circ.wg.plot: Circular visualization CNV and SVC

In ccbiolab/svpluscnv: svpluscnv: analysis and visualization of complex structural variation data

Description

Produces a circos plot combining CNV and SVC of the whole genome

Usage

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

Arguments

cnv	(S4) an object of class svcnvio containing data type 'cnv' initialized by validate.cnv
svc	(S4) an object of class svcnvio containing data type 'svc' initialized by validate.svc
sample.id	(character) the id of the sample to be plotted
genome.v	(character) (hg19 or h38) reference genome version to draw chromosome limits and centromeres
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
chrlist	(character) vector containing chromosomes to plot; by default all chromosomes plotted
add.cnv.legend	(x,y or coordinates) the position parameter passed to legend to plot CNV (outer tracks) description
add.svc.legend	(x,y or coordinates) the position parameter passed to legend to plot SVC (central track) description

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 <- "A549_LUNG"

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

ccbiolab/svpluscnv documentation built on Sept. 9, 2020, 4:52 a.m.