colByChr: colByChr

In karyoploteR: Plot customizable linear genomes displaying arbitrary data

Description

Given a set of data elements, return a color for each one based on their chromosome

Usage

colByChr(data, colors="2grays", all.chrs=NULL, default.col="black")

Arguments

data	Either a vector of characters or a GRanges object
colors	The name of a color set ("2grays", "blackgreen", "rainbow"...) or a vector of colors. If the vector is named, names are expected to be the chromosome names. (defaults to "2grays")
all.chrs	A vector with all possible chromosomes. If NULL, the list will be extracted from data (using seqlevels if available). (defaults to NULL)
default.col	The default color to return when something is unavailable

Details

Returns a color for each data element based on its chromosome. The returned colors might com from one of the predefined color sets or passed in as a parameter.

If colors is the name of one of the available color sets, it the color set is used. If it's a named character vector with the chromosome as names, they will be assigned by name and any missing chromosome will be default.col. If it's a non-named chraracter vector, will be used in order and recycled if necessary.

Data might be either a GRanges object or a vector of chromosomes.

Value

A vector of colors

Note

Available color.sets: "2grays"=c("#888888", "#444444"), "2blues"=c("#6caeff", "#2b5d9b") "blackgreen"=c("black", "green"), "greengray"=c("#c6ffb7", "#888888"), "brewer.set1"=c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#FFFF33", "#A65628", "#F781BF", "#999999") "brewer.set2"=c("#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F", "#E5C494", "#B3B3B3") "brewer.set3"=c("#8DD3C7", "#FFFFB3", "#BEBADA", "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#FCCDE5", "#D9D9D9", "#BC80BD", "#CCEBC5", "#FFED6F") "brewer.pastel1"=c("#FBB4AE", "#B3CDE3", "#CCEBC5", "#DECBE4", "#FED9A6", "#FFFFCC", "#E5D8BD", "#FDDAEC", "#F2F2F2"), "brewer.pastel2"=c("#B3E2CD", "#FDCDAC", "#CBD5E8", "#F4CAE4", "#E6F5C9", "#FFF2AE", "#F1E2CC", "#CCCCCC"), "rainbow"=rainbow(n=length(all.chrs))

See Also

kpPoints

Examples

chrs <- c("chr1", "chr2", "chr2", "chr1", "chr5")
points <- toGRanges(paste0("chr", c(1:22, "X", "Y")), rep(10e6, 24), rep(10e6, 24))

colByChr(chrs)
colByChr(points)

kp <- plotKaryotype(plot.type=4, labels.plotter=NULL, ideogram.plotter=NULL)
kpAddChromosomeNames(kp, srt=45)
kpAddChromosomeSeparators(kp)

total.tracks <- 6

kpPoints(kp, points, col=colByChr(points), y=0.5, cex=1, r0=autotrack(1,total.tracks)$r0, r1=autotrack(1,total.tracks)$r1)
colors <- NULL
kpPoints(kp, points, y=0.5, col=colByChr(points, colors=colors), cex=1, r0=autotrack(2,total.tracks)$r0, r1=autotrack(2,total.tracks)$r1)
colors <- c("red", "blue")
kpPoints(kp, points, y=0.5, col=colByChr(points, colors=colors), cex=1, r0=autotrack(3,total.tracks)$r0, r1=autotrack(3,total.tracks)$r1)
colors <- c(chr1="red", chr7="blue")
kpPoints(kp, points, y=0.5, col=colByChr(points, colors=colors), cex=1, r0=autotrack(4,total.tracks)$r0, r1=autotrack(4,total.tracks)$r1)
kpPoints(kp, points, y=0.5, col=colByChr(points, colors=colors, default.col="green"), cex=1, r0=autotrack(5,total.tracks)$r0, r1=autotrack(5,total.tracks)$r1)
colors <- c("red", "yellow", 3, "orchid", "blue")
kpPoints(kp, points, y=0.5, col=colByChr(points, colors=colors), cex=1, r0=autotrack(6,total.tracks)$r0, r1=autotrack(6,total.tracks)$r1)

#Color sets
pp <- getDefaultPlotParams(plot.type=4)
pp$leftmargin <- 0.2
kp <- plotKaryotype(plot.type=4, labels.plotter=NULL, ideogram.plotter=NULL, plot.params=pp)
kpAddChromosomeNames(kp, srt=45)
kpAddChromosomeSeparators(kp)

color.sets <- c( "2grays", "2blues", "blackgreen", "greengray", "brewer.set1",
                   "brewer.set2", "brewer.set3", "brewer.pastel1", "brewer.pastel2", "rainbow" )
total.tracks <- length(color.sets)
for(i in seq_len(length(color.sets))) {
    kpPoints(kp, points, y=0.5, col=colByChr(points, colors=color.sets[i]), cex=1, r0=autotrack(i,total.tracks)$r0, r1=autotrack(i,total.tracks)$r1)
    kpAddLabels(kp, labels=color.sets[i], cex=0.7, r0=autotrack(i,total.tracks)$r0, r1=autotrack(i,total.tracks)$r1)
}

karyoploteR documentation built on Nov. 8, 2020, 5:52 p.m.