Plot Regime Correlation PCA Results — plot.regime_correlation

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.