Plot Chromosome-wide Heatmap of Copy Number Alterations — plot_chr_all

This function plots a heatmap of copy number alterations (CNA) for a specified chromosome and allele across multiple cells. It supports optional ordering of cells, as well as annotations showing average copy number or gain/loss profiles.

Usage

plot_chr_all_heatmap(
  cna_data,
  chr,
  allele,
  order_heatmap = TRUE,
  add_avg_CN_profile = TRUE,
  add_gain_loss_profile = TRUE,
  use_raster = TRUE,
  raster_quality = 15
)

Arguments

cna_data: A data frame containing copy number data. Must include columns: cell_id, chromosome, bin positions, and a value column specified by allele.
chr: Chromosome to plot (e.g., "1", "X").
allele: Column name in cna_data containing the copy number values to be plotted (e.g., "CN", "cn_a").
order_heatmap: Logical, whether to order the heatmap rows by the number of bins matching a reference value (2 for total CN, 1 for alleles).
add_avg_CN_profile: Logical, whether to add a barplot annotation showing the average CN profile across cells.
add_gain_loss_profile: Logical, whether to add gain/loss annotation bars (proportion of cells with gain/loss).
use_raster: Logical, whether to rasterize the heatmap for faster rendering in large datasets.
raster_quality: Integer, quality of the raster image (relevant only if use_raster = TRUE).

Value

A ComplexHeatmap object representing the CNA heatmap, which can be plotted or combined with other heatmaps.