Plot a composite TCR rearrangement logo panel

Arranges V-gene logos, CDR3 sequence logos (with optional junction bars), and J-gene logos for both alpha and beta chains in a single composite panel. This provides a comprehensive view of TCR rearrangement structure.

Usage

plot_tcr_logo_panel(tcrs, organism, show_junction_bars = TRUE, title = NULL)

Arguments

tcrs

Data.frame with at least columns va, ja, cdr3a, vb, jb, cdr3b. For junction bars, also requires cdr3a_nucseq and cdr3b_nucseq.

organism

Character string. Organism identifier (e.g., "human", "mouse").

show_junction_bars

Logical. If TRUE (default) and nucleotide sequence columns are present, display V/N/D/J junction bars below each CDR3 logo.

title

Optional character string. Overall panel title.

Value

A patchwork object.

See also

plot_vj_gene_logo, plot_cdr3_logo, plot_junction_bars, compute_nucseq_src

Examples

if (FALSE) { # \dontrun{
data(dash)
pa <- dash[dash$epitope == "PA", ][1:30, ]
plot_tcr_logo_panel(pa, organism = "mouse")
plot_tcr_logo_panel(pa, organism = "mouse", show_junction_bars = FALSE)
} # }