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Enzyme Comparison Chart

Source: R/plot_comparison.R
plot_enzyme_comparison.Rd

plot_enzyme_comparison() visualises the output of compare_digests() as a dual-panel chart: component score bars (Panel A) and a composite score lollipop with verdict badge (Panel B).

Usage

plot_enzyme_comparison(
  comparison,
  scores = c("S_coverage", "S_length", "S_count", "S_hydro", "S_charge"),
  recommend = TRUE,
  title = NULL
)

Arguments

comparison

A tibble returned by compare_digests(). Must contain at least the columns enzyme and composite_score, plus whichever component-score columns are requested in scores. If NULL or not a data frame, raises an error.

scores

Character vector of component-score column names to display in Panel A. Any column absent from comparison is silently dropped. Defaults to all five standard component scores. S_unique can be requested when present in a proteome-aware comparison. If NULL, raises an error.

recommend

Logical. When TRUE (default), a "Top model score" badge marks the enzyme with the highest composite score in Panel B. The badge is a model ranking, not an experimental recommendation. If NULL, raises an error.

title

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

Value

A patchwork object with two panels: component-score grouped bar chart (A) and composite-score lollipop with verdict badge (B).

Details

Panel A shows a horizontal grouped bar chart where each enzyme occupies one row and each component score is a separate colored bar, dodged side-by-side. Reference lines at the Moderate and Good verdict thresholds divide the axis into poor / moderate / good regions. Enzymes are sorted by composite score with the highest at the top.

Panel B shows the composite score as a lollipop, color-coded by verdict tier (green >= 0.65, amber 0.40-0.64, red < 0.40). When recommend = TRUE a gold "Top model score" badge is appended next to the top-ranked enzyme.

See also

compare_digests(), recommend_enzyme(), plot_digest_profile(), plot_coverage_map(), plot_batch_comparison()

Examples

if (requireNamespace("ggplot2", quietly = TRUE) &&
  requireNamespace("patchwork", quietly = TRUE)) {
  bsa_path <- system.file("extdata", "P02769.fasta", package = "pepVet")
  comp <- compare_digests(bsa_path,
    enzymes = c(
      "trypsin", "lysc",
      "glutamyl endopeptidase"
    )
  )
  p <- plot_enzyme_comparison(comp)
  print(p)
}