circ.chromo.plot: Circular visualization of shattered regions

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

Description

Produces a circos plot combining CNV and SVC date sooming into the chromosomes harboring shattered regions

Usage

circ.chromo.plot(
  chromo.regs.obj,
  sample.id,
  print.name = TRUE,
  genome.v = "hg19",
  lrr.pct = 0.2,
  lrr.max = 4,
  high.conf = FALSE,
  chrlist = NULL,
  add.cnv.legend = "topleft",
  add.svc.legend = "toprigh",
  ...
)

Arguments

chromo.regs.obj	(chromo.regs) An object of class chromo.regs
sample.id	(character) the id of a sample to be plotted within
print.name	(logical) whether to print the sample id in the center of the circular plot
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 20 percent fold change
lrr.max	(numeric) CNV plot limit
high.conf	(logical) Whether to plot only high confidence shattered regions (see https://github.com/ccbiolab/svpluscnv#identification-of-shattered-regions for more information)
chrlist	(character) vector containing chromosomes to plot; by default only chromosomes with shattered regions are ploted
add.cnv.legend	(x,y or coordinates) the position parameter passed to legend to plot shattered regions and CNV (outer track) description
add.svc.legend	(x,y or coordinates) the position parameter passed to legend to plot SVC (central track) description
...	Additional graphical parameters

Value

circos plot into open device

Examples

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

## obtain shattered regions
shatt.regions <- shattered.regions(cnv,svc)

# select a random sample from the 
id <- "SCLC21H_LUNG"

circ.chromo.plot(shatt.regions, sample.id = id)

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