Plot a CDR3 sequence logo

Renders a sequence logo from CDR3 amino acid sequences using ggseqlogo. Two methods are available: "bits" shows information content per position, "prob" shows amino acid frequencies.

Usage

plot_cdr3_logo(
  cdr3_seqs,
  chain = c("alpha", "beta"),
  trim = TRUE,
  method = c("prob", "bits"),
  gap_character = "-",
  title = NULL,
  nucseq_src = NULL,
  show_junction_bars = FALSE,
  return_junction_pwm = FALSE
)

Arguments

cdr3_seqs

Character vector. CDR3 amino acid sequences.

chain

Character string. "alpha" or "beta".

trim

Logical. If TRUE, trim conserved C/F residues before alignment (first 3, last 2 characters). Default TRUE.

method

Character string. "prob" for frequency-based logo, "bits" for information content. Default "prob".

gap_character

Character string. Gap character for alignment. Default "-".

title

Optional plot title. If NULL, defaults to the chain name with Greek letter.

nucseq_src

List of character vectors with nucleotide source labels (one per CDR3). Required for junction bars.

show_junction_bars

Logical. If TRUE and nucseq_src is provided, stack junction bars below the logo via patchwork.

return_junction_pwm

Logical. If TRUE, return a list with components plot (the ggplot logo) and junction_pwm (the numeric matrix, or NULL). Default FALSE.

Value

A ggplot object (or patchwork object if junction bars are included). When return_junction_pwm = TRUE, a list with plot and junction_pwm.

See also

plot_junction_bars, plot_gene_usage

Examples

if (FALSE) { # \dontrun{
seqs <- c("CAVRDSSYKLIF", "CAVKDSSYKLIF", "CAVRDSYKLIF",
          "CAVRDSSYKLIF", "CAVKDSYKLIF")
plot_cdr3_logo(seqs, chain = "alpha", method = "bits")
plot_cdr3_logo(seqs, chain = "beta", method = "prob")
} # }