Plot clonotype assignment summary across stringency levels — plot_stringency

Creates a two-panel bar chart showing how clonotype counts and cell assignments change across stringency levels. The top panel shows the number of unique clonotypes at each level (decreasing as clones merge). The bottom panel shows the number of cells assigned vs unassigned at each level. Counts are displayed on top of each bar.

Usage

plot_stringency_summary(
  TCR_data,
  mapping_levels = .mapping.levels,
  sample_filter = NULL,
  per_sample = FALSE,
  combined = TRUE,
  title = "Clonotype Assignment Summary"
)

Arguments

TCR_data: A data frame with clone ID columns for each stringency level (as output by assign_clonotype).
mapping_levels: Character vector of stringency level names in order from most to least strict.
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.
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.