plot_gw_ccf: Plot genome-wide CCFs.

In caravagnalab/CNAqc: CNAqc - Copy Number Analysis quality check

Plot genome-wide CCFs.

Description

Plot a genome-wide scatter plot of mutation CCFs, if availbale. The function can randomly subset the points to show.

Usage

plot_gw_ccf(x, N = 5000, chromosomes = paste0("chr", c(1:22, "X", "Y")))

Arguments

x	A CNAqc object.
N	Mutations to use, randomly sampled.
chromosomes	The chromosomes to use for this plot.

Value

A ggplot2 plot.

Examples

data('example_dataset_CNAqc', package = 'CNAqc')
x = init(mutations = example_dataset_CNAqc$mutations, cna = example_dataset_CNAqc$cna, purity = example_dataset_CNAqc$purity)

# Compute CCFs
x = compute_CCF(x)
plot_gw_ccf(x)

# Downsampling examples
plot_gw_ccf(x, N = 100)
plot_gw_ccf(x, N = 1000)
plot_gw_ccf(x, N = 10000)

caravagnalab/CNAqc documentation built on Oct. 31, 2024, 3:54 a.m.