Nothing
R/profile.R
In DMRcaller: Differentially Methylated Regions caller
Defines functions
plotOverlapProfile
computeOverlapProfile
.measureOverlaps
.countOverlaps
plotMethylationProfileFromData
plotMethylationProfile
computeMethylationProfile
Documented in
computeMethylationProfile
computeOverlapProfile
plotMethylationProfile
plotMethylationProfileFromData
plotOverlapProfile
#' This function computes the low resolution profiles for the bisulfite
#' sequencing data.
#'
#' @title Compute methylation profile
#' @param methylationData the methylation data stored as a \code{\link{GRanges}}
#' object with four metadata columns (see \code{\link{methylationDataList}}).
#' @param region a \code{\link{GRanges}} object with the regions where to
#' compute the DMRs.
#' @param windowSize a \code{numeric} value indicating the size of the window in
#' which methylation is averaged.
#' @param context the context in which the DMRs are computed (\code{"CG"},
#' \code{"CHG"} or \code{"CHH"}).
#' @return a \code{\link{GRanges}} object with equal sized tiles of the
#' \code{region}. The object consists of the following metadata
#' \describe{
#' \item{sumReadsM}{the number of methylated reads.}
#' \item{sumReadsN}{the total number of reads.}
#' \item{Proportion}{the proportion of methylated reads.}
#' \item{context}{the context (\code{"CG"}, \code{"CHG"} or \code{"CHH"}).}
#' }
#' @seealso \code{\link{plotMethylationProfileFromData}},
#' \code{\link{plotMethylationProfile}}, \code{\link{methylationDataList}}
#' @examples
#'
#' # load the methylation data
#' data(methylationDataList)
#'
#' # the region where to compute the profile
#' region <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E6))
#'
#' # compute low resolution profile in 20 Kb windows
#' lowResProfileWTCHH <- computeMethylationProfile(methylationDataList[["WT"]],
#' region, windowSize = 20000, context = "CHH")
#'
#' \dontrun{
#' # compute low resolution profile in 10 Kb windows
#' lowResProfileWTCG <- computeMethylationProfile(methylationDataList[["WT"]],
#' region, windowSize = 10000, context = "CG")
#'
#' lowResProfileMet13CG <- computeMethylationProfile(
#' methylationDataList[["met1-3"]], region,
#' windowSize = 10000, context = "CG")
#' }
#'
#' @author Nicolae Radu Zabet and Jonathan Michael Foonlan Tsang
#' @export
computeMethylationProfile <- function(methylationData,
region,
windowSize = floor(width(region)/500),
context = "CG") {
.validateMethylationData(methylationData)
.validateGRanges(region, methylationData, length=1, generateGenomeWide=FALSE)
.validateContext(context)
.stopIfNotAll(c(.isInteger(windowSize, positive=TRUE)),
" the window size used to compute the methylation profile is an integer higher or equal to 0")
seqname <- seqnames(region)
minPos <- start(region)
maxPos <- end(region)
hits <- findOverlaps(methylationData, region)
localMethylationData <- methylationData[queryHits(hits)];
rm(methylationData)
contextMethylationData <- localMethylationData[localMethylationData$context%in%context];
rm(localMethylationData)
cat("Calculating methylation profile for ", .printGenomicRanges(region), " using a window of ", windowSize, " bp \n")
seqs = seq(minPos, maxPos - windowSize, windowSize);
ranges <- GRanges(seqname, IRanges(seqs, seqs+windowSize-1))
#for windowSize <= 2000 Bins method is faster, but for anything else, regions method is faster
if(windowSize <= 2000){
ranges <- .analyseReadsInsideBinsOneSample(contextMethylationData, ranges, region)
} else{
ranges <- .analyseReadsInsideRegionsOneSample(contextMethylationData, ranges)
}
ranges$context <- paste(context, collapse = "_")
return(ranges)
}
#' This function plots the low resolution profiles for the bisulfite sequencing
#' data.
#'
#' @title Plot Methylation Profile
#' @param methylationProfiles a \code{GRangesList} object. Each
#' \code{\link{GRanges}} object in the list is generated by calling the
#' function \code{\link{computeMethylationProfile}}.
#' @param autoscale a \code{logical} value indicating whether the values are
#' autoscalled for each context or not.
#' @param labels a \code{vector} of \code{character} used to add a subfigure
#' characters to the plot. If \code{NULL} nothing is added.
#' @param title the plot title.
#' @param col a \code{character} vector with the colours. It needs to contain a
#' minimum of 2 colours per context. If not or if NULL, the defalut colours will
#' be used.
#' @param pch the R symbols used to plot the data.
#' @param lty the line types used to plot the data.
#' @return Invisibly returns \code{NULL}
#' @seealso \code{\link{plotMethylationProfileFromData}},
#' \code{\link{computeMethylationProfile}} and \code{\link{methylationDataList}}
#' @examples
#'
#'
#' # load the methylation data
#' data(methylationDataList)
#'
#' # the region where to compute the profile
#' region <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E6))
#'
#' # compute low resolution profile in 20 Kb windows
#' lowResProfileWTCG <- computeMethylationProfile(methylationDataList[["WT"]],
#' region, windowSize = 20000, context = "CG")
#'
#' lowResProfilsCG <- GRangesList("WT" = lowResProfileWTCG)
#'
#' #plot the low resolution profile
#' par(mar=c(4, 4, 3, 1)+0.1)
#' par(mfrow=c(1,1))
#' plotMethylationProfile(lowResProfilsCG, autoscale = FALSE,
#' title="CG methylation on Chromosome 3",
#' col=c("#D55E00","#E69F00"), pch = c(1,0),
#' lty = c(4,1))
#'
#' \dontrun{
#' # compute low resolution profile in 10 Kb windows in CG context
#' lowResProfileWTCG <- computeMethylationProfile(methylationDataList[["WT"]],
#' region, windowSize = 10000, context = "CG")
#'
#' lowResProfileMet13CG <- computeMethylationProfile(
#' methylationDataList[["met1-3"]], region,
#' windowSize = 10000, context = "CG")
#'
#' lowResProfileCG <- GRangesList("WT" = lowResProfileWTCG,
#' "met1-3" = lowResProfileMet13CG)
#'
#' # compute low resolution profile in 10 Kb windows in CHG context
#' lowResProfileWTCHG <- computeMethylationProfile(methylationDataList[["WT"]],
#' region, windowSize = 10000, context = "CHG")
#'
#' lowResProfileMet13CHG <- computeMethylationProfile(
#' methylationDataList[["met1-3"]], region,
#' windowSize = 10000, context = "CHG")
#'
#' lowResProfileCHG <- GRangesList("WT" = lowResProfileWTCHG,
#' "met1-3" = lowResProfileMet13CHG)
#'
#' # plot the low resolution profile
#' par(mar=c(4, 4, 3, 1)+0.1)
#' par(mfrow=c(2,1))
#' plotMethylationProfile(lowResProfileCG, autoscale = FALSE,
#' labels = LETTERS[1],
#' title="CG methylation on Chromosome 3",
#' col=c("#D55E00","#E69F00"), pch = c(1,0),
#' lty = c(4,1))
#' plotMethylationProfile(lowResProfileCHG, autoscale = FALSE,
#' labels = LETTERS[2],
#' title="CHG methylation on Chromosome 3",
#' col=c("#0072B2", "#56B4E9"), pch = c(16,2),
#' lty = c(3,2))
#' }
#'
#' @author Nicolae Radu Zabet
#' @export
plotMethylationProfile <- function(methylationProfiles,
autoscale = FALSE,
labels=NULL,
title = "",
col = NULL,
pch = c(1,0,16,2,15,17),
lty = c(4,1,3,2,6,5)) {
.validateMethylationProfile(methylationProfiles)
defaultConditionsNames <- paste("condition ", (1:length(methylationProfiles)), sep="")
if(is.null(names(methylationProfiles))){
names(methylationProfiles) <- defaultConditionsNames
}
if(!.isColor(col, minLength = length(methylationProfiles) )){
if(length(methylationProfiles) <= 6){
col <- c("#D55E00","#E69F00", "#0072B2", "#56B4E9", "#F0E442", "#009E73")
} else if(length(methylationProfiles) <= 8){
col <- c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
} else{
col <- rainbow(length(methylationProfiles))
}
}
.stopIfNotAll(c(!is.null(autoscale),
is.logical(autoscale),
length(autoscale) == 1),
" autoscale is a logical value")
if(is.null(title)){
title=""
} else if(is.character(title[1]) > 1){
title[1] = as.character(title[1])
}
.stopIfNotAll(c(!is.null(pch),
all(as.integer(pch) == pch),
all(pch >= 0),
length(pch) >= length(methylationProfiles)),
paste(" pch is a vector of positive integers of size ",length(methylationProfiles), sep=""))
.stopIfNotAll(c(!is.null(lty),
all(as.integer(lty) == lty),
all(lty >= 0),
length(lty) >= length(methylationProfiles)),
paste(" lty is a vector of positive integers of size ",length(methylationProfiles), sep=""))
ymax <- 1
if(autoscale){
ymax <- 0
for(i in 1:length(methylationProfiles)){
if(ymax < max(methylationProfiles[[i]]$Proportion)){
ymax = max(methylationProfiles[[i]]$Proportion)
}
}
}
options(scipen=10)
pos <- (start(methylationProfiles[[1]])+end(methylationProfiles[[1]]))/2
plot(pos, methylationProfiles[[1]]$Proportion, type = "o", ylim = c(0,ymax),
xlab="genomic coordinate", ylab="methylation", col=col[1], yaxt="n",
pch = pch[1], lty = lty[1], main = title[1])
if(length(methylationProfiles) > 1){
for(i in 2:length(methylationProfiles)){
lines(pos, methylationProfiles[[i]]$Proportion, type = "o", col=col[i], lty = lty[i], pch = pch[i])
}
}
legend("topright", legend = names(methylationProfiles),
lty = lty[1:length(methylationProfiles)],
col = col[1:length(methylationProfiles)],
pch = pch[1:length(methylationProfiles)], bty="n")
if(!is.null(labels)){
mtext(labels[1], line = 0.7, adj = 0, cex=1.4);
}
if(autoscale){
axis(2,c(0,signif(ymax/2, 1),signif(ymax, 1)));
} else{
axis(2,c(0,.5,1));
}
invisible(NULL)
}
#' This function plots the low resolution profiles for all bisulfite sequencing
#' data.
#'
#' @title Plot methylation profile from data
#' @param methylationData1 the methylation data in condition 1
#' (see \code{\link{methylationDataList}}).
#' @param methylationData2 the methylation data in condition 2
#' (see \code{\link{methylationDataList}}). This is optional.
#' @param regions a \code{\link{GRanges}} object with the regions where to plot
#' the profiles.
#' @param conditionsNames the names of the two conditions. This will be used to
#' plot the legend.
#' @param context a \code{vector} with all contexts in which the DMRs are
#' computed (\code{"CG"}, \code{"CHG"} or \code{"CHH"}).
#' @param windowSize a \code{numeric} value indicating the size of the window in
#' which methylation is averaged.
#' @param autoscale a \code{logical} value indicating whether the values are
#' autoscalled for each context or not.
#' @param labels a \code{vector} of \code{character} used to add a subfigure
#' character to the plot. If \code{NULL} nothing is added.
#' @param col a \code{character} vector with the colours. It needs to contain a
#' minimum of 2 colours per condition. If not or if \code{NULL}, the defalut
#' colours will be used.
#' @param pch the R symbols used to plot the data It needs to contain a minimum
#' of 2 symbols per condition. If not or if \code{NULL}, the defalut symbols
#' will be used.
#' @param lty the line types used to plot the data. It needs to contain a
#' minimum of 2 line types per condition. If not or if \code{NULL}, the defalut
#' line types will be used.
#' @param contextPerRow a \code{logical} value indicating if the each row
#' represents an individual context. If \code{FALSE}, each column will represent
#' an individual context.
#' @return Invisibly returns \code{NULL}
#' @seealso \code{\link{plotMethylationProfile}},
#' \code{\link{computeMethylationProfile}} and \code{\link{methylationDataList}}
#' @examples
#'
#'
#' # load the methylation data
#' data(methylationDataList)
#'
#' #plot the low resolution profile at 10 Kb resolution
#' par(mar=c(4, 4, 3, 1)+0.1)
#' plotMethylationProfileFromData(methylationDataList[["WT"]],
#' methylationDataList[["met1-3"]],
#' conditionsNames=c("WT", "met1-3"),
#' windowSize = 20000, autoscale = TRUE,
#' context = c("CHG"))
#'
#' \dontrun{
#' #plot the low resolution profile at 5 Kb resolution
#' par(mar=c(4, 4, 3, 1)+0.1)
#' plotMethylationProfileFromData(methylationDataList[["WT"]],
#' methylationDataList[["met1-3"]],
#' conditionsNames=c("WT", "met1-3"),
#' windowSize = 5000, autoscale = TRUE,
#' context = c("CG", "CHG", "CHH"),
#' labels = LETTERS)
#' }
#'
#' @author Nicolae Radu Zabet
#' @export
plotMethylationProfileFromData <- function(methylationData1,
methylationData2 = NULL,
regions = NULL,
conditionsNames = NULL,
context = "CG",
windowSize = NULL,
autoscale = FALSE,
labels=NULL,
col=NULL,
pch = c(1,0,16,2,15,17),
lty = c(4,1,3,2,6,5),
contextPerRow = TRUE) {
.validateContext(context)
.validateMethylationData(methylationData1, variableName="methylationData1")
numberOfConditions <- 1
if(!is.null(methylationData2)){
.validateMethylationData(methylationData2, variableName="methylationData2")
numberOfConditions <- 2
}
if(is.null(conditionsNames) | length(conditionsNames) < numberOfConditions){
conditionsNames <- paste("condition ",(1:numberOfConditions),sep="")
}
number_of_symbols <-numberOfConditions*length(context)
if(!.isColor(col, minLength = number_of_symbols )){
if(number_of_symbols <= 6){
col <- c("#D55E00","#E69F00", "#0072B2", "#56B4E9", "#F0E442", "#009E73")
} else if(number_of_symbols <= 8){
col <- c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
} else{
col <- rainbow(number_of_symbols)
}
}
.stopIfNotAll(c(!is.null(pch),
all(as.integer(pch) == pch),
all(pch >= 0),
length(pch) >= number_of_symbols),
paste(" pch is a vector of positive integers of size ",number_of_symbols, sep=""))
.stopIfNotAll(c(!is.null(lty),
all(as.integer(lty) == lty),
all(lty >= 0),
length(lty) >= number_of_symbols),
paste(" lty is a vector of positive integers of size ",number_of_symbols, sep=""))
#compute all genomic regions for which data is available
recomputeRegions <- FALSE
if(is.null(regions)){
recomputeRegions <- TRUE
}
if(!recomputeRegions & (!is(regions, "GRanges") | length(regions) < 1)){
recomputeRegions <- TRUE
}
if(recomputeRegions){
cat("Recompute regions... \n")
regions <- GRanges()
regions <- union(regions, getWholeChromosomes(methylationData1))
if(numberOfConditions > 1){
regions <- union(regions, getWholeChromosomes(methylationData2))
}
}
if(is.null(windowSize)){
windowSize = floor(min(width(regions))/500)
}
index <- 1;
cat("Computing low resolution profiles... \n")
par(mar=c(4, 4, 3, 1)+0.1)
if(contextPerRow){
par(mfrow=c(length(context),length(regions)))
for(i in 1:length(context)){
for(j in 1:length(regions)){
buffer_profile <- GRangesList(computeMethylationProfile(methylationData1, regions[j], windowSize = windowSize, context = context[i]))
if(numberOfConditions > 1){
buffer_profile <- c(buffer_profile, GRangesList(computeMethylationProfile(methylationData2, regions[j], windowSize = windowSize, context = context[i])))
}
names(buffer_profile) <- conditionsNames
symbols_ind <- (numberOfConditions*(i-1) + 1):(numberOfConditions*i)
plotMethylationProfile(buffer_profile, autoscale = autoscale, labels = labels[index],
title=paste(context[i], " methylation on chromosome ", as.character(seqnames(regions)[j]),sep=""), col=col[symbols_ind],
pch = pch[symbols_ind], lty = lty[symbols_ind])
index <- index + 1
}
}
} else{
par(mfrow=c(length(regions),length(context)))
for(j in 1:length(regions)){
for(i in 1:length(context)){
buffer_profile <- GRangesList(computeMethylationProfile(methylationData1, regions[j], windowSize = windowSize, context = context[i]))
if(numberOfConditions > 1){
buffer_profile <- c(buffer_profile, GRangesList(computeMethylationProfile(methylationData2, regions[j], windowSize = windowSize, context = context[i])))
}
names(buffer_profile) <- conditionsNames
symbols_ind <- (numberOfConditions*(i-1) + 1):(numberOfConditions*i)
plotMethylationProfile(buffer_profile, autoscale = autoscale, labels = labels[index],
title=paste(context[i], " methylation on chromosome ", as.character(seqnames(regions)[j]),sep=""), col=col[symbols_ind],
pch = pch[symbols_ind], lty = lty[symbols_ind])
index <- index + 1
}
}
}
invisible(NULL)
}
.countOverlaps <- function(region, subRegions){
return(sum(countOverlaps(subRegions, region)))
}
.measureOverlaps <- function(region, subRegions){
return(sum(width(intersect(subRegions, region))))
}
#' This function computes the distribution of a subset of regions
#' (\code{\link{GRanges}} object) over a large region (\code{\link{GRanges}}
#' object)
#'
#' @title Compute Overlaps Profile
#' @param subRegions a \code{\link{GRanges}} object with the sub regions; e.g.
#' can be the DMRs.
#' @param largeRegion a \code{\link{GRanges}} object with the region where to
#' compute the overlaps; e.g. a chromosome
#' @param windowSize The \code{largeRegion} is partitioned into equal sized
#' tiles of width \code{windowSize}.
#' @param binary a value indicating whether to count 1 for each overlap or to
#' compute the width of the overlap
#' @param cores the number of cores used to compute the DMRs.
#' @return a \code{\link{GRanges}} object with equal sized tiles of the regions.
#' The object has one metadata file \code{score} which represents: the number of
#' subRegions overlapping with the tile, in the case of \code{binary = TRUE},
#' and the width of the subRegions overlapping with the tile , in the case of
#' \code{binary = FALSE}.
#' @seealso \code{\link{plotOverlapProfile}}, \code{\link{filterDMRs}},
#' \code{\link{computeDMRs}} and \code{\link{mergeDMRsIteratively}}
#' @examples
#' # load the methylation data
#' data(methylationDataList)
#'
#' # load the DMRs in CG context
#' data(DMRsNoiseFilterCG)
#'
#' # the coordinates of the area to be plotted
#' largeRegion <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E5))
#'
#' # compute overlaps distribution
#' hotspots <- computeOverlapProfile(DMRsNoiseFilterCG, largeRegion,
#' windowSize = 10000, binary = FALSE)
#' @author Nicolae Radu Zabet
#' @export
computeOverlapProfile <- function(subRegions,
largeRegion,
windowSize = floor(width(largeRegion)/500),
binary=TRUE,
cores = 1){
.stopIfNotAll(c(!is.null(subRegions),
is(subRegions, "GRanges")),
paste(" subRegions neads to be a GRanges object.",sep=""))
.stopIfNotAll(c(!is.null(largeRegion),
is(largeRegion, "GRanges"),
length(largeRegion) == 1),
paste(" largeRegion neads to be a GRanges object with one location (e.g. entire chromosome).",sep=""))
.stopIfNotAll(c(!is.null(binary),
is.logical(binary),
length(binary) == 1),
paste(" binary neads to be a logical variable.",sep=""))
.stopIfNotAll(c(.isInteger(windowSize, positive=TRUE)),
" the window size used to compute the methylation profile is an integer higher or equal to 0")
.stopIfNotAll(c(.isInteger(cores, positive=TRUE)),
" the number of cores to used when computing the DMRs needs to be an integer hirger or equal to 1.")
seqname <- seqnames(largeRegion)
minPos <- start(largeRegion)
maxPos <- end(largeRegion)
cat("Calculating overlaps for ", .printGenomicRanges(largeRegion), " using a window of ", windowSize, " bp \n")
seqs = seq(minPos, maxPos - windowSize, windowSize);
ranges <- GRanges(seqname, IRanges(seqs, seqs+windowSize-1))
ranges$score <- 0
rangesList <- tile(ranges, cores)
if(binary){
if(cores > 1){
scores <- parallel::mclapply(rangesList, .countOverlaps, subRegions = subRegions, mc.cores = cores)
} else {
scores <- lapply(rangesList, .countOverlaps, subRegions = subRegions)
}
} else{
if(cores > 1){
scores <- parallel::mclapply(rangesList, .measureOverlaps, subRegions = subRegions, mc.cores = cores)
} else {
scores <- lapply(rangesList, .measureOverlaps, subRegions = subRegions)
}
}
ranges$score <- unlist(scores)
return(ranges)
}
#' This function plots the distribution of a set of subregions on a large
#' region.
#'
#' @title Plot overlap profile
#' @param overlapsProfiles1 a \code{\link{GRanges}} object with the overlaps
#' profile; see \code{\link{computeOverlapProfile}}.
#' @param overlapsProfiles2 a \code{\link{GRanges}} object with the overlaps
#' profile; see \code{\link{computeOverlapProfile}}. This is optional. For
#' example, one can be use \code{overlapsProfiles1} to display hypomethylated
#' regions and \code{overlapsProfiles2} the hypermethylated regions.
#' @param names a \code{vector} of \code{character} to add labels for the two
#' overlapsProfiles. This is an optinal parameter.
#' @param labels a \code{vector} of \code{character} used to add a subfigure
#' character to the plot. If \code{NULL} nothing is added.
#' @param col a \code{character} vector with the colours. It needs to contain 2
#' colours. If not or if \code{NULL}, the defalut colours will be used.
#' @param title the title of the plot.
#' @param logscale a \code{logical} value indicating if the colours are on
#' logscale or not.
#' @param maxValue a maximum value in a region. Used for the colour scheme.
#' @return Invisibly returns \code{NULL}.
#' @seealso \code{\link{computeOverlapProfile}}, \code{\link{filterDMRs}},
#' \code{\link{computeDMRs}} and \code{\link{mergeDMRsIteratively}}
#' @examples
#'
#' # load the methylation data
#' data(methylationDataList)
#'
#' # load the DMRs in CG context
#' data(DMRsNoiseFilterCG)
#'
#' # the coordinates of the area to be plotted
#' largeRegion <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E5))
#'
#' # compute overlaps distribution
#' hotspotsHypo <- computeOverlapProfile(DMRsNoiseFilterCG, largeRegion,
#' windowSize = 10000, binary = FALSE)
#'
#' plotOverlapProfile(GRangesList("Chr3"=hotspotsHypo),
#' names = c("hypomethylated"), title = "CG methylation")
#'
#' \dontrun{
#'
#' largeRegion <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E6))
#'
#' hotspotsHypo <- computeOverlapProfile(
#' DMRsNoiseFilterCG[(DMRsNoiseFilterCG$regionType == "loss")],
#' largeRegion, windowSize=2000, binary=TRUE, cores=1)
#'
#' hotspotsHyper <- computeOverlapProfile(
#' DMRsNoiseFilterCG[(DMRsNoiseFilterCG$regionType == "gain")],
#' largeRegion, windowSize=2000, binary=TRUE, cores=1)
#'
#' plotOverlapProfile(GRangesList("Chr3"=hotspotsHypo),
#' GRangesList("Chr3"=hotspotsHyper),
#' names=c("loss", "gain"), title="CG methylation")
#' }
#'
#' @author Nicolae Radu Zabet
#' @export
plotOverlapProfile <- function(overlapsProfiles1, overlapsProfiles2=NULL, names=NULL,
labels=NULL, col=NULL, title="", logscale=FALSE, maxValue=NULL) {
.stopIfNotAll(c(!is.null(overlapsProfiles1),
is(overlapsProfiles1, "GRangesList"),
length(overlapsProfiles1) > 0),
" overlapsProfiles1 needs to be a GRangesList object")
unlisted_overlapsProfiles1 <- unlist(overlapsProfiles1, use.names=FALSE)
score <- mcols(unlisted_overlapsProfiles1)$score
if(is.null(score)) stop("elements of the overlapsProfiles1 are incorrect")
maxScore <- max(score)
minScore <- min(score)
numberOfConditions <- 1
if(!is.null(overlapsProfiles2)){
.stopIfNotAll(c(is(overlapsProfiles2, "GRangesList"),
length(overlapsProfiles2) == length(overlapsProfiles1)),
" overlapsProfiles2 needs to be a GRangesList object with the same number of elements as overlapsProfiles1")
unlisted_overlapsProfiles2 <- unlist(overlapsProfiles2, use.names=FALSE)
score <- mcols(unlisted_overlapsProfiles2)$score
if(is.null(score)) stop("elements of the overlapsProfiles2 are incorrect")
maxScore <- max(maxScore, score)
minScore <- min(minScore, score)
numberOfConditions <- 2
}
.stopIfNotAll(c(!is.null(logscale),
is.logical(logscale),
length(logscale) == 1),
paste(" logscale neads to be a logical variable.",sep=""))
if(!.isColor(col) | length(col) < numberOfConditions){
col <- c("#0072B2", "#D55E00")
}
if(!is.null(maxValue)){
if(is.numeric(maxValue)){
if(round(maxValue) > 0){
maxScore <- round(maxValue)
}
}
}
if(logscale){
minScore <- log10(1)
maxScore <- log10(maxScore)
}
minScore <- round(minScore)
maxScore <- round(maxScore)
cols1 <- c(colorRampPalette(c("white",col[1]))(1 + maxScore - minScore))
cols2 <- c(colorRampPalette(c("white",col[2]))(1 + maxScore - minScore))
numberOfProfiles<-length(overlapsProfiles1)
xmin <- min(unlist(lapply(overlapsProfiles1, start)))
xmax <- max(unlist(lapply(overlapsProfiles1, end)))
par(mar=c(4, 4, 3, 1)+0.1)
plot(c(xmin,xmax),c(0, 1*numberOfProfiles), type="n",xlab="position (bp)", ylab="", yaxt="n", bty="n", main=title)
for(i in 1:length(overlapsProfiles1)){
if(!is.null(overlapsProfiles2)){
#plot two conditions
for(j in 1:length(overlapsProfiles1[[i]])){
colId <- overlapsProfiles1[[i]][j]$score
if(colId > 0){
if(logscale){
colId <- log10(colId)
}
rect(start(overlapsProfiles1[[i]][j]), (length(overlapsProfiles1) - i + 0.4), end(overlapsProfiles1[[i]][j]), (length(overlapsProfiles1) - i + 0.7), col=cols1[round(colId)+1], border = NA)
}
}
for(j in 1:length(overlapsProfiles2[[i]])){
colId <- overlapsProfiles2[[i]][j]$score
if(colId > 0){
if(logscale){
colId <- log10(colId)
}
rect(start(overlapsProfiles2[[i]][j]), (length(overlapsProfiles2) - i + 0.1), end(overlapsProfiles2[[i]][j]), (length(overlapsProfiles2) - i + 0.4), col=cols2[round(colId)+1], border = NA)
}
}
if(!is.null(names)){
if(all(is.character(names)) & length(names) >= numberOfConditions){
at_pos <- c(0.55,0.25)
for(j in 1:numberOfConditions){
mtext(names[j], side = 2, line=-0.5, at=(length(overlapsProfiles1) - i + at_pos[j]), col="black", las=2)
}
}
}
} else{
#plot one conditions
for(j in 1:length(overlapsProfiles1[[i]])){
colId <- overlapsProfiles1[[i]][j]$score
if(colId > 0){
if(logscale){
colId <- log10(colId)
}
rect(start(overlapsProfiles1[[i]][j]), (length(overlapsProfiles1) - i + 0.1), end(overlapsProfiles1[[i]][j]), (length(overlapsProfiles1) - i + 0.7), col=cols1[round(colId)+1], border = NA)
}
}
if(!is.null(names)){
if(all(is.character(names)) & length(names) >= numberOfConditions){
at_pos <- c(0.4)
mtext(names[1], side = 2, line=-0.5, at=(length(overlapsProfiles1) - i + at_pos[1]), col="black")
}
}
}
rect(xmin, (length(overlapsProfiles1) - i + 0.1), max(end(overlapsProfiles1[[i]])), (length(overlapsProfiles1) - i + 0.7), col=NA, border="#999999")
text(0, (length(overlapsProfiles1) - i + 0.80), names(overlapsProfiles1)[i], pos=4, col="black")
}
if(!is.null(labels)){
mtext(labels[1], line = 0.7, adj = 0, cex=1.4);
}
invisible(NULL)
}
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Defines functions plotOverlapProfile computeOverlapProfile .measureOverlaps .countOverlaps plotMethylationProfileFromData plotMethylationProfile computeMethylationProfile
Documented in computeMethylationProfile computeOverlapProfile plotMethylationProfile plotMethylationProfileFromData plotOverlapProfile
#' This function computes the low resolution profiles for the bisulfite
#' sequencing data.
#'
#' @title Compute methylation profile
#' @param methylationData the methylation data stored as a \code{\link{GRanges}}
#' object with four metadata columns (see \code{\link{methylationDataList}}).
#' @param region a \code{\link{GRanges}} object with the regions where to
#' compute the DMRs.
#' @param windowSize a \code{numeric} value indicating the size of the window in
#' which methylation is averaged.
#' @param context the context in which the DMRs are computed (\code{"CG"},
#' \code{"CHG"} or \code{"CHH"}).
#' @return a \code{\link{GRanges}} object with equal sized tiles of the
#' \code{region}. The object consists of the following metadata
#' \describe{
#' \item{sumReadsM}{the number of methylated reads.}
#' \item{sumReadsN}{the total number of reads.}
#' \item{Proportion}{the proportion of methylated reads.}
#' \item{context}{the context (\code{"CG"}, \code{"CHG"} or \code{"CHH"}).}
#' }
#' @seealso \code{\link{plotMethylationProfileFromData}},
#' \code{\link{plotMethylationProfile}}, \code{\link{methylationDataList}}
#' @examples
#'
#' # load the methylation data
#' data(methylationDataList)
#'
#' # the region where to compute the profile
#' region <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E6))
#'
#' # compute low resolution profile in 20 Kb windows
#' lowResProfileWTCHH <- computeMethylationProfile(methylationDataList[["WT"]],
#' region, windowSize = 20000, context = "CHH")
#'
#' \dontrun{
#' # compute low resolution profile in 10 Kb windows
#' lowResProfileWTCG <- computeMethylationProfile(methylationDataList[["WT"]],
#' region, windowSize = 10000, context = "CG")
#'
#' lowResProfileMet13CG <- computeMethylationProfile(
#' methylationDataList[["met1-3"]], region,
#' windowSize = 10000, context = "CG")
#' }
#'
#' @author Nicolae Radu Zabet and Jonathan Michael Foonlan Tsang
#' @export
computeMethylationProfile <- function(methylationData,
region,
windowSize = floor(width(region)/500),
context = "CG") {
.validateMethylationData(methylationData)
.validateGRanges(region, methylationData, length=1, generateGenomeWide=FALSE)
.validateContext(context)
.stopIfNotAll(c(.isInteger(windowSize, positive=TRUE)),
" the window size used to compute the methylation profile is an integer higher or equal to 0")
seqname <- seqnames(region)
minPos <- start(region)
maxPos <- end(region)
hits <- findOverlaps(methylationData, region)
localMethylationData <- methylationData[queryHits(hits)];
rm(methylationData)
contextMethylationData <- localMethylationData[localMethylationData$context%in%context];
rm(localMethylationData)
cat("Calculating methylation profile for ", .printGenomicRanges(region), " using a window of ", windowSize, " bp \n")
seqs = seq(minPos, maxPos - windowSize, windowSize);
ranges <- GRanges(seqname, IRanges(seqs, seqs+windowSize-1))
#for windowSize <= 2000 Bins method is faster, but for anything else, regions method is faster
if(windowSize <= 2000){
ranges <- .analyseReadsInsideBinsOneSample(contextMethylationData, ranges, region)
} else{
ranges <- .analyseReadsInsideRegionsOneSample(contextMethylationData, ranges)
}
ranges$context <- paste(context, collapse = "_")
return(ranges)
}
#' This function plots the low resolution profiles for the bisulfite sequencing
#' data.
#'
#' @title Plot Methylation Profile
#' @param methylationProfiles a \code{GRangesList} object. Each
#' \code{\link{GRanges}} object in the list is generated by calling the
#' function \code{\link{computeMethylationProfile}}.
#' @param autoscale a \code{logical} value indicating whether the values are
#' autoscalled for each context or not.
#' @param labels a \code{vector} of \code{character} used to add a subfigure
#' characters to the plot. If \code{NULL} nothing is added.
#' @param title the plot title.
#' @param col a \code{character} vector with the colours. It needs to contain a
#' minimum of 2 colours per context. If not or if NULL, the defalut colours will
#' be used.
#' @param pch the R symbols used to plot the data.
#' @param lty the line types used to plot the data.
#' @return Invisibly returns \code{NULL}
#' @seealso \code{\link{plotMethylationProfileFromData}},
#' \code{\link{computeMethylationProfile}} and \code{\link{methylationDataList}}
#' @examples
#'
#'
#' # load the methylation data
#' data(methylationDataList)
#'
#' # the region where to compute the profile
#' region <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E6))
#'
#' # compute low resolution profile in 20 Kb windows
#' lowResProfileWTCG <- computeMethylationProfile(methylationDataList[["WT"]],
#' region, windowSize = 20000, context = "CG")
#'
#' lowResProfilsCG <- GRangesList("WT" = lowResProfileWTCG)
#'
#' #plot the low resolution profile
#' par(mar=c(4, 4, 3, 1)+0.1)
#' par(mfrow=c(1,1))
#' plotMethylationProfile(lowResProfilsCG, autoscale = FALSE,
#' title="CG methylation on Chromosome 3",
#' col=c("#D55E00","#E69F00"), pch = c(1,0),
#' lty = c(4,1))
#'
#' \dontrun{
#' # compute low resolution profile in 10 Kb windows in CG context
#' lowResProfileWTCG <- computeMethylationProfile(methylationDataList[["WT"]],
#' region, windowSize = 10000, context = "CG")
#'
#' lowResProfileMet13CG <- computeMethylationProfile(
#' methylationDataList[["met1-3"]], region,
#' windowSize = 10000, context = "CG")
#'
#' lowResProfileCG <- GRangesList("WT" = lowResProfileWTCG,
#' "met1-3" = lowResProfileMet13CG)
#'
#' # compute low resolution profile in 10 Kb windows in CHG context
#' lowResProfileWTCHG <- computeMethylationProfile(methylationDataList[["WT"]],
#' region, windowSize = 10000, context = "CHG")
#'
#' lowResProfileMet13CHG <- computeMethylationProfile(
#' methylationDataList[["met1-3"]], region,
#' windowSize = 10000, context = "CHG")
#'
#' lowResProfileCHG <- GRangesList("WT" = lowResProfileWTCHG,
#' "met1-3" = lowResProfileMet13CHG)
#'
#' # plot the low resolution profile
#' par(mar=c(4, 4, 3, 1)+0.1)
#' par(mfrow=c(2,1))
#' plotMethylationProfile(lowResProfileCG, autoscale = FALSE,
#' labels = LETTERS[1],
#' title="CG methylation on Chromosome 3",
#' col=c("#D55E00","#E69F00"), pch = c(1,0),
#' lty = c(4,1))
#' plotMethylationProfile(lowResProfileCHG, autoscale = FALSE,
#' labels = LETTERS[2],
#' title="CHG methylation on Chromosome 3",
#' col=c("#0072B2", "#56B4E9"), pch = c(16,2),
#' lty = c(3,2))
#' }
#'
#' @author Nicolae Radu Zabet
#' @export
plotMethylationProfile <- function(methylationProfiles,
autoscale = FALSE,
labels=NULL,
title = "",
col = NULL,
pch = c(1,0,16,2,15,17),
lty = c(4,1,3,2,6,5)) {
.validateMethylationProfile(methylationProfiles)
defaultConditionsNames <- paste("condition ", (1:length(methylationProfiles)), sep="")
if(is.null(names(methylationProfiles))){
names(methylationProfiles) <- defaultConditionsNames
}
if(!.isColor(col, minLength = length(methylationProfiles) )){
if(length(methylationProfiles) <= 6){
col <- c("#D55E00","#E69F00", "#0072B2", "#56B4E9", "#F0E442", "#009E73")
} else if(length(methylationProfiles) <= 8){
col <- c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
} else{
col <- rainbow(length(methylationProfiles))
}
}
.stopIfNotAll(c(!is.null(autoscale),
is.logical(autoscale),
length(autoscale) == 1),
" autoscale is a logical value")
if(is.null(title)){
title=""
} else if(is.character(title[1]) > 1){
title[1] = as.character(title[1])
}
.stopIfNotAll(c(!is.null(pch),
all(as.integer(pch) == pch),
all(pch >= 0),
length(pch) >= length(methylationProfiles)),
paste(" pch is a vector of positive integers of size ",length(methylationProfiles), sep=""))
.stopIfNotAll(c(!is.null(lty),
all(as.integer(lty) == lty),
all(lty >= 0),
length(lty) >= length(methylationProfiles)),
paste(" lty is a vector of positive integers of size ",length(methylationProfiles), sep=""))
ymax <- 1
if(autoscale){
ymax <- 0
for(i in 1:length(methylationProfiles)){
if(ymax < max(methylationProfiles[[i]]$Proportion)){
ymax = max(methylationProfiles[[i]]$Proportion)
}
}
}
options(scipen=10)
pos <- (start(methylationProfiles[[1]])+end(methylationProfiles[[1]]))/2
plot(pos, methylationProfiles[[1]]$Proportion, type = "o", ylim = c(0,ymax),
xlab="genomic coordinate", ylab="methylation", col=col[1], yaxt="n",
pch = pch[1], lty = lty[1], main = title[1])
if(length(methylationProfiles) > 1){
for(i in 2:length(methylationProfiles)){
lines(pos, methylationProfiles[[i]]$Proportion, type = "o", col=col[i], lty = lty[i], pch = pch[i])
}
}
legend("topright", legend = names(methylationProfiles),
lty = lty[1:length(methylationProfiles)],
col = col[1:length(methylationProfiles)],
pch = pch[1:length(methylationProfiles)], bty="n")
if(!is.null(labels)){
mtext(labels[1], line = 0.7, adj = 0, cex=1.4);
}
if(autoscale){
axis(2,c(0,signif(ymax/2, 1),signif(ymax, 1)));
} else{
axis(2,c(0,.5,1));
}
invisible(NULL)
}
#' This function plots the low resolution profiles for all bisulfite sequencing
#' data.
#'
#' @title Plot methylation profile from data
#' @param methylationData1 the methylation data in condition 1
#' (see \code{\link{methylationDataList}}).
#' @param methylationData2 the methylation data in condition 2
#' (see \code{\link{methylationDataList}}). This is optional.
#' @param regions a \code{\link{GRanges}} object with the regions where to plot
#' the profiles.
#' @param conditionsNames the names of the two conditions. This will be used to
#' plot the legend.
#' @param context a \code{vector} with all contexts in which the DMRs are
#' computed (\code{"CG"}, \code{"CHG"} or \code{"CHH"}).
#' @param windowSize a \code{numeric} value indicating the size of the window in
#' which methylation is averaged.
#' @param autoscale a \code{logical} value indicating whether the values are
#' autoscalled for each context or not.
#' @param labels a \code{vector} of \code{character} used to add a subfigure
#' character to the plot. If \code{NULL} nothing is added.
#' @param col a \code{character} vector with the colours. It needs to contain a
#' minimum of 2 colours per condition. If not or if \code{NULL}, the defalut
#' colours will be used.
#' @param pch the R symbols used to plot the data It needs to contain a minimum
#' of 2 symbols per condition. If not or if \code{NULL}, the defalut symbols
#' will be used.
#' @param lty the line types used to plot the data. It needs to contain a
#' minimum of 2 line types per condition. If not or if \code{NULL}, the defalut
#' line types will be used.
#' @param contextPerRow a \code{logical} value indicating if the each row
#' represents an individual context. If \code{FALSE}, each column will represent
#' an individual context.
#' @return Invisibly returns \code{NULL}
#' @seealso \code{\link{plotMethylationProfile}},
#' \code{\link{computeMethylationProfile}} and \code{\link{methylationDataList}}
#' @examples
#'
#'
#' # load the methylation data
#' data(methylationDataList)
#'
#' #plot the low resolution profile at 10 Kb resolution
#' par(mar=c(4, 4, 3, 1)+0.1)
#' plotMethylationProfileFromData(methylationDataList[["WT"]],
#' methylationDataList[["met1-3"]],
#' conditionsNames=c("WT", "met1-3"),
#' windowSize = 20000, autoscale = TRUE,
#' context = c("CHG"))
#'
#' \dontrun{
#' #plot the low resolution profile at 5 Kb resolution
#' par(mar=c(4, 4, 3, 1)+0.1)
#' plotMethylationProfileFromData(methylationDataList[["WT"]],
#' methylationDataList[["met1-3"]],
#' conditionsNames=c("WT", "met1-3"),
#' windowSize = 5000, autoscale = TRUE,
#' context = c("CG", "CHG", "CHH"),
#' labels = LETTERS)
#' }
#'
#' @author Nicolae Radu Zabet
#' @export
plotMethylationProfileFromData <- function(methylationData1,
methylationData2 = NULL,
regions = NULL,
conditionsNames = NULL,
context = "CG",
windowSize = NULL,
autoscale = FALSE,
labels=NULL,
col=NULL,
pch = c(1,0,16,2,15,17),
lty = c(4,1,3,2,6,5),
contextPerRow = TRUE) {
.validateContext(context)
.validateMethylationData(methylationData1, variableName="methylationData1")
numberOfConditions <- 1
if(!is.null(methylationData2)){
.validateMethylationData(methylationData2, variableName="methylationData2")
numberOfConditions <- 2
}
if(is.null(conditionsNames) | length(conditionsNames) < numberOfConditions){
conditionsNames <- paste("condition ",(1:numberOfConditions),sep="")
}
number_of_symbols <-numberOfConditions*length(context)
if(!.isColor(col, minLength = number_of_symbols )){
if(number_of_symbols <= 6){
col <- c("#D55E00","#E69F00", "#0072B2", "#56B4E9", "#F0E442", "#009E73")
} else if(number_of_symbols <= 8){
col <- c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
} else{
col <- rainbow(number_of_symbols)
}
}
.stopIfNotAll(c(!is.null(pch),
all(as.integer(pch) == pch),
all(pch >= 0),
length(pch) >= number_of_symbols),
paste(" pch is a vector of positive integers of size ",number_of_symbols, sep=""))
.stopIfNotAll(c(!is.null(lty),
all(as.integer(lty) == lty),
all(lty >= 0),
length(lty) >= number_of_symbols),
paste(" lty is a vector of positive integers of size ",number_of_symbols, sep=""))
#compute all genomic regions for which data is available
recomputeRegions <- FALSE
if(is.null(regions)){
recomputeRegions <- TRUE
}
if(!recomputeRegions & (!is(regions, "GRanges") | length(regions) < 1)){
recomputeRegions <- TRUE
}
if(recomputeRegions){
cat("Recompute regions... \n")
regions <- GRanges()
regions <- union(regions, getWholeChromosomes(methylationData1))
if(numberOfConditions > 1){
regions <- union(regions, getWholeChromosomes(methylationData2))
}
}
if(is.null(windowSize)){
windowSize = floor(min(width(regions))/500)
}
index <- 1;
cat("Computing low resolution profiles... \n")
par(mar=c(4, 4, 3, 1)+0.1)
if(contextPerRow){
par(mfrow=c(length(context),length(regions)))
for(i in 1:length(context)){
for(j in 1:length(regions)){
buffer_profile <- GRangesList(computeMethylationProfile(methylationData1, regions[j], windowSize = windowSize, context = context[i]))
if(numberOfConditions > 1){
buffer_profile <- c(buffer_profile, GRangesList(computeMethylationProfile(methylationData2, regions[j], windowSize = windowSize, context = context[i])))
}
names(buffer_profile) <- conditionsNames
symbols_ind <- (numberOfConditions*(i-1) + 1):(numberOfConditions*i)
plotMethylationProfile(buffer_profile, autoscale = autoscale, labels = labels[index],
title=paste(context[i], " methylation on chromosome ", as.character(seqnames(regions)[j]),sep=""), col=col[symbols_ind],
pch = pch[symbols_ind], lty = lty[symbols_ind])
index <- index + 1
}
}
} else{
par(mfrow=c(length(regions),length(context)))
for(j in 1:length(regions)){
for(i in 1:length(context)){
buffer_profile <- GRangesList(computeMethylationProfile(methylationData1, regions[j], windowSize = windowSize, context = context[i]))
if(numberOfConditions > 1){
buffer_profile <- c(buffer_profile, GRangesList(computeMethylationProfile(methylationData2, regions[j], windowSize = windowSize, context = context[i])))
}
names(buffer_profile) <- conditionsNames
symbols_ind <- (numberOfConditions*(i-1) + 1):(numberOfConditions*i)
plotMethylationProfile(buffer_profile, autoscale = autoscale, labels = labels[index],
title=paste(context[i], " methylation on chromosome ", as.character(seqnames(regions)[j]),sep=""), col=col[symbols_ind],
pch = pch[symbols_ind], lty = lty[symbols_ind])
index <- index + 1
}
}
}
invisible(NULL)
}
.countOverlaps <- function(region, subRegions){
return(sum(countOverlaps(subRegions, region)))
}
.measureOverlaps <- function(region, subRegions){
return(sum(width(intersect(subRegions, region))))
}
#' This function computes the distribution of a subset of regions
#' (\code{\link{GRanges}} object) over a large region (\code{\link{GRanges}}
#' object)
#'
#' @title Compute Overlaps Profile
#' @param subRegions a \code{\link{GRanges}} object with the sub regions; e.g.
#' can be the DMRs.
#' @param largeRegion a \code{\link{GRanges}} object with the region where to
#' compute the overlaps; e.g. a chromosome
#' @param windowSize The \code{largeRegion} is partitioned into equal sized
#' tiles of width \code{windowSize}.
#' @param binary a value indicating whether to count 1 for each overlap or to
#' compute the width of the overlap
#' @param cores the number of cores used to compute the DMRs.
#' @return a \code{\link{GRanges}} object with equal sized tiles of the regions.
#' The object has one metadata file \code{score} which represents: the number of
#' subRegions overlapping with the tile, in the case of \code{binary = TRUE},
#' and the width of the subRegions overlapping with the tile , in the case of
#' \code{binary = FALSE}.
#' @seealso \code{\link{plotOverlapProfile}}, \code{\link{filterDMRs}},
#' \code{\link{computeDMRs}} and \code{\link{mergeDMRsIteratively}}
#' @examples
#' # load the methylation data
#' data(methylationDataList)
#'
#' # load the DMRs in CG context
#' data(DMRsNoiseFilterCG)
#'
#' # the coordinates of the area to be plotted
#' largeRegion <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E5))
#'
#' # compute overlaps distribution
#' hotspots <- computeOverlapProfile(DMRsNoiseFilterCG, largeRegion,
#' windowSize = 10000, binary = FALSE)
#' @author Nicolae Radu Zabet
#' @export
computeOverlapProfile <- function(subRegions,
largeRegion,
windowSize = floor(width(largeRegion)/500),
binary=TRUE,
cores = 1){
.stopIfNotAll(c(!is.null(subRegions),
is(subRegions, "GRanges")),
paste(" subRegions neads to be a GRanges object.",sep=""))
.stopIfNotAll(c(!is.null(largeRegion),
is(largeRegion, "GRanges"),
length(largeRegion) == 1),
paste(" largeRegion neads to be a GRanges object with one location (e.g. entire chromosome).",sep=""))
.stopIfNotAll(c(!is.null(binary),
is.logical(binary),
length(binary) == 1),
paste(" binary neads to be a logical variable.",sep=""))
.stopIfNotAll(c(.isInteger(windowSize, positive=TRUE)),
" the window size used to compute the methylation profile is an integer higher or equal to 0")
.stopIfNotAll(c(.isInteger(cores, positive=TRUE)),
" the number of cores to used when computing the DMRs needs to be an integer hirger or equal to 1.")
seqname <- seqnames(largeRegion)
minPos <- start(largeRegion)
maxPos <- end(largeRegion)
cat("Calculating overlaps for ", .printGenomicRanges(largeRegion), " using a window of ", windowSize, " bp \n")
seqs = seq(minPos, maxPos - windowSize, windowSize);
ranges <- GRanges(seqname, IRanges(seqs, seqs+windowSize-1))
ranges$score <- 0
rangesList <- tile(ranges, cores)
if(binary){
if(cores > 1){
scores <- parallel::mclapply(rangesList, .countOverlaps, subRegions = subRegions, mc.cores = cores)
} else {
scores <- lapply(rangesList, .countOverlaps, subRegions = subRegions)
}
} else{
if(cores > 1){
scores <- parallel::mclapply(rangesList, .measureOverlaps, subRegions = subRegions, mc.cores = cores)
} else {
scores <- lapply(rangesList, .measureOverlaps, subRegions = subRegions)
}
}
ranges$score <- unlist(scores)
return(ranges)
}
#' This function plots the distribution of a set of subregions on a large
#' region.
#'
#' @title Plot overlap profile
#' @param overlapsProfiles1 a \code{\link{GRanges}} object with the overlaps
#' profile; see \code{\link{computeOverlapProfile}}.
#' @param overlapsProfiles2 a \code{\link{GRanges}} object with the overlaps
#' profile; see \code{\link{computeOverlapProfile}}. This is optional. For
#' example, one can be use \code{overlapsProfiles1} to display hypomethylated
#' regions and \code{overlapsProfiles2} the hypermethylated regions.
#' @param names a \code{vector} of \code{character} to add labels for the two
#' overlapsProfiles. This is an optinal parameter.
#' @param labels a \code{vector} of \code{character} used to add a subfigure
#' character to the plot. If \code{NULL} nothing is added.
#' @param col a \code{character} vector with the colours. It needs to contain 2
#' colours. If not or if \code{NULL}, the defalut colours will be used.
#' @param title the title of the plot.
#' @param logscale a \code{logical} value indicating if the colours are on
#' logscale or not.
#' @param maxValue a maximum value in a region. Used for the colour scheme.
#' @return Invisibly returns \code{NULL}.
#' @seealso \code{\link{computeOverlapProfile}}, \code{\link{filterDMRs}},
#' \code{\link{computeDMRs}} and \code{\link{mergeDMRsIteratively}}
#' @examples
#'
#' # load the methylation data
#' data(methylationDataList)
#'
#' # load the DMRs in CG context
#' data(DMRsNoiseFilterCG)
#'
#' # the coordinates of the area to be plotted
#' largeRegion <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E5))
#'
#' # compute overlaps distribution
#' hotspotsHypo <- computeOverlapProfile(DMRsNoiseFilterCG, largeRegion,
#' windowSize = 10000, binary = FALSE)
#'
#' plotOverlapProfile(GRangesList("Chr3"=hotspotsHypo),
#' names = c("hypomethylated"), title = "CG methylation")
#'
#' \dontrun{
#'
#' largeRegion <- GRanges(seqnames = Rle("Chr3"), ranges = IRanges(1,1E6))
#'
#' hotspotsHypo <- computeOverlapProfile(
#' DMRsNoiseFilterCG[(DMRsNoiseFilterCG$regionType == "loss")],
#' largeRegion, windowSize=2000, binary=TRUE, cores=1)
#'
#' hotspotsHyper <- computeOverlapProfile(
#' DMRsNoiseFilterCG[(DMRsNoiseFilterCG$regionType == "gain")],
#' largeRegion, windowSize=2000, binary=TRUE, cores=1)
#'
#' plotOverlapProfile(GRangesList("Chr3"=hotspotsHypo),
#' GRangesList("Chr3"=hotspotsHyper),
#' names=c("loss", "gain"), title="CG methylation")
#' }
#'
#' @author Nicolae Radu Zabet
#' @export
plotOverlapProfile <- function(overlapsProfiles1, overlapsProfiles2=NULL, names=NULL,
labels=NULL, col=NULL, title="", logscale=FALSE, maxValue=NULL) {
.stopIfNotAll(c(!is.null(overlapsProfiles1),
is(overlapsProfiles1, "GRangesList"),
length(overlapsProfiles1) > 0),
" overlapsProfiles1 needs to be a GRangesList object")
unlisted_overlapsProfiles1 <- unlist(overlapsProfiles1, use.names=FALSE)
score <- mcols(unlisted_overlapsProfiles1)$score
if(is.null(score)) stop("elements of the overlapsProfiles1 are incorrect")
maxScore <- max(score)
minScore <- min(score)
numberOfConditions <- 1
if(!is.null(overlapsProfiles2)){
.stopIfNotAll(c(is(overlapsProfiles2, "GRangesList"),
length(overlapsProfiles2) == length(overlapsProfiles1)),
" overlapsProfiles2 needs to be a GRangesList object with the same number of elements as overlapsProfiles1")
unlisted_overlapsProfiles2 <- unlist(overlapsProfiles2, use.names=FALSE)
score <- mcols(unlisted_overlapsProfiles2)$score
if(is.null(score)) stop("elements of the overlapsProfiles2 are incorrect")
maxScore <- max(maxScore, score)
minScore <- min(minScore, score)
numberOfConditions <- 2
}
.stopIfNotAll(c(!is.null(logscale),
is.logical(logscale),
length(logscale) == 1),
paste(" logscale neads to be a logical variable.",sep=""))
if(!.isColor(col) | length(col) < numberOfConditions){
col <- c("#0072B2", "#D55E00")
}
if(!is.null(maxValue)){
if(is.numeric(maxValue)){
if(round(maxValue) > 0){
maxScore <- round(maxValue)
}
}
}
if(logscale){
minScore <- log10(1)
maxScore <- log10(maxScore)
}
minScore <- round(minScore)
maxScore <- round(maxScore)
cols1 <- c(colorRampPalette(c("white",col[1]))(1 + maxScore - minScore))
cols2 <- c(colorRampPalette(c("white",col[2]))(1 + maxScore - minScore))
numberOfProfiles<-length(overlapsProfiles1)
xmin <- min(unlist(lapply(overlapsProfiles1, start)))
xmax <- max(unlist(lapply(overlapsProfiles1, end)))
par(mar=c(4, 4, 3, 1)+0.1)
plot(c(xmin,xmax),c(0, 1*numberOfProfiles), type="n",xlab="position (bp)", ylab="", yaxt="n", bty="n", main=title)
for(i in 1:length(overlapsProfiles1)){
if(!is.null(overlapsProfiles2)){
#plot two conditions
for(j in 1:length(overlapsProfiles1[[i]])){
colId <- overlapsProfiles1[[i]][j]$score
if(colId > 0){
if(logscale){
colId <- log10(colId)
}
rect(start(overlapsProfiles1[[i]][j]), (length(overlapsProfiles1) - i + 0.4), end(overlapsProfiles1[[i]][j]), (length(overlapsProfiles1) - i + 0.7), col=cols1[round(colId)+1], border = NA)
}
}
for(j in 1:length(overlapsProfiles2[[i]])){
colId <- overlapsProfiles2[[i]][j]$score
if(colId > 0){
if(logscale){
colId <- log10(colId)
}
rect(start(overlapsProfiles2[[i]][j]), (length(overlapsProfiles2) - i + 0.1), end(overlapsProfiles2[[i]][j]), (length(overlapsProfiles2) - i + 0.4), col=cols2[round(colId)+1], border = NA)
}
}
if(!is.null(names)){
if(all(is.character(names)) & length(names) >= numberOfConditions){
at_pos <- c(0.55,0.25)
for(j in 1:numberOfConditions){
mtext(names[j], side = 2, line=-0.5, at=(length(overlapsProfiles1) - i + at_pos[j]), col="black", las=2)
}
}
}
} else{
#plot one conditions
for(j in 1:length(overlapsProfiles1[[i]])){
colId <- overlapsProfiles1[[i]][j]$score
if(colId > 0){
if(logscale){
colId <- log10(colId)
}
rect(start(overlapsProfiles1[[i]][j]), (length(overlapsProfiles1) - i + 0.1), end(overlapsProfiles1[[i]][j]), (length(overlapsProfiles1) - i + 0.7), col=cols1[round(colId)+1], border = NA)
}
}
if(!is.null(names)){
if(all(is.character(names)) & length(names) >= numberOfConditions){
at_pos <- c(0.4)
mtext(names[1], side = 2, line=-0.5, at=(length(overlapsProfiles1) - i + at_pos[1]), col="black")
}
}
}
rect(xmin, (length(overlapsProfiles1) - i + 0.1), max(end(overlapsProfiles1[[i]])), (length(overlapsProfiles1) - i + 0.7), col=NA, border="#999999")
text(0, (length(overlapsProfiles1) - i + 0.80), names(overlapsProfiles1)[i], pos=4, col="black")
}
if(!is.null(labels)){
mtext(labels[1], line = 0.7, adj = 0, cex=1.4);
}
invisible(NULL)
}
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