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Four-Panel Digest Diagnostic Plot

Source: R/plot_single.R
plot_digest_profile.Rd

plot_digest_profile() assembles a four-panel figure for a single protein-enzyme pair from an evaluate_digest() result. The panels are:

Usage

plot_digest_profile(
  result,
  length_range = c(7L, 25L),
  gravy_range = c(-1, 0.6),
  title = NULL
)

Arguments

result

A named list returned by evaluate_digest(). Must describe a single protein (one unique protein_id in result$peptides). If NULL or invalid, raises an error.

length_range

Integer vector of length 2. Defines the valid peptide length window, passed to the length and coverage panels. Defaults to c(7L, 25L).

gravy_range

Numeric vector of length 2. Defines the LC-friendly GRAVY range shaded in panel B. Defaults to c(-1.0, 0.6).

title

Optional character string for the figure title. When NULL (default) a title is auto-generated from the protein accession, enzyme, and missed-cleavage count.

Value

A patchwork object with four panels: length distribution (A), GRAVY distribution (B), coverage map (C), and component scores (D).

Details

  • (A) Length distribution: histogram of peptide lengths with the valid window shaded. Bars are colored by length class: valid (blue), too short (amber), too long (rose).

  • (B) GRAVY distribution: histogram of GRAVY hydrophobicity scores. The LC-friendly range is shaded and bounded by dashed lines.

  • (C) Coverage map: protein drawn as horizontal lanes (one per missed-cleavage level) with valid-length peptides stacked via a greedy interval-packing algorithm. Uncovered regions are highlighted in red. Peptide length labels appear inside segments of 8 aa or longer.

  • (D) Component scores: horizontal bar chart for each scoring component, colored by tier (green \(\geq\) 0.65, amber 0.40-0.64, red < 0.40). The composite score is marked with a dashed vertical line.

GRAVY scores are computed internally from the peptide sequences in result$peptides using the Kyte-Doolittle scale. No external columns are required beyond the standard evaluate_digest() output.

Panel C labels peptide lengths inside segments of 8 aa or longer. For heavily digested proteins this keeps the map readable without overlap. When multiple missed-cleavage levels are present, each level occupies its own horizontal lane with peptides stacked using the same greedy interval-packing algorithm as plot_coverage_map().

See also

evaluate_digest() for the upstream digestion step, plot_enzyme_comparison() for enzyme comparison across digests.

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

Examples

if (requireNamespace("ggplot2", quietly = TRUE) &&
  requireNamespace("patchwork", quietly = TRUE)) {
  bsa_path <- system.file("extdata", "P02769.fasta", package = "pepVet")
  res <- evaluate_digest(bsa_path, enzyme = "trypsin", missed_cleavages = 1L)
  p <- plot_digest_profile(res)
  print(p)
}