plot_CCF: Plot the CCF estimates in the data.

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

Plot the CCF estimates in the data.

Description

This function extracts the plots of the Cancer Cell Fractions (CCFs) estimates from a 'CNAqc' object, after they have been computed using function 'compute_CCF'. The plots - one per computed karyotype - are assembled into a 'ggpubr' figure.

Usage

plot_CCF(x, strip = FALSE, empty_plot = TRUE, assembly_plot = TRUE)

Arguments

x	An object of class cnaqc, where CCF have been computed using function 'compute_CCF'.
strip	If TRUE, shows little detail and a strip horizontal plot. Otherwise it shows a detailed report (multiple rows). This parameter is now deprecated.
empty_plot	If data for one karyotype is missing, an empty plot is returned. Otherwise the plot is not returned (NULL is forwarded).
assembly_plot	If TRUE, a unique figure is returned with all the plots assembled. Otherwise a list of plot is returned.

Value

A 'ggpubr' figure of the CCF estimates.

Examples

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

x = compute_CCF(x)
plot_CCF(x)

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