show_cn_freq_circos: Show Copy Number Variation Frequency Profile with Circos

In sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Show Copy Number Variation Frequency Profile with Circos

Description

Show Copy Number Variation Frequency Profile with Circos

Usage

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

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

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

sigminer documentation built on May 29, 2024, 3:11 a.m.