plot.regime_correlation_pca: Plot Regime Correlation PCA Results

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

Plot Regime Correlation PCA Results

Description

Draw compact PCA views from regime_correlation_pca(). The default "loadings" view reconstructs upper-triangle loading vectors as symmetric trait-by-trait heatmaps, matching the Supplementary Figure 4B-style interpretation of correlation-structure axes.

Usage

## S3 method for class 'regime_correlation_pca'
plot(
  x,
  type = c("loadings", "scores", "variance"),
  components = 1:4,
  pc_x = 1L,
  pc_y = 2L,
  palette = NULL,
  main = NULL,
  cluster = c("none", "global", "local"),
  heatmap_engine = c("auto", "base", "ComplexHeatmap"),
  show_dendrogram = TRUE,
  show_legend = TRUE,
  cex.axis = 0.62,
  ...
)

Arguments

x	A regime_correlation_pca object.
type	Plot type: "loadings", "scores", or "variance".
components	Principal components to draw for loading or variance plots. Supply numeric indices or names such as "PC1". By default, the first four available components, or all components when fewer exist, are drawn.
pc_x, pc_y	Components for the score scatter plot. The default uses PC1 and PC2 when available, or PC1 for both axes when only one component exists.
palette	Optional color vector for loading heatmaps.
main	Optional plot title. For loading plots with multiple components, supply one title per component.
cluster	Loading-heatmap clustering style: "none" preserves trait order, "global" reuses the first selected PC's clustered row/column order for all panels, and "local" reclusters each PC panel.
heatmap_engine	Loading-heatmap renderer. "auto" uses ComplexHeatmap for clustered heatmaps when that optional package is installed and otherwise falls back to base graphics.
show_dendrogram, show_legend	Logical controls used by the optional ComplexHeatmap renderer.
cex.axis	Axis label size for loading heatmaps.
...	Additional graphical parameters passed to base plotting functions.

Value

Invisibly returns x.

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