plot_baf_hist: Plot BAF Histogram

Description

This function generates a histogram of BAF (B-allele frequency) values. It supports options for adding estimated and expected peaks, area colors, and filtering homozygous calls.

Usage

plot_baf_hist(
  data_sample,
  area_single,
  ploidy,
  colors = FALSE,
  add_estimated_peaks = TRUE,
  add_expected_peaks = FALSE,
  BAF_hist_overall = FALSE,
  ratio = FALSE,
  rm_homozygous = FALSE,
  font_size = 12
)

Value

A ggplot object representing the BAF histogram.

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`.
colors: Logical. If TRUE, adds area colors to the histogram. Default is FALSE.
add_estimated_peaks: Logical. If TRUE, adds lines for estimated peaks. Default is TRUE.
add_expected_peaks: Logical. If TRUE, adds lines for expected peaks. Default is FALSE.
BAF_hist_overall: Logical. If TRUE, plots the BAF histogram for the entire genome. Default is FALSE.
ratio: Logical. If TRUE, plots the raw ratio instead of BAF. Default is FALSE.
rm_homozygous: Logical. If TRUE, removes homozygous calls from the histogram. Default is FALSE.
font_size: Numeric value for the font size of plot labels. Default is 12.