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Multi-enzyme proteome comparison

Source: R/plot_batch.R
plot_batch_comparison.Rd

plot_batch_comparison() produces a four-panel side-by-side comparison of enzyme performance across a full proteome, using output from batch_compare_enzymes():

Usage

plot_batch_comparison(comparison, title = NULL)

Arguments

comparison

A pepvet_batch_comparison tibble returned by batch_compare_enzymes(), with columns protein_id, enzyme, composite_score, verdict, and the five component score columns. A proteome-aware comparison may also contain S_unique, which is included in the component heatmap. If NULL or empty, raises an error.

title

Optional character title for the combined figure. When NULL (default), generates an auto-title with protein and enzyme counts.

Value

A patchwork object with four panels: verdict summary bars (A), score distribution violins (B), component-score heatmap (C), and per-protein win-rate bars (D).

Details

  • (A) Verdict summary: 100% stacked horizontal bars showing the Good/Moderate/Poor verdict breakdown per enzyme. Enzymes are ordered by descending Good%, and the highest model summary is marked with a star.

  • (B) Score distributions: horizontal violin plots for each enzyme, showing the full distribution of composite scores. An IQR boxplot is overlaid on each violin. Violin fill color reflects the enzyme's median verdict.

  • (C) Component heatmap: median component scores in an enzyme-by-component grid, filled by the verdict gradient (red to amber to green). Reveals which digest quality dimension differentiates the enzymes.

  • (D) Per-protein win rate: bar chart showing the proportion of proteins for which each enzyme achieves the highest composite score. The starred enzyme matches the top model summary in panel A.

Limitations

At proteome sizes exceeding 2000 proteins the figure panels become dense and text labels may overlap. Consider filtering the comparison to a representative subset or increasing the output dimensions.

See also

batch_compare_enzymes() for the upstream comparison step.

Other plot-batch: plot_proteome_overview()

Examples

if (requireNamespace("ggplot2", quietly = TRUE) &&
  requireNamespace("patchwork", quietly = TRUE)) {
  small <- system.file(
    "extdata", "small_proteome_50_proteins.fasta",
    package = "pepVet"
  )
  comp <- batch_compare_enzymes(small, enzymes = c("trypsin", "lysc"))
  plot_batch_comparison(comp)
}
#> Scoring 50 proteins against 2 enzymes.
#> Warning: Protein "sp|P08246|ELNE_HUMAN Neutrophil elastase OS=Homo sapiens OX=9606
#> GN=ELANE PE=1 SV=1" has no cleavage sites for "lysc". S_count and composite
#> score set to 0; verdict set to Poor.