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Addressing issues due to nan values, causing need finite 'ylim' value… #136

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Addressing issues due to nan values, causing need finite 'ylim' value… #136

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23 changes: 12 additions & 11 deletions scripts/makeGraph2.0.R
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Original file line number Diff line number Diff line change
Expand Up @@ -37,22 +37,23 @@ if (ratioFileInd) {

#Plotting in the log scale:
offset = 0.01

ratio$log2ratio <- log2(ratio$Ratio+offset) #added calculated column to main table so that the operation is only done once

png(filename = paste(args[ratioFileInd],".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$Chromosome==i)
tt <- which(ratio$Chromosome==i & is.na(ratio$log2ratio)==FALSE) #filtering rows with na values in log2ratio and it uses the calculated column instead of calculating it every time
if (length(tt)>0) {
plot(ratio$Start[tt],log2(ratio$Ratio[tt]+offset),xlab = paste ("position, chr",i),ylab = "normalized copy number profile (log2)",pch = ".",col = colors()[88])
tt <- which(ratio$Chromosome==i & ratio$CopyNumber>ploidy )
points(ratio$Start[tt],log2(ratio$Ratio[tt]+offset),pch = ".",col = colors()[136])
plot(ratio$Start[tt],ratio$log2ratio[tt],xlab = paste ("position, chr",i),ylab = "normalized copy number profile (log2)",pch = ".",col = colors()[88]) #it uses the calculated log2 column
tt <- which(ratio$Chromosome==i & ratio$CopyNumber>ploidy & is.na(ratio$log2ratio)==FALSE) #added the na filter to the points too and it uses the calculated column
points(ratio$Start[tt],ratio$log2ratio[tt],pch = ".",col = colors()[136])


tt <- which(ratio$Chromosome==i & ratio$CopyNumber<ploidy & ratio$CopyNumber!= -1)
points(ratio$Start[tt],log2(ratio$Ratio[tt]+offset),pch = ".",col = colors()[461])
tt <- which(ratio$Chromosome==i & ratio$CopyNumber<ploidy & ratio$CopyNumber!= -1 & is.na(ratio$log2ratio)==FALSE) #added the na filter to the points too and it uses the calculated column
points(ratio$Start[tt],ratio$log2ratio[tt],pch = ".",col = colors()[461])
tt <- which(ratio$Chromosome==i)

#UNCOMMENT HERE TO SEE THE PREDICTED COPY NUMBER LEVEL:
Expand All @@ -66,7 +67,7 @@ if (ratioFileInd) {

}
dev.off()

#------------------------------------------------------
#Plotting in raw ratio values:
png(filename = paste(args[ratioFileInd],".png",sep = ""), width = 1180, height = 1180,
Expand All @@ -77,12 +78,12 @@ if (ratioFileInd) {
#replace high values of ratio with value "maxLevelToPlot":
maxLevelToPlot <- 3
ratio$Ratio[ratio$Ratio>maxLevelToPlot]=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$CopyNumber>ploidy )
tt <- which(ratio$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)
Expand Down Expand Up @@ -161,4 +162,4 @@ if (BAFfileInd) {
}
dev.off()

} else {cat ("WARNING: To get a .png image with BAF profile, you can provide as input a file with suffix 'BAF.txt'\n")}
} else {cat ("WARNING: To get a .png image with BAF profile, you can provide as input a file with suffix 'BAF.txt'\n")}