shattered.map.plot: Visualize the aggregate map of shattered regions for all...

In gonzolgarcia/svcnvplus: Integrative analyses of CNV segmentation and SV variant calls

Description

Visualize the aggregate map of shattered regions for all samples

Usage

shattered.map.plot(
  chromo.regs.obj,
  conf = "hc",
  genome.v = "hg19",
  freq.cut = NULL,
  add.legend = "top"
)

Arguments

chromo.regs.obj	(chromo.regs) An object of class chromo.regs
conf	(character) either 'hc' for high confidence objects or else all included
genome.v	(hg19 or hg38) reference genome version to draw chromosome limits and centromeres
freq.cut	the value to draw an horizontal line; use 'freq.p.test' to obtain a threshold for statisticaly significant hot spots
add.legend	the position of the legend in the plot; if null, no legend will be draw

Value

a plot into open device

Examples

require(circlize)

## validate input data.frames
cnv <- validate.cnv(segdat_lung_ccle)
svc <- validate.svc(svdat_lung_ccle)

## obtain shattered regions
chromo.regs.obj <- shattered.regions(cnv,svc)

shattered.map.plot(chromo.regs.obj)

gonzolgarcia/svcnvplus documentation built on March 4, 2020, 6:02 p.m.