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Amino-Acid Peptide Overlap Map

Source: R/plot_single.R
plot_peptide_overlap_map.Rd

plot_peptide_overlap_map() renders a wrapped residue-level view of a single protein and colors each amino-acid tile by how many peptides cover that residue (MC=0 only by default). Uncovered residues are white; increasing overlap depth gets progressively stronger blue fills. The subtitle reports the maximum overlap, which helps gauge whether the 6-color scale (0, 1, 2-3, 4-7, 8-15, 16+) is sufficient for your data.

Usage

plot_peptide_overlap_map(
  result,
  length_range = c(7L, 25L),
  missed_cleavages = 1L,
  residues_per_line = 50L,
  title = NULL
)

Arguments

result

A named list returned by evaluate_digest(). Must describe a single protein. If NULL or invalid, raises an error.

length_range

Optional integer vector of length 2 defining which peptide lengths count toward overlap. Defaults to c(7L, 25L). Peptides are counted from the MC level specified by missed_cleavages. Use length_range = NULL to count all digested peptides at all missed-cleavage levels.

missed_cleavages

Integer. Which missed-cleavage level to use for the overlap count. Defaults to 1L (standard bottom-up practice). Pass 0L for strict non-overlapping fragments, or NULL to count all MC levels (automatically set when length_range = NULL).

residues_per_line

Positive integer. Number of residues to show before wrapping to the next display row. Defaults to 50L. If NULL or non-integer, raises an error.

title

Optional character string for the plot title. Auto-generated from the protein accession and enzyme when NULL (default).

Value

A ggplot object showing one tile per residue colored by peptide overlap depth (white for uncovered, escalating blue fills for 1, 2-3, 4-7, 8-15, or 16+ covering peptides).

Details

The plotted letters are reconstructed from the MC=0 peptide set in result$peptides, so the plot can be generated directly from an evaluate_digest() result without re-reading the original FASTA input. Overlap counts are computed from valid-length MC=1 peptides by default (configurable via missed_cleavages). Pass missed_cleavages = 0L for strict non-overlapping fragments, or length_range = NULL to count all digested peptides at all missed-cleavage levels.

See also

evaluate_digest() for the upstream digestion step.

Other plot-single: plot_cleavage_map(), plot_coverage_map(), plot_digest_profile(), 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", missed_cleavages = 1)
  p <- plot_peptide_overlap_map(res)
  print(p)
}