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GRAVY Landscape: 2D Scatter of Peptide Length vs. Hydrophobicity

Source: R/plot_distribution.R
plot_gravy_landscape.Rd

plot_gravy_landscape() plots each peptide as a point in the length \(\times\) GRAVY physicochemical space. The selected length-and-GRAVY region is shaded, points are colour-coded by window class, and marginal density panels show the 1D distributions on each axis. Peptides outside the selected region are labelled with their sequences when their count is below label_outliers_n.

Usage

plot_gravy_landscape(
  result,
  length_range = c(7L, 25L),
  gravy_range = c(-1, 0.6),
  label_outliers_n = 15L,
  title = NULL
)

Arguments

result

A named list returned by evaluate_digest(), or a data.frame / tibble with at least length and gravy columns. When a bare data.frame lacks a gravy column but has a peptide column, GRAVY scores are computed automatically. If NULL or an unrecognised type, raises an error.

length_range

Integer vector of length 2. Valid length window. Defaults to c(7L, 25L). Read from result$params when a full evaluate_digest() result is supplied.

gravy_range

Numeric vector of length 2. LC-friendly GRAVY window. Defaults to c(-1.0, 0.6). Read from result$params when available.

label_outliers_n

Integer. Maximum number of outlier points to label with their peptide sequences. Labels are suppressed when the count exceeds this threshold. Defaults to 15L. If NULL, raises an error.

title

Optional character string for the plot title. Auto-generated when NULL (default).

Value

A patchwork object with a central scatter of length vs GRAVY coloured by window class, and marginal density panels on the top and right axes.

Details

When result is a named list of evaluate_digest() results (multi-input mode), produces a faceted scatter with one panel per result (no marginal densities). GRAVY scores are computed automatically when a bare data.frame has a peptide column but no gravy column.

See also

evaluate_digest() for the upstream digestion step, plot_digest_profile() for a single-protein digest summary.

Other plot-distribution: plot_length_distribution(), plot_missed_cleavage_impact(), plot_mz_distribution(), plot_pI_distribution()

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")
  p <- plot_gravy_landscape(res)
  print(p)
}