Skip to contents

Plot a V/J gene usage logo

Source: R/plot_logo.R
plot_vj_gene_logo.Rd

Renders gene names as stacked text glyphs with heights proportional to their frequency — a "sequence logo" style for gene usage. Each gene name is rendered as a coloured raster image and vertically stacked so that more frequent genes occupy more vertical space.

Usage

plot_vj_gene_logo(
  genes,
  organism,
  gene_type = c("V", "J"),
  chain = c("alpha", "beta"),
  max_genes = 10L
)

Arguments

genes

Character vector. V-gene or J-gene allele names (e.g., "TRAV1-2*01").

organism

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

gene_type

Character string. "V" or "J".

chain

Character string. "alpha" or "beta".

max_genes

Integer. Maximum number of genes to display. Default 10L.

Value

A ggplot object.

See also

plot_gene_usage, plot_tcr_logo_panel

Examples

if (FALSE) { # \dontrun{
data(dash)
pa <- dash[dash$epitope == "PA", ]
plot_vj_gene_logo(pa$vb, organism = "mouse", gene_type = "V",
                  chain = "beta")
plot_vj_gene_logo(pa$ja, organism = "mouse", gene_type = "J",
                  chain = "alpha")
} # }