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R/plotting.R
In TitanCNA: Subclonal copy number and LOH prediction from whole genome sequencing of tumours
Defines functions
plotSegmentMedians
plotAllelicCN
plotSubcloneProfiles
plotCNlogRByChr
plotClonalFrequency
plotAllelicRatio
Documented in
plotAllelicRatio
plotClonalFrequency
plotCNlogRByChr
plotSegmentMedians
plotSubcloneProfiles
# author: Gavin Ha
# Dana-Farber Cancer Institute
# Broad Institute
# contact: <gavinha@gmail.com> or <gavinha@broadinstitute.org>
# date: July 26, 2018
# data is the output format of TITAN cytoBand = {T,
# F} alphaVal = [0,1] geneAnnot is a dataframe with
# 4 columns: geneSymbol, chr, start, stop spacing
# is the distance between each track
plotAllelicRatio <- function(dataIn, chr = c(1:22), geneAnnot = NULL,
spacing = 4, xlim = NULL, ...) {
# color coding alphaVal <- ceiling(alphaVal * 255);
# class(alphaVal) = 'hexmode'
lohCol <- c("#00FF00", "#006400", "#0000FF", "#8B0000",
"#006400", "#BEBEBE", "#FF0000", "#BEBEBE",
"#FF0000")
# lohCol <- paste(lohCol,alphaVal,sep='') lohCol <-
# col2rgb(c('green','darkgreen','blue','darkgreen','grey','red'))
names(lohCol) <- c("HOMD", "DLOH", "NLOH", "GAIN",
"ALOH", "HET", "ASCNA", "BCNA", "UBCNA")
# use consistent chromosome naming convention
chr <- as.character(chr)
genomeStyle <- seqlevelsStyle(as.character(dataIn$Chr))[1]
chr <- mapSeqlevels(chr, genomeStyle, drop = FALSE)[1, ]
dataIn <- copy(dataIn)
if (!is.null(chr) && length(chr) == 1) {
for (i in chr) {
dataByChr <- dataIn[Chr == i]
dataByChr <- dataByChr[TITANcall != "OUT"]
# plot the data if (outfile!=''){
# pdf(outfile,width=10,height=6) }
par(mar = c(spacing, 8, 2, 2))
# par(xpd=NA)
if (missing(xlim)) {
xlim <- as.numeric(c(1, dataByChr[nrow(dataByChr), Position]))
}
plot(dataByChr[, Position], dataByChr[,
AllelicRatio], col = lohCol[dataByChr[,
TITANcall]], pch = 16, xaxt = "n",
las = 1, ylab = "Allelic Ratio", xlim = xlim,
...)
lines(as.numeric(c(1, dataByChr[nrow(dataByChr),
Position])), rep(0.5, 2), type = "l",
col = "grey", lwd = 3)
if (!is.null(geneAnnot)) {
plotGeneAnnotation(geneAnnot, i)
}
}
} else {
# plot for all chromosomes specified
dataIn <- dataIn[Chr %in% chr, ]
coord <- getGenomeWidePositions(dataIn[, Chr],
dataIn[, Position])
plot(coord$posns, as.numeric(dataIn[, AllelicRatio]),
col = lohCol[dataIn[, TITANcall]], pch = 16,
xaxt = "n", bty = "n", las = 1, ylab = "Allelic Fraction",
...)
lines(as.numeric(c(1, coord$posns[length(coord$posns)])),
rep(0.5, 2), type = "l", col = "grey",
lwd = 3)
plotChrLines(unique(dataIn[, Chr]), coord$chrBkpt,
c(-0.1, 1.1))
}
}
# data is the output format of TITAN alphaVal =
# [0,1] geneAnnot is a dataframe with 4 columns:
# geneSymbol, chr, start, stop spacing is the
# distance between each track
plotClonalFrequency <- function(dataIn, chr = c(1:22),
normal = NULL, geneAnnot = NULL, spacing = 4, xlim = NULL, ...) {
# color coding
lohCol <- c("#00FF00", "#006400", "#0000FF", "#8B0000",
"#006400", "#BEBEBE", "#FF0000", "#FF0000",
"#FF0000", "#FF0000", "#FF0000")
names(lohCol) <- c("HOMD", "DLOH", "NLOH", "GAIN",
"ALOH", "HET", "ASCNA", "BCNA", "UBCNA", "AMP", "HLAMP")
# use consistent chromosome naming convention
chr <- as.character(chr)
genomeStyle <- seqlevelsStyle(as.character(dataIn$Chr))[1]
chr <- mapSeqlevels(chr, genomeStyle, drop = FALSE)[1, ]
# get unique set of cluster and estimates table:
# 1st column is cluster number, 2nd column is
# clonal freq
clusters <- unique(dataIn[, list(ClonalCluster, CellularPrevalence)])
clusters <- clusters[!is.na(ClonalCluster), ] #exclude NA
if (!is.null(normal)) {
clusters[, CellularPrevalence := CellularPrevalence * (1 - as.numeric(normal))]
}
dataToUse <- copy(dataIn)
dataToUse <- dataToUse[TITANcall != "OUT", ]
#dataToUse[CellularPrevalence == "NA" | is.na(CellularPrevalence),
# list(ClonalCluster, CellularPrevalence) := c(NA, NA)]
# extract clonal info
clonalFreq <- dataToUse[, list(ClonalCluster, CellularPrevalence)]
# mode(clonalFreq) <- 'numeric' clonalFreq[,2] <- 1 - clonalFreq[,2]
if (!is.null(normal)) {
clonalFreq[, CellularPrevalence := CellularPrevalence * (1 - normal)]
}
clonalFreq[is.na(CellularPrevalence) | CellularPrevalence == "0" |
CellularPrevalence == "NA", CellularPrevalence := 0]
# plot per chromosome
if (!is.null(chr) && length(chr) == 1) {
for (i in chr) {
ind <- dataToUse[, Chr] == as.character(i)
dataByChr <- dataToUse[ind, ]
clonalFreq <- clonalFreq[ind, ]
# plot the data
par(mar = c(spacing, 8, 2, 2), xpd = NA)
# par(xpd=NA)
# PLOT CLONAL FREQUENCIES
if (missing(xlim)) {
xlim <- as.numeric(c(1, dataByChr[nrow(dataByChr), Position]))
}
plot(dataByChr[, Position], clonalFreq[, CellularPrevalence], type = "h",
col = lohCol[dataByChr[, TITANcall]], las = 1, xaxt = "n",
ylab = "Cellular Prevalence", xlim = xlim, ...)
# plot cluster lines and labels
if (nrow(clusters) > 0){
for (row in 1:nrow(clusters)) {
prevalence <- clusters[row, CellularPrevalence]
clustnum <- clusters[row, ClonalCluster]
chrLen <- as.numeric(dataByChr[dim(dataByChr)[1], Position])
lines(c(1 - chrLen * 0.02, chrLen * 1.02),
rep(prevalence , 2), type = "l", col = "grey", lwd = 3)
mtext(side = 4, at = prevalence,
text = paste("Z", clustnum, "", sep = ""),
cex = 1, padj = 0.5, adj = 1, las = 2, outer = FALSE)
mtext(side = 2, at = prevalence,
text = paste("Z", clustnum, "", sep = ""),
cex = 1, padj = 0.5,
adj = 0, las = 2, outer = FALSE)
}
}
if (!is.null(normal)) {
chrLen <- as.numeric(dataByChr[nrow(dataByChr), Position])
lines(c(1 - chrLen * 0.02, chrLen *
1.02), rep((1 - normal), 2), type = "l",
col = "#000000", lwd = 3)
#mtext(side = 4, at = (1 - normal),
#text = paste("-T-", sep = ""), padj = 0.5,
#adj = 1, cex = 1, las = 2, outer = FALSE)
#mtext(side = 2, at = (1 - normal),
#text = paste("-T-", sep = ""), padj = 0.5,
#adj = 0, cex = 1, las = 2, outer = FALSE)
}
if (!is.null(geneAnnot)) {
plotGeneAnnotation(geneAnnot, i)
}
}
} else {
# plot for all chromosomes specified
ind <- dataIn[Chr %in% chr, which=TRUE]
dataIn <- dataIn[ind]
clonalFreq <- clonalFreq[ind]
coord <- getGenomeWidePositions(dataIn[, Chr],
dataIn[, Position])
plot(coord$posns, clonalFreq[, CellularPrevalence], type = "h",
col = lohCol[dataIn[, TITANcall]], pch = 16,
xaxt = "n", las = 1, bty = "n", ylab = "Cellular Prevalence",
...)
plotChrLines(unique(dataIn[, Chr]), coord$chrBkpt,
c(-0.1, 1.1))
# plot cluster lines and labels
if (nrow(clusters) > 0){
for (row in 1:nrow(clusters)) {
prevalence <- clusters[row, CellularPrevalence]
clustnum <- clusters[row, ClonalCluster]
chrLen <- as.numeric(coord$posns[length(coord$posns)])
lines(c(1 - chrLen * 0.02, chrLen * 1.02),
rep(prevalence, 2), type = "l",
col = "grey", lwd = 3)
mtext(side = 4, at = prevalence, text = paste("Z",
clustnum, "", sep = ""), cex = 1,
padj = 0.5, adj = 1, las = 2, outer = FALSE)
mtext(side = 2, at = prevalence, text = paste("Z",
clustnum, "", sep = ""), cex = 1,
padj = 0.5, adj = 0, las = 2, outer = FALSE)
}
}
if (!is.null(normal)) {
chrLen <- as.numeric(coord$posns[length(coord$posns)])
lines(c(1 - chrLen * 0.02, chrLen * 1.02),
rep((1 - normal), 2), type = "l", col = "#000000",
lwd = 3)
}
}
}
# data is the output format of TITAN (*loh.txt)
# alphaVal = [0,1] geneAnnot is a dataframe with 4
# columns: geneSymbol, chr, start, stop spacing is
# the distance between each track
plotCNlogRByChr <- function(dataIn, chr = c(1:22), segs = NULL,
plotCorrectedCN = TRUE, geneAnnot = NULL,
ploidy = NULL, normal = NULL, spacing = 4, alphaVal = 1, xlim = NULL, ...) {
# color coding
alphaVal <- ceiling(alphaVal * 255)
class(alphaVal) = "hexmode"
cnCol <- c("#00FF00", "#006400", "#0000FF", "#880000",
"#BB0000", "#CC0000", "#DD0000", "#EE0000", rep("#FF0000",493))
cnCol <- paste(cnCol, alphaVal, sep = "")
# cnCol <-
# col2rgb(c('green','darkgreen','blue','darkred','red','brightred'))
names(cnCol) <- c(0:500)
# use consistent chromosome naming convention
chr <- as.character(chr)
genomeStyle <- seqlevelsStyle(as.character(dataIn$Chr))[1]
chr <- mapSeqlevels(chr, genomeStyle, drop = FALSE)[1, ]
if (plotCorrectedCN && "Corrected_Copy_Number" %in% colnames(dataIn)){
binCN <- "Corrected_Copy_Number"
segCN <- "Corrected_Copy_Number"
}else{
binCN <- "CopyNumber"
segCN <- "Copy_Number"
}
dataIn <- copy(dataIn)
## adjust logR values for ploidy ##
if (!is.null(ploidy)) {
if (is.null(normal)){
stop("plotCNlogRByChr: Please provide \"normal\" contamination estimate.")
}
dataIn[, LogRatio := LogRatio + log2(((1-normal)*ploidy+normal*2)/2)]
if (!is.null(segs)){
segs.sample <- copy(segs)
segs.sample[, Median_logR := Median_logR + log2(((1-normal)*ploidy+normal*2) / 2)]
}
}
if (!is.null(chr) && length(chr) == 1) {
for (i in chr) {
dataByChr <- dataIn[dataIn[, Chr] == i, ]
dataByChr <- dataByChr[dataByChr[, TITANcall] != "OUT", ]
# plot the data if (outfile!=''){
# pdf(outfile,width=10,height=6) }
par(mar = c(spacing, 8, 2, 2))
# par(xpd=NA)
if (missing(xlim)) {
xlim <- as.numeric(c(1, dataByChr[nrow(dataByChr), Position]))
}
coord <- as.numeric(dataByChr[, Position])
plot(coord, as.numeric(dataByChr[, LogRatio]),
col = cnCol[as.character(dataByChr[, get(binCN)])], pch = 16, xaxt = "n", las = 1, ylab = "Copy Number (log ratio)", xlim = xlim, ...)
lines(xlim, rep(0, 2), type = "l", col = "grey", lwd = 0.75)
if (!is.null(segs)){
segsByChr <- segs.sample[Chromosome == as.character(i), ]
tmp <- apply(segsByChr, 1, function(x){
lines(x[c("Start_Position.bp.","End_Position.bp.")],
rep(x["Median_logR"], 2), col = cnCol[as.character(x[segCN])], lwd = 3, lend = 1)
})
}
if (!is.null(geneAnnot)) {
plotGeneAnnotation(geneAnnot, i)
}
}
} else {
# plot for all chromosomes specified
dataIn <- dataIn[Chr %in% chr, ]
coord <- getGenomeWidePositions(dataIn[, Chr], dataIn[, Position])
plot(coord$posns, as.numeric(dataIn[, LogRatio]),
col = cnCol[as.character(dataIn[, get(binCN)])],
pch = 16, xaxt = "n", las = 1, bty = "n",
ylab = "Copy Number (log ratio)", ...)
lines(as.numeric(c(1, coord$posns[length(coord$posns)])),
rep(0, 2), type = "l", col = "grey", lwd = 2)
plotChrLines(dataIn[, Chr], coord$chrBkpt, par("yaxp")[1:2])
#plot segments
if (!is.null(segs)){
segs.sample <- segs.sample[Chromosome %in% chr]
coordEnd <- getGenomeWidePositions(segs.sample[, Chromosome], segs.sample[, End_Position.bp.])
coordStart <- coordEnd$posns - (segs.sample[, End_Position.bp.] - segs.sample[, Start_Position.bp.] + 1)
xlim <- as.numeric(c(1, coordEnd$posns[length(coordEnd$posns)]))
col <- cnCol[as.character(segs.sample[, get(segCN)])]
value <- as.numeric(segs.sample[, Median_logR])
mat <- as.data.frame(cbind(coordStart, coordEnd$posns, value, col))
rownames(mat) <- 1:nrow(mat)
tmp <- apply(mat, 1, function(x){
lines(x[1:2], rep(x[3], 2), col = x[4], lwd = 3, lend = 1)
})
}
}
}
plotSubcloneProfiles <- function(dataIn, chr = c(1:22), geneAnnot = NULL,
spacing = 4, xlim = NULL, ...){
args <- list(...)
lohCol <- c("#00FF00", "#006400", "#0000FF", "#8B0000",
"#006400", "#BEBEBE", "#FF0000", "#FF0000",
"#FF0000")
names(lohCol) <- c("HOMD", "DLOH", "NLOH", "GAIN",
"ALOH", "HET", "ASCNA", "BCNA", "UBCNA")
# use consistent chromosome naming convention
chr <- as.character(chr)
genomeStyle <- seqlevelsStyle(as.character(dataIn$Chr))[1]
chr <- mapSeqlevels(chr, genomeStyle, drop = FALSE)[1, ]
## pull out params from dots ##
if (!is.null(args$cex.axis)) cex.axis <- args$cex.axis else cex.axis <- 0.75
if (!is.null(args$cex.lab)) cex.lab <- args$cex.lab else cex.lab <- 0.75
dataIn <- copy(dataIn)
numClones <- sum(!is.na(unique(as.numeric(dataIn$ClonalCluster))))
if (numClones == 0){ numClones <- 1 }
# plot per chromosome
if (!is.null(chr) && length(chr) == 1) {
for (i in chr) {
ind <- dataIn[, Chr == as.character(i)]
dataByChr <- dataIn[ind, ]
## find x domain #
if (missing(xlim)) {
xlim <- c(1, dataByChr[.N, Position])
}
# plot the data
par(mar = c(spacing, 8, 2, 2), xpd = NA)
# PLOT SUBCLONE PROFILES
# setup plot to include X number of clones (numClones)
maxCN <- dataByChr[, max(CopyNumber)] + 1
ylim <- c(0, numClones * (maxCN + 2) - 1)
plot(0, type = "n", xaxt = "n", ylab = "",
xlim = xlim, ylim = ylim, yaxt = "n", ...)
axis(2, at = seq(ylim[1], ylim[2], 1), las = 1,
labels = rep(c(0:maxCN, "---"), numClones), cex.axis=cex.axis)
for (i in 1:numClones){
val <- dataByChr[, get(paste0("Subclone", i, ".CopyNumber"))]
cellPrev <- suppressWarnings(unique(dataByChr[, get(paste0("Subclone", i, ".Prevalence"))]))
cellPrev <- cellPrev[!is.na(cellPrev)] ## remove NA prevalence, leave subclonal prev
if (length(cellPrev) == 0){ cellPrev <- 0.0 } ## if only NA, then assign 0 prev
if (i > 1){
# shift values up for each subclone
val <- val + (numClones - 1) * (maxCN + 2)
}
call <- dataByChr[, get(paste0("Subclone", i, ".TITANcall"))]
points(dataByChr[, Position], val, col = lohCol[call], pch = 15, ...)
#lines(dataIn[, Position], val, col = lohCol[call], type = "l", lwd = 3, ...)
mtext(text = paste0("Subclone", i, "\n", format(cellPrev, digits = 2)),
side = 2, las = 0, line = 3,
at = i * (maxCN + 2) - (maxCN + 2) / 2 - 1, cex = cex.lab)
chrLen <- as.numeric(dataByChr[.N, Position])
lines(c(1 - chrLen * 0.035, chrLen *
1.035), rep(i * (maxCN + 2) - 1, 2), type = "l",
col = "black", lwd = 1.5)
}
if (!is.null(geneAnnot)) {
plotGeneAnnotation(geneAnnot, i)
}
}
} else {
# plot for all chromosomes specified
dataIn <- dataIn[Chr %in% chr, ]
coord <- getGenomeWidePositions(dataIn[, Chr], dataIn[, Position])
# setup plot to include X number of clones (numClones)
maxCN <- dataIn[, max(CopyNumber)] + 1
ylim <- c(0, numClones * (maxCN + 2) - 1)
xlim <- as.numeric(c(1, coord$posns[length(coord$posns)]))
plot(0, type = "n", xaxt = "n", bty = "n", ylab = "", xlim = xlim,
ylim = ylim, yaxt = "n", ...)
axis(2, at = seq(ylim[1], ylim[2], 1), las = 1,
labels = rep(c(0:maxCN, "---"), numClones))
for (i in 1:numClones){
val <- dataIn[, get(paste0("Subclone", i, ".CopyNumber"))]
if (i > 1){
# shift values up for each subclone
val <- val + (numClones - 1) * (maxCN + 2)
}
call <- dataIn[, get(paste0("Subclone", i, ".TITANcall"))]
points(coord$posns, val, col = lohCol[call], pch = 15, ...)
mtext(text = paste0("Subclone", i), side = 2, las = 0,
line = 2, at = i * (maxCN + 2) - (maxCN + 2) / 2 - 1, cex = 0.75)
chrLen <- xlim[2]
lines(c(1 - chrLen * 0.035, chrLen *
1.035), rep(i * (maxCN + 2) - 1, 2), type = "l",
col = "black", lwd = 1.5)
}
plotChrLines(unique(dataIn[, Chr]), coord$chrBkpt, ylim)
}
}
## TODO: Not completed ##
plotAllelicCN <- function(dataIn, resultType = "AllelicRatio",
chr = NULL, geneAnnot = NULL,
ploidy = 2, spacing = 4, alphaVal = 1, xlim = NULL, ...) {
# color coding
alphaVal <- ceiling(alphaVal * 255)
class(alphaVal) = "hexmode"
cnCol <- c("#00FF00", "#006400", "#0000FF", "#880000",
"#BB0000", "#CC0000", "#DD0000", "#EE0000",
"#FF0000")
cnCol <- paste(cnCol, alphaVal, sep = "")
# cnCol <-
# col2rgb(c('green','darkgreen','blue','darkred','red','brightred'))
names(cnCol) <- c("0", "1", "2", "3", "4", "5", "6", "7", "8")
dataIn <- copy(dataIn)
## compute allelic copy number for each
dataIn[, Allele.1 := get(resultType) * 2^LogRatio*ploidy]
dataIn[, Allele.2 := (1 - get(resultType)) * 2^LogRatio*ploidy]
if (!is.null(chr) && length(chr) == 1) {
for (i in chr) {
dataByChr <- dataIn[Chr == i, ]
dataByChr <- dataByChr[dataByChr[, TITANcall] != "OUT", ]
par(mar = c(spacing, 8, 2, 2))
# par(xpd=NA)
if (missing(xlim)) {
xlim <- as.numeric(c(1, dataByChr[.N, Position]))
}
coord <- dataByChr[, Position]
plot(coord, dataByChr[, Allele.1],
col = cnCol[as.character(dataByChr[, CopyNumber])], pch = 16,
xaxt = "n", las = 1, ylab = "Copy Number",
xlim = xlim, ...)
points(coord, dataByChr[, Allele.2],
col = cnCol[as.character(dataByChr[, CopyNumber])],
pch = 16)
lines(xlim, rep(0, 2), type = "l", col = "grey", lwd = 0.75)
if (!is.null(geneAnnot)) {
plotGeneAnnotation(geneAnnot, i)
}
}
}
}
plotSegmentMedians <- function(dataIn, resultType = "LogRatio",
plotType = "CopyNumber", plotCorrectedCN = TRUE,
chr = c(1:22), geneAnnot = NULL, ploidy = NULL, spacing = 4, alphaVal = 1, xlim = NULL, plot.new = FALSE, lwd = 8, ...){
## check for the possible resultType to plot ##
if (!resultType %in% c("LogRatio", "AllelicRatio", "HaplotypeRatio")){
stop("plotSegmentMedians: resultType must be 'LogRatio', 'AllelicRatio', or 'HaplotypeRatio'")
}
if (!plotType %in% c("CopyNumber", "Ratio")){
stop("plotSegmentMedians: plotType must be 'CopyNumber' or 'Ratio'")
}
# use consistent chromosome naming convention
chr <- as.character(chr)
genomeStyle <- seqlevelsStyle(as.character(dataIn$Chr))[1]
chr <- mapSeqlevels(chr, genomeStyle, drop = FALSE)[1, ]
dataType <- c("Median_logR", "Median_Ratio", "Median_HaplotypeRatio")
names(dataType) <- c("LogRatio", "AllelicRatio", "HaplotypeRatio")
axisName <- c("Copy Number (log ratio)", "Allelic Ratio", "Haplotype Fraction")
names(axisName) <- c("LogRatio", "AllelicRatio", "HaplotypeRatio")
axisNameCN <- c("Copy Number", "Allelic Copy Number")
names(axisNameCN) <- c("LogRatio", "AllelicRatio")
colName <- c("Copy_Number","TITAN_call", "TITAN_call")
names(colName) <- c("LogRatio", "AllelicRatio", "HaplotypeRatio")
if (plotCorrectedCN && "Corrected_Copy_Number" %in% colnames(dataIn)){
colName[1] <- "Corrected_Copy_Number"
}
dataIn <- copy(dataIn)
# color coding
alphaVal <- ceiling(alphaVal * 255)
class(alphaVal) = "hexmode"
if (resultType == "LogRatio"){
cnCol <- c("#00FF00", "#006400", "#0000FF", "#880000",
"#BB0000", "#CC0000", "#DD0000", "#EE0000", rep("#FF0000",493))
cnCol <- paste(cnCol, alphaVal, sep = "")
# cnCol <-
# col2rgb(c('green','darkgreen','blue','darkred','red','brightred'))
names(cnCol) <- c(0:500)
}else if (resultType %in% c("AllelicRatio", "HaplotypeRatio")){
cnCol <- c("#00FF00", "#006400", "#0000FF", "#8B0000",
"#006400", "#BEBEBE", "#FF0000", "#BEBEBE", "#FF0000", "#FF0000", "#FF0000")
# lohCol <- paste(lohCol,alphaVal,sep='') lohCol <-
# col2rgb(c('green','darkgreen','blue','darkgreen','grey','red'))
names(cnCol) <- c("HOMD", "DLOH", "NLOH", "GAIN",
"ALOH", "HET", "ASCNA", "BCNA", "UBCNA", "AMP", "HLAMP")
}
if (plotType == "CopyNumber"){
axisName <- axisNameCN
}
if (is.null(ploidy)){
ploidy <- 2
}
## adjust logR values for ploidy ##
if (resultType == "LogRatio") {
if (plotType == "CopyNumber"){
#dataIn[, (dataType[resultType]) := 2 ^ get(dataType[resultType]) * 2]
}else{
dataIn[, (dataType[resultType]) := get(dataType[resultType]) + log2(ploidy/2)]
}
}
## allelic or haplotype copy number
if (resultType %in% c("AllelicRatio") && plotType == "CopyNumber"){
## compute allelic copy number for each
#dataIn[, Allele.1 := get(dataType[resultType]) * 2 ^ Median_logR * ploidy]
#dataIn[, Allele.2 := (1 - get(dataType[resultType])) * 2 ^ Median_logR * ploidy]
}
# plot for specified chromosomes #
if (!is.null(chr) && length(chr) == 1) {
for (i in chr) {
dataByChr <- dataIn[Chromosome == i, ]
dataByChr <- dataByChr[TITAN_call != "OUT", ]
# plot the data
par(mar = c(spacing, 8, 2, 2))
if (missing(xlim)) {
xlim <- as.numeric(c(1, dataByChr[.N, End_Position.bp.]))
}
col <- cnCol[as.character(dataByChr[, get(colName[resultType])])]
coord <- dataByChr[, .(Start_Position.bp., End_Position.bp.)]
if (plotType == "CopyNumber"){
if (resultType %in% c("AllelicRatio")){
value <- dataByChr[, MajorCN]
value2 <- dataByChr[, MinorCN]
}else{
value <- dataByChr[, get(colName[resultType])]
}
}else{
value <- dataByChr[, get(dataType[resultType])]
}
if (plot.new){
plot(0, type = "n", col = col, xaxt = "n", las = 1,
ylab = axisName[resultType], xlim = xlim, ...)
}
tmp <- apply(cbind(coord, value, col), 1, function(x){
lines(x[1:2], rep(x[3], 2), col = x[4], lend = 1, lwd = lwd)
})
if (plotType == "CopyNumber" && resultType %in% c("AllelicRatio")){
tmp <- apply(cbind(coord, value2, col), 1, function(x){
lines(x[1:2], rep(x[3], 2), col = x[4], lend = 1, lwd = lwd)
})
}
if (plotType == "Ratio"){
lines(xlim, rep(0, 2), type = "l", col = "grey", lwd = 0.75)
}
if (!is.null(geneAnnot)) {
plotGeneAnnotation(geneAnnot, i)
}
}
} else {
# plot for all chromosomes specified
dataIn <- dataIn[Chromosome %in% chr, ]
coordEnd <- getGenomeWidePositions(dataIn[, Chromosome], dataIn[, End_Position.bp.])
coordStart <- coordEnd$posns - (dataIn[, End_Position.bp.] - dataIn[, Start_Position.bp.] + 1)
xlim <- as.numeric(c(1, coordEnd$posns[length(coordEnd$posns)]))
col <- cnCol[as.character(dataIn[, get(colName[resultType])])]
if (plotType == "CopyNumber"){
if (resultType %in% c("AllelicRatio")){
value <- dataIn[, MajorCN]
value2 <- dataIn[, MinorCN]
}else{
value <- dataIn[, Copy_Number]
}
}else{
value <- dataIn[, get(dataType[resultType])]
}
#mat <- data.table(cbind(coordStart, coordEnd$posns, value, col))
#rownames(mat) <- 1:nrow(mat)
if (plot.new){
plot(0, type = "n", col = col, xaxt = "n", las = 1,
ylab = axisName[resultType], xlim = xlim, ...)
}
tmp <- apply(data.table(coordStart, coordEnd$posns, value, col), 1, function(x){
lines(x[1:2], rep(x[3], 2), col = x[4], lend = 1, lwd = lwd)
})
if (plotType == "CopyNumber" && resultType %in% c("AllelicRatio")){
tmp <- apply(data.table(coordStart, coordEnd$posns, value2, col), 1, function(x){
lines(x[1:2], rep(x[3], 2), col = x[4], lend = 1, lwd = lwd)
})
}
if (plotType == "Ratio"){
lines(xlim, rep(0, 2), type = "l", col = "grey", lwd = 2)
}
plotChrLines(dataIn[, Chromosome], coordEnd$chrBkpt, par("yaxp")[1:2])
}
}
plotGeneAnnotation <- function(geneAnnot, chr = 1, ...) {
colnames(geneAnnot) <- c("Gene", "Chr", "Start",
"Stop")
geneAnnot <- geneAnnot[geneAnnot[, "Chr"] == as.character(chr),
]
if (nrow(geneAnnot) != 0) {
for (g in 1:dim(geneAnnot)[1]) {
# print(geneAnnot[g,'Gene'])
abline(v = as.numeric(geneAnnot[g, "Start"]),
col = "black", lty = 3, xpd = FALSE)
abline(v = as.numeric(geneAnnot[g, "Stop"]),
col = "black", lty = 3, xpd = FALSE)
atP <- (as.numeric(geneAnnot[g, "Stop"]) -
as.numeric(geneAnnot[g, "Start"]))/2 +
as.numeric(geneAnnot[g, "Start"])
# if (atP < dataByChr[1,2]){ atP <- dataByChr[1,2]
# }else if (atP > dataByChr[dim(dataByChr)[1],2]){
# atP <- dataByChr[dim(dataByChr)[1],2] }
mtext(geneAnnot[g, "Gene"], side = 3, line = 0,
at = atP, ...)
}
}
}
plotChrLines <- function(chrs, chrBkpt, yrange) {
# plot vertical chromosome lines
for (j in 1:length(chrBkpt)) {
lines(rep(chrBkpt[j], 2), yrange, type = "l",
lty = 2, col = "black", lwd = 0.75)
}
numLines <- length(chrBkpt)
mid <- (chrBkpt[1:(numLines - 1)] + chrBkpt[2:numLines])/2
chrsToShow <- gsub("chr", "", unique(chrs))
axis(side = 1, at = mid, labels = c(chrsToShow),
cex.axis = 1.5, tick = FALSE)
}
getGenomeWidePositions <- function(chrs, posns, seqinfo = NULL) {
# create genome coordinate scaffold
positions <- as.numeric(posns)
chrsNum <- unique(chrs)
chrBkpt <- rep(0, length(chrsNum) + 1)
prevChrPos <- 0
for (i in 2:length(chrsNum)) {
chrInd <- which(chrs == chrsNum[i])
if (!is.null(seqinfo)){
prevChrPos <- seqinfo[i-1, "seqlengths"] + prevChrPos
}else{
prevChrPos <- positions[chrInd[1] - 1]
}
chrBkpt[i] = prevChrPos
positions[chrInd] = positions[chrInd] + prevChrPos
}
chrBkpt[i + 1] <- positions[length(positions)]
return(list(posns = positions, chrBkpt = chrBkpt))
}
### modify SNPchip function "plotIdiogram"
plotIdiogram.hg38 <- function (chromosome, cytoband, seqinfo, cytoband.ycoords, xlim,
ylim = c(0, 2), new = TRUE, label.cytoband = TRUE, label.y = NULL,
srt, cex.axis = 1, outer = FALSE, taper = 0.15, verbose = FALSE,
unit = c("bp", "Mb"), is.lattice = FALSE, ...)
{
def.par <- par(no.readonly = TRUE, mar = c(4.1, 0.1, 3.1,
2.1))
on.exit(def.par)
if (is.lattice) {
segments <- lsegments
polygon <- lpolygon
}
cytoband <- cytoband[cytoband[, "chrom"] == chromosome, ]
unit <- match.arg(unit)
if (unit == "Mb") {
cytoband$start <- cytoband$start/1e+06
cytoband$end <- cytoband$end/1e+06
}
if (missing(cytoband.ycoords)) {
cytoband.ycoords <- ylim
}
rownames(cytoband) <- as.character(cytoband[, "name"])
sl <- seqlengths(seqinfo)[chromosome]
if (missing(xlim))
xlim <- c(0, sl)
if (unit == "Mb")
xlim <- xlim/1e+06
cytoband_p <- cytoband[grep("^p", rownames(cytoband), value = TRUE),
]
cytoband_q <- cytoband[grep("^q", rownames(cytoband), value = TRUE),
]
p.bands <- nrow(cytoband_p)
cut.left <- c()
cut.right <- c()
for (i in seq_len(nrow(cytoband))) {
if (i == 1) {
cut.left[i] <- TRUE
cut.right[i] <- FALSE
}
else if (i == p.bands) {
cut.left[i] <- FALSE
cut.right[i] <- TRUE
}
else if (i == (p.bands + 1)) {
cut.left[i] <- TRUE
cut.right[i] <- FALSE
}
else if (i == nrow(cytoband)) {
cut.left[i] <- FALSE
cut.right[i] <- TRUE
}
else {
cut.left[i] <- FALSE
cut.right[i] <- FALSE
}
}
for (i in seq_len(nrow(cytoband))) {
if (as.character(cytoband[i, "gieStain"]) == "stalk") {
cut.right[i - 1] <- TRUE
cut.left[i] <- NA
cut.right[i] <- NA
cut.left[i + 1] <- TRUE
}
}
include <- cytoband[, "end"] > xlim[1] & cytoband[, "start"] <
xlim[2]
cytoband <- cytoband[include, ]
N <- nrow(cytoband)
cut.left <- cut.left[include]
cut.right <- cut.right[include]
if (new) {
xx <- c(0, cytoband[nrow(cytoband), "end"])
yy <- cytoband.ycoords
plot(xx, yy, xlim = xlim, type = "n", xlab = "", ylab = "",
axes = FALSE, yaxs = "i", ylim = ylim, ...)
}
top <- cytoband.ycoords[2]
bot <- cytoband.ycoords[1]
h <- top - bot
p <- taper
for (i in seq_len(nrow(cytoband))) {
start <- cytoband[i, "start"]
last <- cytoband[i, "end"]
delta = (last - start)/4
getStain <- function(stain) {
switch(stain, gneg = "grey100", gpos25 = "grey90",
gpos50 = "grey70", gpos75 = "grey40", gpos100 = "grey0",
gvar = "grey100", stalk = "brown3", acen = "brown4",
"white")
}
color <- getStain(as.character(cytoband[i, "gieStain"]))
if (is.na(cut.left[i]) & is.na(cut.right[i])) {
delta <- (last - start)/3
segments(start + delta, cytoband.ycoords[1], start +
delta, cytoband.ycoords[2])
segments(last - delta, cytoband.ycoords[1], last -
delta, cytoband.ycoords[2])
}
else if (cut.left[i] & cut.right[i]) {
yy <- c(bot + p * h, bot, bot, bot + p * h, top -
p * h, top, top, top - p * h)
polygon(c(start, start + delta, last - delta, last,
last, last - delta, start + delta, start), yy,
col = color)
}
else if (cut.left[i]) {
yy <- c(bot + p * h, bot, bot, top, top, top - p *
h)
polygon(c(start, start + delta, last, last, start +
delta, start), yy, col = color)
}
else if (cut.right[i]) {
yy <- c(bot, bot, bot + p * h, top - p * h, top,
top)
polygon(c(start, last - delta, last, last, last -
delta, start), yy, col = color)
}
else {
polygon(c(start, last, last, start), c(bot, bot,
top, top), col = color)
}
}
my.x <- (cytoband[, "start"] + cytoband[, "end"])/2
if (label.cytoband & !is.lattice) {
if (is.null(label.y)) {
axis(1, at = my.x, labels = rownames(cytoband), outer = outer,
cex.axis = cex.axis, line = 1, las = 3, tick = FALSE)
axis(1, at = cytoband$start, outer = outer, cex.axis = cex.axis,
line = 1, las = 3, labels = FALSE)
}
else {
if (!is.numeric(label.y)) {
warning("label.y must be numeric -- using default y coordinates for cytoband labels")
label.y <- bot - p * h
}
if (missing(srt))
srt <- 90
text(x = my.x, y = rep(label.y, length(my.x)), labels = rownames(cytoband),
srt = srt)
}
}
return()
}
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Defines functions plotSegmentMedians plotAllelicCN plotSubcloneProfiles plotCNlogRByChr plotClonalFrequency plotAllelicRatio
Documented in plotAllelicRatio plotClonalFrequency plotCNlogRByChr plotSegmentMedians plotSubcloneProfiles
# author: Gavin Ha
# Dana-Farber Cancer Institute
# Broad Institute
# contact: <gavinha@gmail.com> or <gavinha@broadinstitute.org>
# date: July 26, 2018
# data is the output format of TITAN cytoBand = {T,
# F} alphaVal = [0,1] geneAnnot is a dataframe with
# 4 columns: geneSymbol, chr, start, stop spacing
# is the distance between each track
plotAllelicRatio <- function(dataIn, chr = c(1:22), geneAnnot = NULL,
spacing = 4, xlim = NULL, ...) {
# color coding alphaVal <- ceiling(alphaVal * 255);
# class(alphaVal) = 'hexmode'
lohCol <- c("#00FF00", "#006400", "#0000FF", "#8B0000",
"#006400", "#BEBEBE", "#FF0000", "#BEBEBE",
"#FF0000")
# lohCol <- paste(lohCol,alphaVal,sep='') lohCol <-
# col2rgb(c('green','darkgreen','blue','darkgreen','grey','red'))
names(lohCol) <- c("HOMD", "DLOH", "NLOH", "GAIN",
"ALOH", "HET", "ASCNA", "BCNA", "UBCNA")
# use consistent chromosome naming convention
chr <- as.character(chr)
genomeStyle <- seqlevelsStyle(as.character(dataIn$Chr))[1]
chr <- mapSeqlevels(chr, genomeStyle, drop = FALSE)[1, ]
dataIn <- copy(dataIn)
if (!is.null(chr) && length(chr) == 1) {
for (i in chr) {
dataByChr <- dataIn[Chr == i]
dataByChr <- dataByChr[TITANcall != "OUT"]
# plot the data if (outfile!=''){
# pdf(outfile,width=10,height=6) }
par(mar = c(spacing, 8, 2, 2))
# par(xpd=NA)
if (missing(xlim)) {
xlim <- as.numeric(c(1, dataByChr[nrow(dataByChr), Position]))
}
plot(dataByChr[, Position], dataByChr[,
AllelicRatio], col = lohCol[dataByChr[,
TITANcall]], pch = 16, xaxt = "n",
las = 1, ylab = "Allelic Ratio", xlim = xlim,
...)
lines(as.numeric(c(1, dataByChr[nrow(dataByChr),
Position])), rep(0.5, 2), type = "l",
col = "grey", lwd = 3)
if (!is.null(geneAnnot)) {
plotGeneAnnotation(geneAnnot, i)
}
}
} else {
# plot for all chromosomes specified
dataIn <- dataIn[Chr %in% chr, ]
coord <- getGenomeWidePositions(dataIn[, Chr],
dataIn[, Position])
plot(coord$posns, as.numeric(dataIn[, AllelicRatio]),
col = lohCol[dataIn[, TITANcall]], pch = 16,
xaxt = "n", bty = "n", las = 1, ylab = "Allelic Fraction",
...)
lines(as.numeric(c(1, coord$posns[length(coord$posns)])),
rep(0.5, 2), type = "l", col = "grey",
lwd = 3)
plotChrLines(unique(dataIn[, Chr]), coord$chrBkpt,
c(-0.1, 1.1))
}
}
# data is the output format of TITAN alphaVal =
# [0,1] geneAnnot is a dataframe with 4 columns:
# geneSymbol, chr, start, stop spacing is the
# distance between each track
plotClonalFrequency <- function(dataIn, chr = c(1:22),
normal = NULL, geneAnnot = NULL, spacing = 4, xlim = NULL, ...) {
# color coding
lohCol <- c("#00FF00", "#006400", "#0000FF", "#8B0000",
"#006400", "#BEBEBE", "#FF0000", "#FF0000",
"#FF0000", "#FF0000", "#FF0000")
names(lohCol) <- c("HOMD", "DLOH", "NLOH", "GAIN",
"ALOH", "HET", "ASCNA", "BCNA", "UBCNA", "AMP", "HLAMP")
# use consistent chromosome naming convention
chr <- as.character(chr)
genomeStyle <- seqlevelsStyle(as.character(dataIn$Chr))[1]
chr <- mapSeqlevels(chr, genomeStyle, drop = FALSE)[1, ]
# get unique set of cluster and estimates table:
# 1st column is cluster number, 2nd column is
# clonal freq
clusters <- unique(dataIn[, list(ClonalCluster, CellularPrevalence)])
clusters <- clusters[!is.na(ClonalCluster), ] #exclude NA
if (!is.null(normal)) {
clusters[, CellularPrevalence := CellularPrevalence * (1 - as.numeric(normal))]
}
dataToUse <- copy(dataIn)
dataToUse <- dataToUse[TITANcall != "OUT", ]
#dataToUse[CellularPrevalence == "NA" | is.na(CellularPrevalence),
# list(ClonalCluster, CellularPrevalence) := c(NA, NA)]
# extract clonal info
clonalFreq <- dataToUse[, list(ClonalCluster, CellularPrevalence)]
# mode(clonalFreq) <- 'numeric' clonalFreq[,2] <- 1 - clonalFreq[,2]
if (!is.null(normal)) {
clonalFreq[, CellularPrevalence := CellularPrevalence * (1 - normal)]
}
clonalFreq[is.na(CellularPrevalence) | CellularPrevalence == "0" |
CellularPrevalence == "NA", CellularPrevalence := 0]
# plot per chromosome
if (!is.null(chr) && length(chr) == 1) {
for (i in chr) {
ind <- dataToUse[, Chr] == as.character(i)
dataByChr <- dataToUse[ind, ]
clonalFreq <- clonalFreq[ind, ]
# plot the data
par(mar = c(spacing, 8, 2, 2), xpd = NA)
# par(xpd=NA)
# PLOT CLONAL FREQUENCIES
if (missing(xlim)) {
xlim <- as.numeric(c(1, dataByChr[nrow(dataByChr), Position]))
}
plot(dataByChr[, Position], clonalFreq[, CellularPrevalence], type = "h",
col = lohCol[dataByChr[, TITANcall]], las = 1, xaxt = "n",
ylab = "Cellular Prevalence", xlim = xlim, ...)
# plot cluster lines and labels
if (nrow(clusters) > 0){
for (row in 1:nrow(clusters)) {
prevalence <- clusters[row, CellularPrevalence]
clustnum <- clusters[row, ClonalCluster]
chrLen <- as.numeric(dataByChr[dim(dataByChr)[1], Position])
lines(c(1 - chrLen * 0.02, chrLen * 1.02),
rep(prevalence , 2), type = "l", col = "grey", lwd = 3)
mtext(side = 4, at = prevalence,
text = paste("Z", clustnum, "", sep = ""),
cex = 1, padj = 0.5, adj = 1, las = 2, outer = FALSE)
mtext(side = 2, at = prevalence,
text = paste("Z", clustnum, "", sep = ""),
cex = 1, padj = 0.5,
adj = 0, las = 2, outer = FALSE)
}
}
if (!is.null(normal)) {
chrLen <- as.numeric(dataByChr[nrow(dataByChr), Position])
lines(c(1 - chrLen * 0.02, chrLen *
1.02), rep((1 - normal), 2), type = "l",
col = "#000000", lwd = 3)
#mtext(side = 4, at = (1 - normal),
#text = paste("-T-", sep = ""), padj = 0.5,
#adj = 1, cex = 1, las = 2, outer = FALSE)
#mtext(side = 2, at = (1 - normal),
#text = paste("-T-", sep = ""), padj = 0.5,
#adj = 0, cex = 1, las = 2, outer = FALSE)
}
if (!is.null(geneAnnot)) {
plotGeneAnnotation(geneAnnot, i)
}
}
} else {
# plot for all chromosomes specified
ind <- dataIn[Chr %in% chr, which=TRUE]
dataIn <- dataIn[ind]
clonalFreq <- clonalFreq[ind]
coord <- getGenomeWidePositions(dataIn[, Chr],
dataIn[, Position])
plot(coord$posns, clonalFreq[, CellularPrevalence], type = "h",
col = lohCol[dataIn[, TITANcall]], pch = 16,
xaxt = "n", las = 1, bty = "n", ylab = "Cellular Prevalence",
...)
plotChrLines(unique(dataIn[, Chr]), coord$chrBkpt,
c(-0.1, 1.1))
# plot cluster lines and labels
if (nrow(clusters) > 0){
for (row in 1:nrow(clusters)) {
prevalence <- clusters[row, CellularPrevalence]
clustnum <- clusters[row, ClonalCluster]
chrLen <- as.numeric(coord$posns[length(coord$posns)])
lines(c(1 - chrLen * 0.02, chrLen * 1.02),
rep(prevalence, 2), type = "l",
col = "grey", lwd = 3)
mtext(side = 4, at = prevalence, text = paste("Z",
clustnum, "", sep = ""), cex = 1,
padj = 0.5, adj = 1, las = 2, outer = FALSE)
mtext(side = 2, at = prevalence, text = paste("Z",
clustnum, "", sep = ""), cex = 1,
padj = 0.5, adj = 0, las = 2, outer = FALSE)
}
}
if (!is.null(normal)) {
chrLen <- as.numeric(coord$posns[length(coord$posns)])
lines(c(1 - chrLen * 0.02, chrLen * 1.02),
rep((1 - normal), 2), type = "l", col = "#000000",
lwd = 3)
}
}
}
# data is the output format of TITAN (*loh.txt)
# alphaVal = [0,1] geneAnnot is a dataframe with 4
# columns: geneSymbol, chr, start, stop spacing is
# the distance between each track
plotCNlogRByChr <- function(dataIn, chr = c(1:22), segs = NULL,
plotCorrectedCN = TRUE, geneAnnot = NULL,
ploidy = NULL, normal = NULL, spacing = 4, alphaVal = 1, xlim = NULL, ...) {
# color coding
alphaVal <- ceiling(alphaVal * 255)
class(alphaVal) = "hexmode"
cnCol <- c("#00FF00", "#006400", "#0000FF", "#880000",
"#BB0000", "#CC0000", "#DD0000", "#EE0000", rep("#FF0000",493))
cnCol <- paste(cnCol, alphaVal, sep = "")
# cnCol <-
# col2rgb(c('green','darkgreen','blue','darkred','red','brightred'))
names(cnCol) <- c(0:500)
# use consistent chromosome naming convention
chr <- as.character(chr)
genomeStyle <- seqlevelsStyle(as.character(dataIn$Chr))[1]
chr <- mapSeqlevels(chr, genomeStyle, drop = FALSE)[1, ]
if (plotCorrectedCN && "Corrected_Copy_Number" %in% colnames(dataIn)){
binCN <- "Corrected_Copy_Number"
segCN <- "Corrected_Copy_Number"
}else{
binCN <- "CopyNumber"
segCN <- "Copy_Number"
}
dataIn <- copy(dataIn)
## adjust logR values for ploidy ##
if (!is.null(ploidy)) {
if (is.null(normal)){
stop("plotCNlogRByChr: Please provide \"normal\" contamination estimate.")
}
dataIn[, LogRatio := LogRatio + log2(((1-normal)*ploidy+normal*2)/2)]
if (!is.null(segs)){
segs.sample <- copy(segs)
segs.sample[, Median_logR := Median_logR + log2(((1-normal)*ploidy+normal*2) / 2)]
}
}
if (!is.null(chr) && length(chr) == 1) {
for (i in chr) {
dataByChr <- dataIn[dataIn[, Chr] == i, ]
dataByChr <- dataByChr[dataByChr[, TITANcall] != "OUT", ]
# plot the data if (outfile!=''){
# pdf(outfile,width=10,height=6) }
par(mar = c(spacing, 8, 2, 2))
# par(xpd=NA)
if (missing(xlim)) {
xlim <- as.numeric(c(1, dataByChr[nrow(dataByChr), Position]))
}
coord <- as.numeric(dataByChr[, Position])
plot(coord, as.numeric(dataByChr[, LogRatio]),
col = cnCol[as.character(dataByChr[, get(binCN)])], pch = 16, xaxt = "n", las = 1, ylab = "Copy Number (log ratio)", xlim = xlim, ...)
lines(xlim, rep(0, 2), type = "l", col = "grey", lwd = 0.75)
if (!is.null(segs)){
segsByChr <- segs.sample[Chromosome == as.character(i), ]
tmp <- apply(segsByChr, 1, function(x){
lines(x[c("Start_Position.bp.","End_Position.bp.")],
rep(x["Median_logR"], 2), col = cnCol[as.character(x[segCN])], lwd = 3, lend = 1)
})
}
if (!is.null(geneAnnot)) {
plotGeneAnnotation(geneAnnot, i)
}
}
} else {
# plot for all chromosomes specified
dataIn <- dataIn[Chr %in% chr, ]
coord <- getGenomeWidePositions(dataIn[, Chr], dataIn[, Position])
plot(coord$posns, as.numeric(dataIn[, LogRatio]),
col = cnCol[as.character(dataIn[, get(binCN)])],
pch = 16, xaxt = "n", las = 1, bty = "n",
ylab = "Copy Number (log ratio)", ...)
lines(as.numeric(c(1, coord$posns[length(coord$posns)])),
rep(0, 2), type = "l", col = "grey", lwd = 2)
plotChrLines(dataIn[, Chr], coord$chrBkpt, par("yaxp")[1:2])
#plot segments
if (!is.null(segs)){
segs.sample <- segs.sample[Chromosome %in% chr]
coordEnd <- getGenomeWidePositions(segs.sample[, Chromosome], segs.sample[, End_Position.bp.])
coordStart <- coordEnd$posns - (segs.sample[, End_Position.bp.] - segs.sample[, Start_Position.bp.] + 1)
xlim <- as.numeric(c(1, coordEnd$posns[length(coordEnd$posns)]))
col <- cnCol[as.character(segs.sample[, get(segCN)])]
value <- as.numeric(segs.sample[, Median_logR])
mat <- as.data.frame(cbind(coordStart, coordEnd$posns, value, col))
rownames(mat) <- 1:nrow(mat)
tmp <- apply(mat, 1, function(x){
lines(x[1:2], rep(x[3], 2), col = x[4], lwd = 3, lend = 1)
})
}
}
}
plotSubcloneProfiles <- function(dataIn, chr = c(1:22), geneAnnot = NULL,
spacing = 4, xlim = NULL, ...){
args <- list(...)
lohCol <- c("#00FF00", "#006400", "#0000FF", "#8B0000",
"#006400", "#BEBEBE", "#FF0000", "#FF0000",
"#FF0000")
names(lohCol) <- c("HOMD", "DLOH", "NLOH", "GAIN",
"ALOH", "HET", "ASCNA", "BCNA", "UBCNA")
# use consistent chromosome naming convention
chr <- as.character(chr)
genomeStyle <- seqlevelsStyle(as.character(dataIn$Chr))[1]
chr <- mapSeqlevels(chr, genomeStyle, drop = FALSE)[1, ]
## pull out params from dots ##
if (!is.null(args$cex.axis)) cex.axis <- args$cex.axis else cex.axis <- 0.75
if (!is.null(args$cex.lab)) cex.lab <- args$cex.lab else cex.lab <- 0.75
dataIn <- copy(dataIn)
numClones <- sum(!is.na(unique(as.numeric(dataIn$ClonalCluster))))
if (numClones == 0){ numClones <- 1 }
# plot per chromosome
if (!is.null(chr) && length(chr) == 1) {
for (i in chr) {
ind <- dataIn[, Chr == as.character(i)]
dataByChr <- dataIn[ind, ]
## find x domain #
if (missing(xlim)) {
xlim <- c(1, dataByChr[.N, Position])
}
# plot the data
par(mar = c(spacing, 8, 2, 2), xpd = NA)
# PLOT SUBCLONE PROFILES
# setup plot to include X number of clones (numClones)
maxCN <- dataByChr[, max(CopyNumber)] + 1
ylim <- c(0, numClones * (maxCN + 2) - 1)
plot(0, type = "n", xaxt = "n", ylab = "",
xlim = xlim, ylim = ylim, yaxt = "n", ...)
axis(2, at = seq(ylim[1], ylim[2], 1), las = 1,
labels = rep(c(0:maxCN, "---"), numClones), cex.axis=cex.axis)
for (i in 1:numClones){
val <- dataByChr[, get(paste0("Subclone", i, ".CopyNumber"))]
cellPrev <- suppressWarnings(unique(dataByChr[, get(paste0("Subclone", i, ".Prevalence"))]))
cellPrev <- cellPrev[!is.na(cellPrev)] ## remove NA prevalence, leave subclonal prev
if (length(cellPrev) == 0){ cellPrev <- 0.0 } ## if only NA, then assign 0 prev
if (i > 1){
# shift values up for each subclone
val <- val + (numClones - 1) * (maxCN + 2)
}
call <- dataByChr[, get(paste0("Subclone", i, ".TITANcall"))]
points(dataByChr[, Position], val, col = lohCol[call], pch = 15, ...)
#lines(dataIn[, Position], val, col = lohCol[call], type = "l", lwd = 3, ...)
mtext(text = paste0("Subclone", i, "\n", format(cellPrev, digits = 2)),
side = 2, las = 0, line = 3,
at = i * (maxCN + 2) - (maxCN + 2) / 2 - 1, cex = cex.lab)
chrLen <- as.numeric(dataByChr[.N, Position])
lines(c(1 - chrLen * 0.035, chrLen *
1.035), rep(i * (maxCN + 2) - 1, 2), type = "l",
col = "black", lwd = 1.5)
}
if (!is.null(geneAnnot)) {
plotGeneAnnotation(geneAnnot, i)
}
}
} else {
# plot for all chromosomes specified
dataIn <- dataIn[Chr %in% chr, ]
coord <- getGenomeWidePositions(dataIn[, Chr], dataIn[, Position])
# setup plot to include X number of clones (numClones)
maxCN <- dataIn[, max(CopyNumber)] + 1
ylim <- c(0, numClones * (maxCN + 2) - 1)
xlim <- as.numeric(c(1, coord$posns[length(coord$posns)]))
plot(0, type = "n", xaxt = "n", bty = "n", ylab = "", xlim = xlim,
ylim = ylim, yaxt = "n", ...)
axis(2, at = seq(ylim[1], ylim[2], 1), las = 1,
labels = rep(c(0:maxCN, "---"), numClones))
for (i in 1:numClones){
val <- dataIn[, get(paste0("Subclone", i, ".CopyNumber"))]
if (i > 1){
# shift values up for each subclone
val <- val + (numClones - 1) * (maxCN + 2)
}
call <- dataIn[, get(paste0("Subclone", i, ".TITANcall"))]
points(coord$posns, val, col = lohCol[call], pch = 15, ...)
mtext(text = paste0("Subclone", i), side = 2, las = 0,
line = 2, at = i * (maxCN + 2) - (maxCN + 2) / 2 - 1, cex = 0.75)
chrLen <- xlim[2]
lines(c(1 - chrLen * 0.035, chrLen *
1.035), rep(i * (maxCN + 2) - 1, 2), type = "l",
col = "black", lwd = 1.5)
}
plotChrLines(unique(dataIn[, Chr]), coord$chrBkpt, ylim)
}
}
## TODO: Not completed ##
plotAllelicCN <- function(dataIn, resultType = "AllelicRatio",
chr = NULL, geneAnnot = NULL,
ploidy = 2, spacing = 4, alphaVal = 1, xlim = NULL, ...) {
# color coding
alphaVal <- ceiling(alphaVal * 255)
class(alphaVal) = "hexmode"
cnCol <- c("#00FF00", "#006400", "#0000FF", "#880000",
"#BB0000", "#CC0000", "#DD0000", "#EE0000",
"#FF0000")
cnCol <- paste(cnCol, alphaVal, sep = "")
# cnCol <-
# col2rgb(c('green','darkgreen','blue','darkred','red','brightred'))
names(cnCol) <- c("0", "1", "2", "3", "4", "5", "6", "7", "8")
dataIn <- copy(dataIn)
## compute allelic copy number for each
dataIn[, Allele.1 := get(resultType) * 2^LogRatio*ploidy]
dataIn[, Allele.2 := (1 - get(resultType)) * 2^LogRatio*ploidy]
if (!is.null(chr) && length(chr) == 1) {
for (i in chr) {
dataByChr <- dataIn[Chr == i, ]
dataByChr <- dataByChr[dataByChr[, TITANcall] != "OUT", ]
par(mar = c(spacing, 8, 2, 2))
# par(xpd=NA)
if (missing(xlim)) {
xlim <- as.numeric(c(1, dataByChr[.N, Position]))
}
coord <- dataByChr[, Position]
plot(coord, dataByChr[, Allele.1],
col = cnCol[as.character(dataByChr[, CopyNumber])], pch = 16,
xaxt = "n", las = 1, ylab = "Copy Number",
xlim = xlim, ...)
points(coord, dataByChr[, Allele.2],
col = cnCol[as.character(dataByChr[, CopyNumber])],
pch = 16)
lines(xlim, rep(0, 2), type = "l", col = "grey", lwd = 0.75)
if (!is.null(geneAnnot)) {
plotGeneAnnotation(geneAnnot, i)
}
}
}
}
plotSegmentMedians <- function(dataIn, resultType = "LogRatio",
plotType = "CopyNumber", plotCorrectedCN = TRUE,
chr = c(1:22), geneAnnot = NULL, ploidy = NULL, spacing = 4, alphaVal = 1, xlim = NULL, plot.new = FALSE, lwd = 8, ...){
## check for the possible resultType to plot ##
if (!resultType %in% c("LogRatio", "AllelicRatio", "HaplotypeRatio")){
stop("plotSegmentMedians: resultType must be 'LogRatio', 'AllelicRatio', or 'HaplotypeRatio'")
}
if (!plotType %in% c("CopyNumber", "Ratio")){
stop("plotSegmentMedians: plotType must be 'CopyNumber' or 'Ratio'")
}
# use consistent chromosome naming convention
chr <- as.character(chr)
genomeStyle <- seqlevelsStyle(as.character(dataIn$Chr))[1]
chr <- mapSeqlevels(chr, genomeStyle, drop = FALSE)[1, ]
dataType <- c("Median_logR", "Median_Ratio", "Median_HaplotypeRatio")
names(dataType) <- c("LogRatio", "AllelicRatio", "HaplotypeRatio")
axisName <- c("Copy Number (log ratio)", "Allelic Ratio", "Haplotype Fraction")
names(axisName) <- c("LogRatio", "AllelicRatio", "HaplotypeRatio")
axisNameCN <- c("Copy Number", "Allelic Copy Number")
names(axisNameCN) <- c("LogRatio", "AllelicRatio")
colName <- c("Copy_Number","TITAN_call", "TITAN_call")
names(colName) <- c("LogRatio", "AllelicRatio", "HaplotypeRatio")
if (plotCorrectedCN && "Corrected_Copy_Number" %in% colnames(dataIn)){
colName[1] <- "Corrected_Copy_Number"
}
dataIn <- copy(dataIn)
# color coding
alphaVal <- ceiling(alphaVal * 255)
class(alphaVal) = "hexmode"
if (resultType == "LogRatio"){
cnCol <- c("#00FF00", "#006400", "#0000FF", "#880000",
"#BB0000", "#CC0000", "#DD0000", "#EE0000", rep("#FF0000",493))
cnCol <- paste(cnCol, alphaVal, sep = "")
# cnCol <-
# col2rgb(c('green','darkgreen','blue','darkred','red','brightred'))
names(cnCol) <- c(0:500)
}else if (resultType %in% c("AllelicRatio", "HaplotypeRatio")){
cnCol <- c("#00FF00", "#006400", "#0000FF", "#8B0000",
"#006400", "#BEBEBE", "#FF0000", "#BEBEBE", "#FF0000", "#FF0000", "#FF0000")
# lohCol <- paste(lohCol,alphaVal,sep='') lohCol <-
# col2rgb(c('green','darkgreen','blue','darkgreen','grey','red'))
names(cnCol) <- c("HOMD", "DLOH", "NLOH", "GAIN",
"ALOH", "HET", "ASCNA", "BCNA", "UBCNA", "AMP", "HLAMP")
}
if (plotType == "CopyNumber"){
axisName <- axisNameCN
}
if (is.null(ploidy)){
ploidy <- 2
}
## adjust logR values for ploidy ##
if (resultType == "LogRatio") {
if (plotType == "CopyNumber"){
#dataIn[, (dataType[resultType]) := 2 ^ get(dataType[resultType]) * 2]
}else{
dataIn[, (dataType[resultType]) := get(dataType[resultType]) + log2(ploidy/2)]
}
}
## allelic or haplotype copy number
if (resultType %in% c("AllelicRatio") && plotType == "CopyNumber"){
## compute allelic copy number for each
#dataIn[, Allele.1 := get(dataType[resultType]) * 2 ^ Median_logR * ploidy]
#dataIn[, Allele.2 := (1 - get(dataType[resultType])) * 2 ^ Median_logR * ploidy]
}
# plot for specified chromosomes #
if (!is.null(chr) && length(chr) == 1) {
for (i in chr) {
dataByChr <- dataIn[Chromosome == i, ]
dataByChr <- dataByChr[TITAN_call != "OUT", ]
# plot the data
par(mar = c(spacing, 8, 2, 2))
if (missing(xlim)) {
xlim <- as.numeric(c(1, dataByChr[.N, End_Position.bp.]))
}
col <- cnCol[as.character(dataByChr[, get(colName[resultType])])]
coord <- dataByChr[, .(Start_Position.bp., End_Position.bp.)]
if (plotType == "CopyNumber"){
if (resultType %in% c("AllelicRatio")){
value <- dataByChr[, MajorCN]
value2 <- dataByChr[, MinorCN]
}else{
value <- dataByChr[, get(colName[resultType])]
}
}else{
value <- dataByChr[, get(dataType[resultType])]
}
if (plot.new){
plot(0, type = "n", col = col, xaxt = "n", las = 1,
ylab = axisName[resultType], xlim = xlim, ...)
}
tmp <- apply(cbind(coord, value, col), 1, function(x){
lines(x[1:2], rep(x[3], 2), col = x[4], lend = 1, lwd = lwd)
})
if (plotType == "CopyNumber" && resultType %in% c("AllelicRatio")){
tmp <- apply(cbind(coord, value2, col), 1, function(x){
lines(x[1:2], rep(x[3], 2), col = x[4], lend = 1, lwd = lwd)
})
}
if (plotType == "Ratio"){
lines(xlim, rep(0, 2), type = "l", col = "grey", lwd = 0.75)
}
if (!is.null(geneAnnot)) {
plotGeneAnnotation(geneAnnot, i)
}
}
} else {
# plot for all chromosomes specified
dataIn <- dataIn[Chromosome %in% chr, ]
coordEnd <- getGenomeWidePositions(dataIn[, Chromosome], dataIn[, End_Position.bp.])
coordStart <- coordEnd$posns - (dataIn[, End_Position.bp.] - dataIn[, Start_Position.bp.] + 1)
xlim <- as.numeric(c(1, coordEnd$posns[length(coordEnd$posns)]))
col <- cnCol[as.character(dataIn[, get(colName[resultType])])]
if (plotType == "CopyNumber"){
if (resultType %in% c("AllelicRatio")){
value <- dataIn[, MajorCN]
value2 <- dataIn[, MinorCN]
}else{
value <- dataIn[, Copy_Number]
}
}else{
value <- dataIn[, get(dataType[resultType])]
}
#mat <- data.table(cbind(coordStart, coordEnd$posns, value, col))
#rownames(mat) <- 1:nrow(mat)
if (plot.new){
plot(0, type = "n", col = col, xaxt = "n", las = 1,
ylab = axisName[resultType], xlim = xlim, ...)
}
tmp <- apply(data.table(coordStart, coordEnd$posns, value, col), 1, function(x){
lines(x[1:2], rep(x[3], 2), col = x[4], lend = 1, lwd = lwd)
})
if (plotType == "CopyNumber" && resultType %in% c("AllelicRatio")){
tmp <- apply(data.table(coordStart, coordEnd$posns, value2, col), 1, function(x){
lines(x[1:2], rep(x[3], 2), col = x[4], lend = 1, lwd = lwd)
})
}
if (plotType == "Ratio"){
lines(xlim, rep(0, 2), type = "l", col = "grey", lwd = 2)
}
plotChrLines(dataIn[, Chromosome], coordEnd$chrBkpt, par("yaxp")[1:2])
}
}
plotGeneAnnotation <- function(geneAnnot, chr = 1, ...) {
colnames(geneAnnot) <- c("Gene", "Chr", "Start",
"Stop")
geneAnnot <- geneAnnot[geneAnnot[, "Chr"] == as.character(chr),
]
if (nrow(geneAnnot) != 0) {
for (g in 1:dim(geneAnnot)[1]) {
# print(geneAnnot[g,'Gene'])
abline(v = as.numeric(geneAnnot[g, "Start"]),
col = "black", lty = 3, xpd = FALSE)
abline(v = as.numeric(geneAnnot[g, "Stop"]),
col = "black", lty = 3, xpd = FALSE)
atP <- (as.numeric(geneAnnot[g, "Stop"]) -
as.numeric(geneAnnot[g, "Start"]))/2 +
as.numeric(geneAnnot[g, "Start"])
# if (atP < dataByChr[1,2]){ atP <- dataByChr[1,2]
# }else if (atP > dataByChr[dim(dataByChr)[1],2]){
# atP <- dataByChr[dim(dataByChr)[1],2] }
mtext(geneAnnot[g, "Gene"], side = 3, line = 0,
at = atP, ...)
}
}
}
plotChrLines <- function(chrs, chrBkpt, yrange) {
# plot vertical chromosome lines
for (j in 1:length(chrBkpt)) {
lines(rep(chrBkpt[j], 2), yrange, type = "l",
lty = 2, col = "black", lwd = 0.75)
}
numLines <- length(chrBkpt)
mid <- (chrBkpt[1:(numLines - 1)] + chrBkpt[2:numLines])/2
chrsToShow <- gsub("chr", "", unique(chrs))
axis(side = 1, at = mid, labels = c(chrsToShow),
cex.axis = 1.5, tick = FALSE)
}
getGenomeWidePositions <- function(chrs, posns, seqinfo = NULL) {
# create genome coordinate scaffold
positions <- as.numeric(posns)
chrsNum <- unique(chrs)
chrBkpt <- rep(0, length(chrsNum) + 1)
prevChrPos <- 0
for (i in 2:length(chrsNum)) {
chrInd <- which(chrs == chrsNum[i])
if (!is.null(seqinfo)){
prevChrPos <- seqinfo[i-1, "seqlengths"] + prevChrPos
}else{
prevChrPos <- positions[chrInd[1] - 1]
}
chrBkpt[i] = prevChrPos
positions[chrInd] = positions[chrInd] + prevChrPos
}
chrBkpt[i + 1] <- positions[length(positions)]
return(list(posns = positions, chrBkpt = chrBkpt))
}
### modify SNPchip function "plotIdiogram"
plotIdiogram.hg38 <- function (chromosome, cytoband, seqinfo, cytoband.ycoords, xlim,
ylim = c(0, 2), new = TRUE, label.cytoband = TRUE, label.y = NULL,
srt, cex.axis = 1, outer = FALSE, taper = 0.15, verbose = FALSE,
unit = c("bp", "Mb"), is.lattice = FALSE, ...)
{
def.par <- par(no.readonly = TRUE, mar = c(4.1, 0.1, 3.1,
2.1))
on.exit(def.par)
if (is.lattice) {
segments <- lsegments
polygon <- lpolygon
}
cytoband <- cytoband[cytoband[, "chrom"] == chromosome, ]
unit <- match.arg(unit)
if (unit == "Mb") {
cytoband$start <- cytoband$start/1e+06
cytoband$end <- cytoband$end/1e+06
}
if (missing(cytoband.ycoords)) {
cytoband.ycoords <- ylim
}
rownames(cytoband) <- as.character(cytoband[, "name"])
sl <- seqlengths(seqinfo)[chromosome]
if (missing(xlim))
xlim <- c(0, sl)
if (unit == "Mb")
xlim <- xlim/1e+06
cytoband_p <- cytoband[grep("^p", rownames(cytoband), value = TRUE),
]
cytoband_q <- cytoband[grep("^q", rownames(cytoband), value = TRUE),
]
p.bands <- nrow(cytoband_p)
cut.left <- c()
cut.right <- c()
for (i in seq_len(nrow(cytoband))) {
if (i == 1) {
cut.left[i] <- TRUE
cut.right[i] <- FALSE
}
else if (i == p.bands) {
cut.left[i] <- FALSE
cut.right[i] <- TRUE
}
else if (i == (p.bands + 1)) {
cut.left[i] <- TRUE
cut.right[i] <- FALSE
}
else if (i == nrow(cytoband)) {
cut.left[i] <- FALSE
cut.right[i] <- TRUE
}
else {
cut.left[i] <- FALSE
cut.right[i] <- FALSE
}
}
for (i in seq_len(nrow(cytoband))) {
if (as.character(cytoband[i, "gieStain"]) == "stalk") {
cut.right[i - 1] <- TRUE
cut.left[i] <- NA
cut.right[i] <- NA
cut.left[i + 1] <- TRUE
}
}
include <- cytoband[, "end"] > xlim[1] & cytoband[, "start"] <
xlim[2]
cytoband <- cytoband[include, ]
N <- nrow(cytoband)
cut.left <- cut.left[include]
cut.right <- cut.right[include]
if (new) {
xx <- c(0, cytoband[nrow(cytoband), "end"])
yy <- cytoband.ycoords
plot(xx, yy, xlim = xlim, type = "n", xlab = "", ylab = "",
axes = FALSE, yaxs = "i", ylim = ylim, ...)
}
top <- cytoband.ycoords[2]
bot <- cytoband.ycoords[1]
h <- top - bot
p <- taper
for (i in seq_len(nrow(cytoband))) {
start <- cytoband[i, "start"]
last <- cytoband[i, "end"]
delta = (last - start)/4
getStain <- function(stain) {
switch(stain, gneg = "grey100", gpos25 = "grey90",
gpos50 = "grey70", gpos75 = "grey40", gpos100 = "grey0",
gvar = "grey100", stalk = "brown3", acen = "brown4",
"white")
}
color <- getStain(as.character(cytoband[i, "gieStain"]))
if (is.na(cut.left[i]) & is.na(cut.right[i])) {
delta <- (last - start)/3
segments(start + delta, cytoband.ycoords[1], start +
delta, cytoband.ycoords[2])
segments(last - delta, cytoband.ycoords[1], last -
delta, cytoband.ycoords[2])
}
else if (cut.left[i] & cut.right[i]) {
yy <- c(bot + p * h, bot, bot, bot + p * h, top -
p * h, top, top, top - p * h)
polygon(c(start, start + delta, last - delta, last,
last, last - delta, start + delta, start), yy,
col = color)
}
else if (cut.left[i]) {
yy <- c(bot + p * h, bot, bot, top, top, top - p *
h)
polygon(c(start, start + delta, last, last, start +
delta, start), yy, col = color)
}
else if (cut.right[i]) {
yy <- c(bot, bot, bot + p * h, top - p * h, top,
top)
polygon(c(start, last - delta, last, last, last -
delta, start), yy, col = color)
}
else {
polygon(c(start, last, last, start), c(bot, bot,
top, top), col = color)
}
}
my.x <- (cytoband[, "start"] + cytoband[, "end"])/2
if (label.cytoband & !is.lattice) {
if (is.null(label.y)) {
axis(1, at = my.x, labels = rownames(cytoband), outer = outer,
cex.axis = cex.axis, line = 1, las = 3, tick = FALSE)
axis(1, at = cytoband$start, outer = outer, cex.axis = cex.axis,
line = 1, las = 3, labels = FALSE)
}
else {
if (!is.numeric(label.y)) {
warning("label.y must be numeric -- using default y coordinates for cytoband labels")
label.y <- bot - p * h
}
if (missing(srt))
srt <- 90
text(x = my.x, y = rep(label.y, length(my.x)), labels = rownames(cytoband),
srt = srt)
}
}
return()
}
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