Show Copy Number Distribution either by Length or Chromosome

Source: R/show_cn_distribution.R

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.

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

Shixiang Wang w_shixiang@163.com

Examples

# Load copy number object
load(system.file("extdata", "toy_copynumber.RData",
  package = "sigminer", mustWork = TRUE
))
# Plot distribution
p1 <- show_cn_distribution(cn)
p1
#> Warning: The dot-dot notation (`..density..`) was deprecated in ggplot2 3.4.0.
#> ℹ Please use `after_stat(density)` instead.
#> ℹ The deprecated feature was likely used in the sigminer package.
#>   Please report the issue at <https://github.com/ShixiangWang/sigminer/issues>.

p2 <- show_cn_distribution(cn, mode = "cd")
p2

p3 <- show_cn_distribution(cn, mode = "cd", fill = TRUE)
p3