circlizePlus (version 0.9.0)

ccGenomicDensity: 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,
  ...
)

Value

Object ccGenomicTrack

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.

Examples

# \donttest{
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()
# }