Multi-panel Plot of Copy Number, BAF, Clonality, and Quality Across Chromosomes

Produces a summary plot with four panels: copy number, BAF, clonality, and segment quality, faceted by chromosome.

Usage

PlotCov(df_cov, df_ai, call_seg, whitelist, gender, prefix, purity)

Arguments

df_cov

Data frame or tibble. Smoothed coverage data, must include columns seqnames, start, end, and smoothed_bin_cnf.

df_ai

Data frame or tibble. Smoothed AI data, must include columns seqnames, bin_start, and smoothed_ai.

call_seg

Data frame or tibble. Segment calls, must include columns seqnames, loc.start, loc.end, CN, MAF, ccf_final, FILTER.

whitelist

Data frame or tibble. Whitelist regions, must include columns seqnames, start, and end.

gender

Character. Sample gender ("male" or "female").

prefix

Character. Plot title or output prefix.

purity

Numeric. Tumor purity (not directly used in the plot, but included for compatibility).

Value

A grob object (from gridExtra::grid.arrange) representing the combined plot.

Examples

# PlotCov(df_cov, df_ai, call_seg, whitelist, gender = "female", prefix = "Sample1", purity = 0.7)