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Add linear ratio to y-axis #2

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Add linear ratio to y-axis #2

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c07a3c1
add genome wide CNA plot on linear ratio
yunfeiguo Sep 22, 2022
5d46813
fix
yunfeiguo Sep 22, 2022
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29 changes: 27 additions & 2 deletions R/plotting.R
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,11 @@ plotSolutions <- function(hmmResults.cor, tumour_copy, chrs, outDir, counts,
logR.column = logR.column, call.column = call.column,
plotFileType=plotFileType, plotYLim=plotYLim,
plotSegs=plotSegs, estimateScPrevalence=estimateScPrevalence, main=id)
outPlotFile <- paste0(outDir, "/", id, "/", id, "_genomeWide_linearRatio")
plotGWSolution(hmmResults.cor, s, outPlotFile, seqinfo,
logR.column = logR.column, call.column = call.column,
plotFileType=plotFileType, plotYLim=plotYLim,
plotSegs=plotSegs, estimateScPrevalence=estimateScPrevalence, main=id, linear.ratio = TRUE)

### PLOT THE LOG RATIO DATA ALONG WITH COLOUR-CODING FOR PREDICTED CALLS ###
for (i in chrs){
Expand Down Expand Up @@ -140,6 +145,7 @@ plotGWSolution <- function(hmmResults.cor, s, outPlotFile, plotFileType="pdf",
seqinfo = NULL, plotSegs = TRUE,
cex = 0.5, cex.axis = 1.5, cex.lab=1.5, cex.text=1.5,
plotYLim=c(-2,2), estimateScPrevalence, main=NULL, spacing=4,
linear.ratio = FALSE,
turnDevOn=TRUE, turnDevOff=TRUE){
## plot genome wide figures for each solution ##
iter <- hmmResults.cor$results$iter
Expand Down Expand Up @@ -173,6 +179,7 @@ plotGWSolution <- function(hmmResults.cor, s, outPlotFile, plotFileType="pdf",
param = hmmResults.cor$results$param, chr=NULL,
logR.column = logR.column, call.column = call.column,
cex = cex, cex.axis = cex.axis, cex.lab=cex.lab,
linear.ratio = linear.ratio,
ploidy = ploidyAll, cytoBand=T, yrange=plotYLim, spacing=spacing, main=NULL) #ylim for plot
annotStr <- paste0("Tumor Fraction: ", signif(purityEst, digits=4), ", Ploidy: ", signif(ploidyEst, digits=3))
if (!is.null(coverage)){
Expand Down Expand Up @@ -207,6 +214,7 @@ plotGWSolution <- function(hmmResults.cor, s, outPlotFile, plotFileType="pdf",
plotCNlogRByChr <- function(dataIn, segs, param = NULL, logR.column = "logR",
call.column = "event", plotSegs = TRUE, seqinfo=NULL, chr=NULL, ploidy = NULL,
geneAnnot=NULL, yrange=c(-4,6), xlim=NULL, xaxt = "n", cex = 0.5, cex.axis = 1.5, cex.lab=1.5, gene.cex = 0.5,
linear.ratio = FALSE,
plot.title = NULL, spacing=4, cytoBand=T, alphaVal=1, main){
#color coding
alphaVal <- ceiling(alphaVal * 255); class(alphaVal) = "hexmode"
Expand Down Expand Up @@ -250,10 +258,17 @@ plotCNlogRByChr <- function(dataIn, segs, param = NULL, logR.column = "logR",
plot.title <- paste("Chromosome ",i,sep="")
}
## plot logR for bins ##
plot(coord,as.numeric(dataByChr[, logR.column]),col=cnCol[dataByChr[, call.column]],
if (linear.ratio){
plot(coord,as.numeric(dataByChr[, logR.column])^2,col=cnCol[dataByChr[, call.column]],
pch=16, ylim=yrange,
xlim=xlim, xaxt = xaxt, xlab="",ylab="Copy Number Ratio",
cex.lab=cex.lab,cex.axis=cex.axis, cex=cex,las=1)
} else {
plot(coord,as.numeric(dataByChr[, logR.column]),col=cnCol[dataByChr[, call.column]],
pch=16, ylim=yrange,
xlim=xlim, xaxt = xaxt, xlab="",ylab="Copy Number (log2 ratio)",
cex.lab=cex.lab,cex.axis=cex.axis, cex=cex,las=1)
}
title(plot.title, line = 1.25, xpd=NA, cex.main=1.5)
## plot centre line ##
lines(c(1,as.numeric(dataByChr[dim(dataByChr)[1],3])),rep(0,2),type="l",col="grey",lwd=0.75)
Expand Down Expand Up @@ -293,13 +308,23 @@ plotCNlogRByChr <- function(dataIn, segs, param = NULL, logR.column = "logR",
#midpt <- (as.numeric(dataIn[,"end"]) + as.numeric(dataIn[,"start"]))/2
#coord <- getGenomeWidePositions(dataIn[,"chr"],midpt)
coord <- getGenomeWidePositions(dataIn[,"chr"],dataIn[,"end"], seqinfo)
plot(coord$posns,as.numeric(dataIn[, logR.column]),
if (linear.ratio){
plot(coord$posns,as.numeric(dataIn[, logR.column])^2,
col=cnCol[as.character(dataIn[,call.column])],pch=16,xaxt="n", ylim=yrange,
xlim=c(1,as.numeric(coord$posns[length(coord$posns)])),
xlab="",ylab="Copy Number Ratio",
cex.lab=cex.lab,cex.axis=cex.axis,cex.main=1.5,cex=cex,las=1,bty="n",
#main=dataIn[1,"sample"])
main=main)
} else {
plot(coord$posns,as.numeric(dataIn[, logR.column]),
col=cnCol[as.character(dataIn[,call.column])],pch=16,xaxt="n", ylim=yrange,
xlim=c(1,as.numeric(coord$posns[length(coord$posns)])),
xlab="",ylab="Copy Number (log2 ratio)",
cex.lab=cex.lab,cex.axis=cex.axis,cex.main=1.5,cex=cex,las=1,bty="n",
#main=dataIn[1,"sample"])
main=main)
}
#plot segments

if (plotSegs){
Expand Down