plot_baf: 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
)

Value

A ggplot object representing the BAF plot.

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.