Plot score diagnostics

plot_score_diagnostics() visualises the result of score_diagnostics() as a three-panel figure: (A) VIF bar chart with threshold lines at 5 and 10, (B) PCA scree plot with cumulative variance line and an 80% reference, (C) ablation waterfall showing the mean composite drop with error bars when each component is set to zero, annotated with the number of verdicts that flip.

Usage

plot_score_diagnostics(x, title = NULL)

Arguments

x

A list returned by score_diagnostics(). If NULL or missing required elements, raises an error.

title

Optional character string for an overall figure title. When NULL (default), generates "Score Diagnostics" with the protein and component counts.

Value

A patchwork object with three panels: VIF (A), PCA (B), ablation (C).

Limitations

Shows what score_diagnostics() returns. Interpretation needs domain knowledge.

See also

score_diagnostics() for the upstream analysis.

Other diagnostics: score_diagnostics()

Examples

if (requireNamespace("ggplot2", quietly = TRUE) &&
    requireNamespace("patchwork", quietly = TRUE)) {
  small_fasta <- system.file(
    "extdata", "small_proteome_50_proteins.fasta",
    package = "pepVet"
  )
  batch <- batch_evaluate(small_fasta, enzyme = "trypsin")
  diag <- score_diagnostics(batch)
  p <- plot_score_diagnostics(diag)
  print(p)
}