plot.regime_module_diagnostics: Plot Regime Module Diagnostics

In bifrost: Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits

Plot Regime Module Diagnostics

Description

Draw scatterplots comparing selected PCA scores with selected module summaries from regime_module_diagnostics().

Usage

## S3 method for class 'regime_module_diagnostics'
plot(
  x,
  pc,
  comparison,
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  point_col = "#4C78A8",
  line_col = "#1B4F72",
  ribbon_col = "grey70",
  point_alpha = 0.5,
  pch = 21,
  lwd = 2,
  n_boot = 1000,
  ci_level = 0.99,
  seed = 1L,
  ...
)

Arguments

x	A regime_module_diagnostics object.
pc	Principal component name(s), such as "PC1".
comparison	Module comparison name(s).
main	Optional panel title(s).
xlab, ylab	Optional axis labels. Recycled across panels.
point_col, line_col	Point fill and fitted-line colors.
ribbon_col	Ribbon color for bootstrap confidence intervals.
point_alpha, pch, lwd	Graphical controls.
n_boot	Number of bootstrap replicates for confidence ribbons. Set to 0 to omit the ribbon and draw only the fitted line.
ci_level	Confidence level for bootstrap ribbons.
seed	Optional random seed for reproducible bootstrap curves.
...	Additional graphical parameters passed to graphics::plot().

Value

Invisibly returns x.

bifrost documentation built on Nov. 5, 2026, 9:07 a.m.