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R Scripts — PCA & Ordination

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PCA & Ordination

Principal component analyses, Procrustes and correlation plots

make.PCA(TRAITS, dimensionsAux, savePCA)

Run a PCA on a trait matrix and return axes scores, loadings and explained variance.

make.PCA.groups(traitsImputed, traitsMissing, ...)

PCA with separate point sets for imputed and missing-trait species.

PCA_plot(PCoAPlot, PCoACorPlot, multAx1, multAx, title, legend)

Biplot of PCA scores with correlation arrows and optional group legend.

PCA_plot_funspace(PCoAPlot, PCoACorPlot, ...)

Functional-space biplot with KDE density shading and phylopic image overlays.

make_pca_plot(pca_object, correlation_data, ...)

PCA correlation plot with 2D density legend (axes 1–2).

make_pca_plot_34(pca_object, correlation_data, ...)

Same as make_pca_plot but for axes 3–4.

format_correlation_table(PCoACorPlot, shortNames)

Format a PCA loading table with colour-coded cells and abbreviated trait names.

run_procrustes(PCA_list)

Procrustes analysis comparing PCA spaces across multiple groups or datasets.