Plot an integrated PCA fit — plot.dp

Uses the stored estimates without estimating loading, scree or score again. Use set.seed() before plotting to reproduce synthetic samples.

Usage

# S3 method for class 'dp_pca'
plot(
  x,
  display = "all",
  scree = list(),
  score = list(),
  loading = list(),
  variable = list(),
  biplot = list(),
  sampling = NULL,
  center = TRUE,
  variables = 10,
  base_size = 12,
  ...
)

Arguments

x: A fitted dp_pca() object.
display: "all" (default) or a vector selecting "scree", "score", "loading", "variable", and "biplot".
scree: Plot options: type = "pve" or "scree", and plot_control = NULL (scree_plot_control()).
score: Plot options: type = "histogram" or "sample", and plot_control = NULL (score_plot_control()). For grouped plots, the color map and legend settings also apply to the biplot.
loading: Plot options: type = "vector", "point", or "heatmap", heatmap_components = NULL, and plot_control = NULL (loading_plot_control()). Multiple types require display = "loading".
variable: Plot options: plot_control = NULL. Shows labeled arrows and the correlation-style unit circle.
biplot: Plot options: alpha = 0 (between 0 and 1), labels = TRUE, and plot_control = NULL.
sampling: A sampling_control() object with one method, shared by the score sample plot and biplot. By default, DP sample size is the input sample size, and non-private plots use observed scores. An explicit sample_size samples both versions from their histograms. For groups, sizes are allocated across groups; zero-mass groups yield no points.
center: Whether to shift displayed private scores by the midpoint of the private frame (TRUE by default). Shared by score and biplot; the biplot arrows start at the origin when TRUE. Ordinary reference scores remain centered at zero. This is display-only post-processing.
variables: Variables to display: positive top-N count (10 by default), "all", NULL, names, or indices. Top-N selection uses norms of private loading coefficients on the two selected axes. Selection is shared by loading, variable and biplot panels, including non-private comparisons.
base_size: Base font size (12 by default); local plot controls override it.
...: Unused arguments are rejected.

Value

Invisibly returns private and, when requested, nonprivate lists. Each contains plots, page, sampled_points (unshifted), biplot, frames and direction_sign. Biplot metadata includes the alpha-transformed and displayed coordinates, scale, arrow_scale, score_center, score_radius, estimated_center, centered, arrow_start, arrow_endpoints and display frame. The plots are always drawn; out <- plot(fit) also keeps these results for reuse. Multiple loading displays with both versions additionally return a comparison patchwork.

Details

Plotting reuses the stored estimates; non-private panels appear automatically if the fit contains them. Synthetic sampling is post-processing, and set.seed() can reproduce sampled displays.

Variable-plot coordinates use the covariance reconstructed from the k private scree estimates and directions; they need not equal observed variable–score correlations. Variables with zero implied variance are omitted.

Biplot coordinates divide sampled scores by d^alpha and multiply private direction coefficients by d^alpha, where d = sqrt((n - 1) * scree) on the selected axes. A zero scree value with positive alpha suppresses that axis. Arrows use one display multiplier computed from the private sample and shared with the ordinary comparison; empty or zero-radius samples omit arrows. The comparison uses the same square biplot frame.

Centering translates only displayed coordinates. Combined grouped pages show one group legend, while individual ggplot objects retain their own. The returned object stores both the combined pages and individual plots.