colByRegion: colByRegion

In bernatgel/karyoploteR: Plot customizable linear genomes displaying arbitrary data

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, original.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)
original.colors	(color vector) The original colors of the data points. They will be use instead of the default color for data points not overlapping the regions. If NULL, the default color will be used. (defaults to NULL)
default.col	The default color to return for data elements not overlapping the regions. Only used if original.colors is NULL (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. Data points not in the specified region can take either a default color or keep their "original.color" if given. This is useful when using colByRegion to highlight data points as in kpPlotManhattan.

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))

bernatgel/karyoploteR documentation built on Feb. 1, 2024, 11:48 p.m.