plot_baf: Plot BAF

In Qploidy: Estimation of Ploidy and Detection of Aneuploidy Using Genotyping Data

Plot BAF

Description

This function generates a BAF (B-allele frequency) plot for visualizing genomic data. It allows customization of dot size, expected and estimated peaks, centromere positions, and area colors.

Usage

plot_baf(
  data_sample,
  area_single,
  ploidy,
  dot.size = 1,
  add_estimated_peaks = FALSE,
  add_expected_peaks = FALSE,
  centromeres = NULL,
  add_centromeres = FALSE,
  colors = FALSE,
  font_size = 12
)

Arguments

data_sample	A data.frame containing BAF and genomic position information. Must include columns 'Chr', 'Position', and 'sample'.
area_single	Numeric value defining the area around the expected peak to be considered.
ploidy	Integer or vector specifying the expected ploidy. If a vector, it must match the number of chromosomes in 'data_sample'.
dot.size	Numeric value for the size of the dots in the plot. Default is 1.
add_estimated_peaks	Logical. If TRUE, adds lines for estimated peaks. Default is FALSE.
add_expected_peaks	Logical. If TRUE, adds lines for expected peaks. Default is FALSE.
centromeres	Named vector defining centromere positions for each chromosome. Names must match chromosome IDs in 'data_sample'.
add_centromeres	Logical. If TRUE, adds vertical lines at centromere positions. Default is FALSE.
colors	Logical. If TRUE, adds area colors to the plot. Default is FALSE.
font_size	Numeric value for the font size of plot labels. Default is 12.

Value

A ggplot object representing the BAF plot.

Qploidy documentation built on June 8, 2025, 10 a.m.