colorby: Handle plotgardener color scaling parameters

In PhanstielLab/BentoBox: Coordinate-Based Genomic Visualization Package for R

Handle plotgardener color scaling parameters

Description

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

Usage

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,
)

PhanstielLab/BentoBox documentation built on June 30, 2024, 12:50 p.m.