = c()
+args[8] = 0
+args[7] = 0
+args[6] = "ratios_0.txt"
+args[5] = 2
+args[4] = 1
+
+dataTable <-read.table(args[6], header=T, na.strings="NA");
+print(paste (args[6],"read"))
 ratio<-data.frame(dataTable)
 chr <- type.convert(args[4])
-#chr <- 'X'
-ploidy <- type.convert(args[5])
+ploidy <- type.convert(args[5])
+CN_subc = ratio$Subclones
 
-maxLevelToPlot <- 3
-for (i in c(1:length(ratio$Ratio))) {
-	if (ratio$Ratio[i]>maxLevelToPlot) {
-		ratio$Ratio[i]=maxLevelToPlot;
-	}
-}
+max_value = 10#max(ratio$CopyNumber)
 
-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);
+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$Subclones[ttt]),j,j))
+            j = j-1
+		     }
+
+         x = NA
+         y = NA
+         if (round(length(ttt)/2) > 0 && (-ratio$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);
 	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
@@ -56,4 +120,4 @@ if (length(args)>=7) {
 	print( paste (args[7],"read"))
 }
 dev.off()
-
+}