ccGenomicDensity: Create a track of density plot

In circlizePlus: Using 'ggplot2' Feature to Write Readable R Code for Circular Visualization

Create a track of density plot

Description

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

Usage

ccGenomicDensity(
  data,
  ylim.force = FALSE,
  window.size = NULL,
  overlap = TRUE,
  count_by = c("percent", "number"),
  col = ifelse(area, "grey", "black"),
  lwd = par("lwd"),
  lty = par("lty"),
  type = "l",
  area = TRUE,
  area.baseline = NULL,
  baseline = 0,
  border = NA,
  ...
)

Arguments

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.
...	Pass to circos.trackPlotRegion.

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()

circlizePlus documentation built on June 8, 2025, 10:42 a.m.