show_cn_profile: Show Sample Copy Number Profile

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

Show Sample Copy Number Profile

Description

Sometimes it is very useful to check details about copy number profile for one or multiple samples. This function is designed to do this job and can be further modified by ggplot2 related packages.

Usage

show_cn_profile(
  data,
  samples = NULL,
  show_n = NULL,
  show_title = FALSE,
  show_labels = NULL,
  chrs = paste0("chr", 1:22),
  position = NULL,
  genome_build = c("hg19", "hg38", "T2T", "mm10", "mm9", "ce11"),
  ylim = NULL,
  nrow = NULL,
  ncol = NULL,
  return_plotlist = FALSE
)

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. If data argument is a data.frame, a column called sample must exist.
show_n	number of samples to show, this is used for checking.
show_title	if TRUE, show title for multiple samples.
show_labels	one of NULL, "s" (for labelling short segments < 1e7) or "a" (all segments).
chrs	chromosomes start with 'chr'.
position	a position range, e.g. "chr1:3218923-116319008". Only data overlaps with this range will be shown.
genome_build	genome build version, used when data is a data.frame, should be 'hg19' or 'hg38'.
ylim	limites for y axis.
nrow	number of rows in the plot grid when multiple samples are selected.
ncol	number of columns in the plot grid when multiple samples are selected.
return_plotlist	default is FALSE, if TRUE, return a plot list instead of a combined plot.

Value

a ggplot object or a list

Examples

# Load copy number object
load(system.file("extdata", "toy_copynumber.RData",
  package = "sigminer", mustWork = TRUE
))

p <- show_cn_profile(cn, nrow = 2, ncol = 1)
p

p2 <- show_cn_profile(cn,
  nrow = 2, ncol = 1,
  position = "chr1:3218923-116319008"
)
p2

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