Nothing
.plotMethMap <- function(object, region, groups, intervals=FALSE, ...) {
if (length(region) != 1) {
stop("Argument \"region\" must contain exactly one genomic region.")
}
strand(object) <- "*"
object <- sort(object)
ind <- overlapsAny(rowRanges(object), region)
if (sum(ind) == 0) {
stop("No data to plot within the given region/samples.")
}
md <- methLevel(object)[ind, ]
pos <- start(rowRanges(object))[ind]
rownames(md) <- as.character(pos)
md <- t(md)
ind <- !apply(is.na(md), 2, all)
md <- md[, ind]
pos <- pos[ind]
if (intervals) {
fullMd <- matrix(NA, nrow=nrow(md), ncol=pos[length(pos)]-pos[1]+1)
rownames(fullMd) <- rownames(md)
colnames(fullMd) <- as.character(pos[1]:pos[length(pos)])
fullMd[, colnames(md)] <- md
md <- fullMd
rm(fullMd)
}
ind.na <- apply(md, 1, function(x) all(is.na(x)))
if (sum(ind.na) > 0) {
names.na <- names(which(ind.na))
md <- md[!ind.na, ]
object <- object[, !ind.na]
if (is.element("RowSideColors", names(args))) {
args$RowSideColors <- args$RowSideColors[!ind.na]
}
warning("Sample(s) ", names.na, " omitted due to missing data within \"region\".")
}
if (intervals) {
cn <- as.character(pretty(colnames(md), n=5))
colnames(md)[!is.element(colnames(md), cn)] <- ""
}
args <- list(...)
# set RowSideColors if groups is given
if (!missing(groups) & !is.element("RowSideColors", names(args))) {
pDat <- as.character(groups)
uPDat <- unique(pDat)
cols <- .categorialColors(length(uPDat))
names(cols) <- uPDat
args <- c(list(RowSideColors=cols[pDat]), args)
}
# default scale="none"
if (!is.element("scale", names(args))) {
args <- c(args, list(scale="none"))
}
# default zlim=c(0,1)
if (!is.element("zlim", names(args))) {
args <- c(args, list(zlim=c(0,1)))
}
# default Colv = NA
if (!is.element("Colv", names(args))) {
args <- c(args, list(Colv=NA))
}
# default cexCol=0.8 if intervals=TRUE and no labCol given
if (intervals &
!is.element("labCol", names(args)) &
!is.element("cexCol", names(args))) {
args <- c(args, list(cexCol=0.8))
}
# default colors green - black - red
if (!is.element("col", names(args))) {
colF <- colorRampPalette(colors=c("green", "black", "red"))
args <- c(args, list(col=colF(64)))
}
args <- c(list(x=md), args)
do.call(heatmap, args)
}
setMethod("plotMethMap",
signature=c(object="BSrel", region="GRanges", groups="factor", intervals="logical"),
.plotMethMap)
setMethod("plotMethMap",
signature=c(object="BSrel", region="GRanges", groups="missing", intervals="logical"),
.plotMethMap)
setMethod("plotMethMap",
signature=c(object="BSrel", region="GRanges", groups="factor", intervals="missing"),
.plotMethMap)
setMethod("plotMethMap",
signature=c(object="BSrel", region="GRanges", groups="missing", intervals="missing"),
.plotMethMap)
setMethod("plotMethMap",
signature=c(object="BSraw", region="GRanges", groups="factor", intervals="logical"),
function(object, region, groups, intervals, ...) {
.plotMethMap(object=rawToRel(object), region=region, groups=groups, intervals=intervals, ...)
})
setMethod("plotMethMap",
signature=c(object="BSraw", region="GRanges", groups="missing", intervals="logical"),
function(object, region, intervals, ...) {
.plotMethMap(object=rawToRel(object), region=region, intervals=intervals, ...)
})
setMethod("plotMethMap",
signature=c(object="BSraw", region="GRanges", groups="factor", intervals="missing"),
function(object, region, groups, ...) {
.plotMethMap(object=rawToRel(object), region=region, groups=groups, ...)
})
setMethod("plotMethMap",
signature=c(object="BSraw", region="GRanges", groups="missing", intervals="missing"),
function(object, region, ...) {
.plotMethMap(object=rawToRel(object), region=region, ...)
})
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