show_cn_distribution: Show Copy Number Distribution either by Length or Chromosome

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

Show Copy Number Distribution either by Length or Chromosome

Description

Visually summarize copy number distribution either by copy number segment length or chromosome. Input is a CopyNumber object, genome_build option will read from genome_build slot of object.

Usage

show_cn_distribution(
  data,
  rm_normal = TRUE,
  mode = c("ld", "cd"),
  fill = FALSE,
  scale_chr = TRUE,
  base_size = 14
)

Arguments

data	a CopyNumber object.
rm_normal	logical. Whether remove normal copy (i.e. "segVal" equals 2), default is TRUE.
mode	either "ld" for distribution by CN length or "cd" for distribution by chromosome.
fill	when mode is "cd" and fill is TRUE, plot percentage instead of count.
scale_chr	logical. If TRUE, normalize count to per Megabase unit.
base_size	overall font size.

Value

a ggplot object

Author(s)

Shixiang Wang [e-mail]

Examples

# Load copy number object
load(system.file("extdata", "toy_copynumber.RData",
  package = "sigminer", mustWork = TRUE
))
# Plot distribution
p1 <- show_cn_distribution(cn)
p1
p2 <- show_cn_distribution(cn, mode = "cd")
p2
p3 <- show_cn_distribution(cn, mode = "cd", fill = TRUE)
p3

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