colByRegion {karyoploteR}R Documentation

colByRegion

Description

Given a set of data elements, return a color for each one based on whether they overlap a given set of regions. This might be useful, for example, to set a different color for data points overlapping a certain region of interest.

Usage

colByRegion(data, regions, colors=NULL, default.col="black")

Arguments

data

Either a vector of characters or a GRanges object

regions

(GRanges or equivalent) A set of regions where the color will be modified. Internally it will be converted into a Genomic Ranges object by toGRanges (from regioneR package) and so it can be either a GRanges, a data.frame, a character or any other value type accepted by that function. If colors is NULL (the default) and regions has additional columns in addition to chr, start and end, if any has a name in c("color", "colors", "col", "cols") it will be used. Otherwise the first additional column will be used.

colors

(color) The colors to be used for each region. The content will be recycled if needed. If NULL, the colors are assumed to be available in the regions object. (defaults to NULL)

default.col

The default color to return for data elements not overlapping the regions. (defaults to "black")

Details

Given a set of data elements, return a color for each one based on whether they overlap a given set of regions. The colors might be different for each region and can be specified either in the regions object itself or in a separate colors parameter. If specified in colors, the values will be recycled as needed.

Value

A vector of colors

See Also

kpPoints, colByChr, toGRanges

Examples


data <- toGRanges("chr1", c(1e6*1:245), c(1e6*1:245)+10)
data$y <- rnorm(n = length(data), mean = 0.5, sd = 0.15)

regions <- toGRanges(c("chr1:10e6-20e6", "chr1:100e6-150e6"))
regions$col <- c("red", "blue")

kp <- plotKaryotype(chromosomes="chr1")
kpPoints(kp, data=data, r0=0, r1=0.2)
kpPoints(kp, data=data, r0=0.2, r1=0.4, col=colByRegion(data, regions = regions) )
kpText(kp, data=data, r0=0.4, r1=0.6, col=colByRegion(data, regions = regions), label="A", cex=0.5 )
kpBars(kp, data=data, y0=0, y1=data$y, r0=0.6, r1=0.8, border=colByRegion(data, regions = regions))
#It might not work wor objects where R expects a single color such as lines. Segments should be used instead
kpLines(kp, data=data, r0=0.8, r1=1, col=colByRegion(data, regions = regions) )


kp <- plotKaryotype(chromosomes="chr1")
kpPoints(kp, data=data, r0=0, r1=0.25)
kpPoints(kp, data=data, r0=0.25, r1=0.5, col=colByRegion(data, regions = regions, colors="green") )
kpText(kp, data=data, r0=0.5, r1=0.75, col=colByRegion(data, regions = regions, color=c("gray", "gold")), label="A", cex=0.5 )
kpBars(kp, data=data, y0=0, y1=data$y, r0=0.75, r1=1, border=colByRegion(data, regions = regions))


[Package karyoploteR version 1.10.2 Index]