colorby should be used to create a set of parameters that specify color scaling for the functions plotPairs, plotPairsArches, and plotRanges.

colorby(column, palette = NULL, range = NULL, scalePerRegion = FALSE)

Arguments

column

String specifying name of data column to scale colors by.

palette

(optional) A function describing the color palette to use for color scaling.

range

(optional) A numeric vector specifying the range of values to apply a color scale to.

scalePerRegion

A logical value indicating whether to adjust NULL range of numerical `colorby` values to subset of data in a plotted genomic regoin. Default value is scalePerRegion = FALSE.

Value

Returns a "colorby" object.

Examples

## Load paired ranges data in BEDPE format
library(plotgardenerData)
data("IMR90_DNAloops_pairs")

## Add a length column
IMR90_DNAloops_pairs$length <- 
        (IMR90_DNAloops_pairs$start2 - IMR90_DNAloops_pairs$start1) / 1000

## Plot pairs with colorby object set for `length` column
bedpePlot <- plotPairs(
    data = IMR90_DNAloops_pairs,
    chrom = "chr21",
    chromstart = 27900000, chromend = 30700000,
    assembly = "hg19",
    fill = colorby("length", palette = 
                colorRampPalette(c("dodgerblue2", "firebrick2"))),
    lwd = 2, spaceHeight = .7,
)
#> pairs[pairs1]