copy_number_density_plot: Copy number density plot

In crukci-bioinformatics/rascal: Shiny app and functions for scaling relative copy number data to absolute values

Description

Creates a ggplot for the density of the given copy numbers values.

Usage

copy_number_density_plot(
  copy_numbers,
  copy_number_steps = NULL,
  min_copy_number = NULL,
  max_copy_number = NULL,
  copy_number_step_colour = "blue",
  copy_number_step_alpha = 0.35,
  copy_number_step_line_size = 0.75,
  xlabel = "copy number",
  ylabel = "density"
)

Arguments

copy_numbers	a numeric vector containing copy number values.
copy_number_steps	a data frame containing copy_number and absolute_copy_number columns.
min_copy_number	the minimum relative copy number to display.
max_copy_number	the maximum relative copy number to display.
copy_number_step_colour	the colour of the copy number step lines.
copy_number_step_alpha	the transparency of the copy number step lines.
copy_number_step_line_size	the size of the lines for the copy number steps.
xlabel, ylabel	x- and y-axis labels.

Value

a ggplot object

Examples

data(copy_number)
copy_number <- copy_number[copy_number$sample == "X17222", ]

copy_number_density_plot(copy_number$segmented)

absolute_copy_numbers <- 0:8
relative_copy_numbers <- absolute_to_relative_copy_number(absolute_copy_numbers, ploidy = 4.01, cellularity = 0.81)
copy_number_steps <- data.frame(absolute_copy_number = absolute_copy_numbers, copy_number = relative_copy_numbers)

copy_number_density_plot(copy_number$segmented, copy_number_steps, 0, 2.5)

crukci-bioinformatics/rascal documentation built on Dec. 19, 2021, 6:21 p.m.