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pI Distribution: Histogram of Peptide Isoelectric Points

Source: R/plot_distribution.R
plot_pI_distribution.Rd

plot_pI_distribution() draws a histogram of peptide isoelectric points coloured by SCX fraction bin (e.g., pH 3-4, 4-5, ...) to preview fractionation outcomes. Vertical boundary lines and per-fraction count annotations are optionally overlaid.

Usage

plot_pI_distribution(
  result,
  fraction_breaks = c(3, 4, 5, 6, 7, 8, 9, 10),
  show_fraction_lines = TRUE,
  title = NULL
)

Arguments

result

Accepted inputs:

  • A named list returned by evaluate_digest(). pI values are computed automatically from the valid-peptide sequences.

  • A tibble returned by score_peptides() with include_pI = TRUE (contains a pI list column).

  • A plain data.frame / tibble with a numeric pI column.

  • A bare numeric vector of pI values. If NULL, raises an error.

fraction_breaks

Numeric vector of pH boundary values defining the fraction bins. Defaults to c(3, 4, 5, 6, 7, 8, 9, 10), which produces eight bins: <3, 3-4, ..., 9-10, >10. If NULL, raises an error.

show_fraction_lines

Logical. When TRUE (default) vertical dashed lines are drawn at each interior fraction boundary. If NULL, treated as FALSE.

title

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

Value

A ggplot object showing a histogram of isoelectric points coloured by SCX fraction bin with optional fraction boundary lines.

Details

The function accepts four input types with the following precedence: (1) named list of evaluate_digest() results (multi-input mode, produces overlaid density curves per result), (2) single evaluate_digest() result, (3) data.frame with a pI column, (4) raw numeric vector of pI values. When a full evaluate_digest() result is supplied, pI values are computed from valid-peptide sequences via calculate_pI().

See also

evaluate_digest() and score_peptides() for upstream peptide scoring.

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

Examples

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