circlizePlus (version 0.9.0)

ccGenomicRainfall: Create a rainfall plot

Description

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

Usage

ccGenomicRainfall(
  data,
  mode = "min",
  ylim = NULL,
  col = "black",
  pch = par("pch"),
  cex = par("cex"),
  normalize_to_width = FALSE,
  ...
)

Value

Object ccGenomicTrack

Arguments

data

A bed-file-like data frame or a list of data frames.

mode

How to calculate the distance of two neighbouring regions, pass to rainfallTransform.

ylim

ylim for rainfall plot track. If normalize_to_width is FALSE, the value should correspond to log10(dist+1), and if normalize_to_width is TRUE, the value should correspond to log2(rel_dist).

col

Color of points. It should be length of one. If data is a list, the length of col can also be the length of the list.

pch

Style of points.

cex

Size of points.

normalize_to_width

If it is TRUE, the value is the relative distance divided by the width of the region.

...

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))
bed_list = list(DMR_hyper, DMR_hypo)
t1 = ccGenomicRainfall(bed_list, pch = 16, cex = 0.4, col = c("#FF000080", "#0000FF80"))
cc + t1
circos.clear()
# }