Merge branch 'ReleaseBranch_1.2.166' of https://github.com/DKFZ-ODCF/SNVCallingWorkflow into ReleaseBranch_1.2.166

m into a topic branch.

Author: warsow

resources/analysisTools/snvPipeline/MAF_plots.r

@@ -19,39 +19,41 @@ maf=read.table(infile,sep="\t",as.is=TRUE)
 
 pdf(outfile, width=7, height=7)
 
-if(nr_in_dbSNP > 3 && length(which(maf[,1]==1))>1){
-
-	dens_in_dbSNP <- density(x = maf[maf[,1]==1,3])
-	dens_in_all <- density(x = maf[,3])
-	perc_in_dbSNP <- round((100*nr_in_dbSNP/snvnum),2)
-
-	maxy <- max(dens_in_all$y)
-	if(max(dens_in_all$y) < max(dens_in_dbSNP$y)){
-		maxy <- max(dens_in_dbSNP$y)
+if(nrow(maf)>1) {
+	if(nr_in_dbSNP > 3 && length(which(maf[,1]==1))>1){
+
+		dens_in_dbSNP <- density(x = maf[maf[,1]==1,3])
+		dens_in_all <- density(x = maf[,3])
+		perc_in_dbSNP <- round((100*nr_in_dbSNP/snvnum),2)
+
+		maxy <- max(dens_in_all$y)
+		if(max(dens_in_all$y) < max(dens_in_dbSNP$y)){
+			maxy <- max(dens_in_dbSNP$y)
+		}
+
+		plot(dens_in_dbSNP, ylim = c(0,maxy), col = "red", cex.lab=1.5, cex.axis=1.5, lwd=3, xlab=paste("Mutant allele frequency from ", snvnum, " SNVs and ", nr_in_dbSNP, " in dbSNP", sep=""), xlim=c(0, 1.0),main="")
+		lines(dens_in_all,col = "blue", lwd = 3)
+		abline(v=0.5,col="black",lty=2)
+		title(main=paste(pid, perc_in_dbSNP, "% in dbSNP", sep=" "), cex.main = 1.5)
+
+		legend("topright", c("ALL","IN dbSNP"), fill=c("blue","red"), cex = 0.7, lwd=1, bty="n")
+	}else{
+	#	dens_in_dbSNP <- density(x = maf[maf[,1]==1,3])
+		dens_in_all <- density(x = maf[,3])
+		perc_in_dbSNP <- round((100*nr_in_dbSNP/snvnum),2)
+
+		maxy <- max(dens_in_all$y)
+	#    if(max(dens_in_all$y) < max(dens_in_dbSNP$y)){
+	#        maxy <- max(dens_in_dbSNP$y)
+	#    }
+
+		plot(dens_in_all, ylim = c(0,maxy), col = "red", cex.lab=1.5, cex.axis=1.5, lwd=3, xlab=paste("Mutant allele frequency from ", snvnum, " SNVs and ", nr_in_dbSNP,     " in dbSNP", sep=""), xlim=c(0, 1.0),main="")
+	#    lines(dens_in_all,col = "blue", lwd = 3)
+		abline(v=0.5,col="black",lty=2)
+		title(main=paste(pid, perc_in_dbSNP, "% in dbSNP", sep=" "), cex.main = 1.5)
+
+		legend("topright", c("ALL","IN dbSNP"), fill=c("blue","red"), cex = 0.7, lwd=1, bty="n")
 	}
-
-	plot(dens_in_dbSNP, ylim = c(0,maxy), col = "red", cex.lab=1.5, cex.axis=1.5, lwd=3, xlab=paste("Mutant allele frequency from ", snvnum, " SNVs and ", nr_in_dbSNP, " in dbSNP", sep=""), xlim=c(0, 1.0),main="")
-	lines(dens_in_all,col = "blue", lwd = 3)
-	abline(v=0.5,col="black",lty=2)
-	title(main=paste(pid, perc_in_dbSNP, "% in dbSNP", sep=" "), cex.main = 1.5)
-
-	legend("topright", c("ALL","IN dbSNP"), fill=c("blue","red"), cex = 0.7, lwd=1, bty="n")
-}else{
-#	dens_in_dbSNP <- density(x = maf[maf[,1]==1,3])
-    dens_in_all <- density(x = maf[,3])
-    perc_in_dbSNP <- round((100*nr_in_dbSNP/snvnum),2)
-
-    maxy <- max(dens_in_all$y)
-#    if(max(dens_in_all$y) < max(dens_in_dbSNP$y)){
-#        maxy <- max(dens_in_dbSNP$y)
-#    }
-
-    plot(dens_in_all, ylim = c(0,maxy), col = "red", cex.lab=1.5, cex.axis=1.5, lwd=3, xlab=paste("Mutant allele frequency from ", snvnum, " SNVs and ", nr_in_dbSNP,     " in dbSNP", sep=""), xlim=c(0, 1.0),main="")
-#    lines(dens_in_all,col = "blue", lwd = 3)
-    abline(v=0.5,col="black",lty=2)
-    title(main=paste(pid, perc_in_dbSNP, "% in dbSNP", sep=" "), cex.main = 1.5)
-
-    legend("topright", c("ALL","IN dbSNP"), fill=c("blue","red"), cex = 0.7, lwd=1, bty="n")
 }
 
 dev.off()