Create a track of density plot — ccGenomicDensity • circlizePlus

Object ccGenomicTrack will call the function circlize::circos.genomicDensity while drawing.

Usage

ccGenomicDensity(...)

Arguments

...

Arguments passed on to circlize::circos.genomicDensity

data: A bed-file-like data frame or a list of data frames. If the input is a list of data frames. there will be multiple density plot in one same track.
ylim.force: Whether to force upper bound of ylim to be 1. Ignored if count_by is set to number.
window.size: Pass to genomicDensity.
overlap: Pass to genomicDensity.
count_by: Pass to genomicDensity.
col: Colors. It should be length of one. If data is a list of data frames, the length of col can also be the length of the list. If multiple sets of genomic regions are visualized in one single track, you should set the colors with transparency to distinguish them.
lwd: Width of lines, the same setting as col argument.
lty: Style of lines, the same setting as col argument.
type: Type of lines, see circos.lines.
area: See circos.lines.
area.baseline: Deprecated, use baseline instead.
baseline: See circos.lines.
border: See circos.lines.

Value

Object ccGenomicTrack

Examples

library(circlizePlus)
load(system.file(package = "circlize", "extdata", "DMR.RData"))
cc = ccPlot(initMode="initializeWithIdeogram", chromosome.index = paste0("chr", 1:22))
t2 = ccGenomicDensity(DMR_hyper, col = c("#FF000080"), track.height = 0.1)
t3 = ccGenomicDensity(DMR_hypo, col = c("#0000FF80"), track.height = 0.1)
cc + t2 + t3

circos.clear()