Plot clonotype chain composition — plot_clone

Creates a tile chart showing the V gene usage for each chain position (TRA_1, TRA_2, TRB_1, TRB_2) across clonotypes at a given stringency level. Each tile is colored by V gene identity, making it easy to see which clones share V gene segments and which chains are present or absent.

Usage

plot_clone_composition(
  ref_table,
  top_n = 20,
  sample_filter = NULL,
  per_sample = FALSE,
  combined = TRUE,
  title = "Clonotype Chain Composition"
)

Arguments

ref_table: A reference table from identify_clonotypes or assign_clonotype output (e.g., result$ref_tables$dual_chain_both_partial). Must contain columns: TRA_1, TRB_1.
top_n: Maximum number of clones to display. Clones are ranked by chain richness (number of non-NA chains). Remaining clones are excluded.
sample_filter: Optional sample name to filter to. If NULL, all samples are included. Ignored when per_sample = TRUE.
per_sample: Logical. If TRUE, create a separate plot for each unique sample in the reference table.
combined: Logical. If TRUE and per_sample = TRUE, combine all per-sample plots into a single figure using patchwork. If FALSE, return a named list of plots.
title: Plot title.

Value

A ggplot object, or a named list of ggplot objects when per_sample = TRUE and combined = FALSE.