colByChr {karyoploteR} | R Documentation

## colByChr

### 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)
    }

[Package karyoploteR version 1.14.1 Index]