circ.wg.plot: Circos plot combining segmentation and SV calls

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

Description

Circos plot combining segmentation and SV calls

Usage

circ.wg.plot(
  cnv,
  svc,
  sample.id = NULL,
  lrr.pct = 0.2,
  lrr.max = 4,
  genome.v = "hg19",
  chrlist = NULL
)

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' validated by validate.cnv
svc	(S4) an object of class svcnvio containing data type 'svc' validated by validate.svc
sample.id	(character) the id of the sample to be plotted
lrr.pct	(numeric) copy number change between 2 consecutive segments: i.e (default) cutoff = 0.2 represents a fold change of 0.8 or 1.2
lrr.max	(numeric) maximum CNV to be plotted
genome.v	(hg19 or h38) reference genome version to draw chromosome limits and centromeres
chrlist	(character) vector containing chromosomes to plot; by default all chromosomes plotted

Value

circos plot into open device

Examples

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

## select a random sample id
id <-  sample(intersect(cnv$sample,svc$sample))[1]

circ.wg.plot(cnv, svc, sample.id=id)

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