Cleavage Site Map

plot_cleavage_map() draws the full protein as a horizontal bar and marks every cleavage site as a vertical tick, colored by efficiency (high=green, medium=amber, low=red). Peptide fragments between consecutive cleavage sites are drawn as colored blocks, with invalid peptides dimmed. When cleavage_sites data is not available, sites are inferred from the peptide boundaries and all rendered as the same default color.

Usage

plot_cleavage_map(
  result,
  cleavage_sites = NULL,
  length_range = c(7L, 25L),
  title = NULL
)

Arguments

result

A named list returned by evaluate_digest(). If NULL or invalid, raises an error.

cleavage_sites

Optional data.frame from annotate_cleavage_sites() with columns position, efficiency (character: "high", "medium", "low"), and optionally rule. When NULL (default) sites are inferred from peptide boundaries.

length_range

Integer vector of length 2. Valid peptide window. Defaults to c(7L, 25L).

title

Optional character title. Auto-generated when NULL.

Value

A ggplot object showing a protein bar with cleavage-site ticks colored by efficiency and peptide fragment blocks between sites.

Details

When cleavage_sites is not supplied, cleavage positions are inferred from the C-terminal ends of MC=0 peptides (excluding the true C-terminus of the protein). Inferred sites all render in the same default color. Pass the output of annotate_cleavage_sites() for efficiency-aware coloring.

See also

evaluate_digest() for the upstream digestion step, annotate_cleavage_sites() for efficiency-annotated cleavage sites.

Other plot-single: plot_coverage_map(), plot_digest_profile(), plot_peptide_overlap_map(), plot_weight_sensitivity()

Examples

if (requireNamespace("ggplot2", quietly = TRUE)) {
  bsa_path <- system.file("extdata", "P02769.fasta", package = "pepVet")
  res <- evaluate_digest(bsa_path, enzyme = "trypsin")
  p <- plot_cleavage_map(res)
  print(p)
}