colorby {plotgardener} | R Documentation |
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)
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 |
Returns a "colorby
" object.
## 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, )