show_cn_circos {sigminer}

Show Copy Number Profile in Circos

Description

Another visualization method for copy number profile like show_cn_profile.

Usage

show_cn_circos(
  data,
  samples = NULL,
  show_title = TRUE,
  chrs = paste0("chr", 1:22),
  genome_build = c("hg19", "hg38", "T2T", "mm10", "mm9", "ce11"),
  col = NULL,
  side = "inside",
  ...
)

Arguments

data

a CopyNumber object or a data.frame containing at least 'chromosome', 'start', 'end', 'segVal' these columns.

samples

default is NULL, can be a chracter vector representing multiple samples or number of samples to show. If data argument is a data.frame, a column called sample must exist.

show_title

if TRUE (default), show title with sample ID.

chrs

chromosomes start with 'chr'.

genome_build

genome build version, used when data is a data.frame, should be 'hg19' or 'hg38'.

col

colors for the heatmaps. If it is NULL, set to circlize::colorRamp2(c(1, 2, 4), c("blue", "black", "red")).

side

side of the heatmaps.

...

other parameters passing to circlize::circos.genomicHeatmap.

Value

a circos plot

Examples

load(system.file("extdata", "toy_copynumber.RData",
  package = "sigminer", mustWork = TRUE
))

show_cn_circos(cn, samples = 1)
show_cn_circos(cn, samples = "TCGA-99-7458-01A-11D-2035-01")

## Remove title
show_cn_circos(cn, samples = 1, show_title = FALSE)

## Subset chromosomes
show_cn_circos(cn, samples = 1, chrs = c("chr1", "chr2", "chr3"))

## Arrange plots
layout(matrix(1:4, 2, 2))
show_cn_circos(cn, samples = 4)

layout(1) # reset layout