Show Sample Copy Number Profile — show_cn

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.

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

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

# }