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

Description Usage Arguments Value Examples

View source: R/circular.plot.r

Description

Circos plot combining segmentation and SV calls

Usage

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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

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## 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.