Show Copy Number Variation Frequency Profile with Circos

show_cn_freq_circos(
  data,
  groups = NULL,
  cutoff = 2L,
  resolution_factor = 1L,
  title = c("AMP", "DEL"),
  chrs = paste0("chr", 1:22),
  genome_build = c("hg19", "hg38", "T2T", "mm10", "mm9", "ce11"),
  cols = NULL,
  plot_ideogram = TRUE,
  track_height = 0.5,
  ideogram_height = 1,
  ...
)

Arguments

data: a CopyNumber object or a data.frame containing at least 'chromosome', 'start', 'end', 'segVal', 'sample' these columns.
groups: a named list or a column name for specifying groups.
cutoff: copy number value cutoff for splitting data into AMP and DEL. The values equal to cutoff are discarded. Default is 2, you can also set a length-2 vector, e.g. c(2, 2).
resolution_factor: an integer to control the resolution. When it is 1 (default), compute frequency in each cytoband. When it is 2, use compute frequency in each half cytoband.
title: length-2 titles for AMP and DEL.
chrs: chromosomes start with 'chr'.
genome_build: genome build version, used when data is a data.frame, should be 'hg19' or 'hg38'.
cols: length-2 colors for AMP and DEL.
plot_ideogram: default is TRUE, show ideogram.
track_height: track height in mm unit.
ideogram_height: ideogram height in mm unit.
...: other parameters passing to circlize::circos.genomicLines.

Value

Nothing.

Examples

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

show_cn_freq_circos(cn)
#> Plotting AMP
#> Plotting group 1
#> Plotting DEL
#> Plotting group 1

ss <- unique(cn@data$sample)
show_cn_freq_circos(cn, groups = list(a = ss[1:5], b = ss[6:10]), cols = c("red", "green"))
#> Plotting AMP
#> Plotting group a
#> Plotting group b
#> Plotting DEL
#> Plotting group a
#> Plotting group b

# }