Plot BFB-like Signatures Along the Genome

This function visualizes the distribution of BFB-like events (asymmetric CN differences) across genomic segments for a given chromosome and allele. The plot highlights which genomic regions are most frequently affected by potential BFB events in the reconstructed phylogeny.

Usage

plot_bfb_signature(res, chr_of_interest, allele_of_interest)

Arguments

res

A fitted object returned by the fit() function. It must contain the reconstructions field populated via compute_reconstructions().

chr_of_interest

A character string indicating the chromosome to plot (e.g., "8" or "X").

allele_of_interest

A character string indicating the allele to analyze, typically "A" or "B".

Value

A ggplot object displaying a bar plot where each bar corresponds to a genomic segment, with its height and color intensity proportional to the number of BFB-like events affecting that segment.

Details

The function extracts the reconstructed merged profiles and identifies the internal nodes in the phylogeny that show asymmetric copy number changes (i.e., delta > 0). It computes the difference between the left and right child profiles for these nodes, identifies affected segments, and counts the number of times each segment is involved in a BFB-like event. The output is a genomic bar plot showing the number of BFB-like events per segment.