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 region. 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]
