Plot junction bars showing V/N/D/J nucleotide composition

Renders stacked coloured bars showing the fraction of nucleotides derived from V-gene, N-region, D-gene, or J-gene segments at each codon position within a CDR3 alignment. Designed to sit below a CDR3 sequence logo.

Usage

plot_junction_bars(
  junction_pwm,
  chain = c("alpha", "beta"),
  gap_character = "-"
)

Arguments

junction_pwm

Numeric matrix. Rows are junction source labels, columns are nucleotide positions (3 per codon).

chain

Character string. "alpha" or "beta".

gap_character

Character string. Gap character. Default "-".

Value

A ggplot object.

See also

plot_cdr3_logo