SIGNIFICANT USER-VISIBLE CHANGES
enrich_p_threshold renamed to enrich_threshold in plot_modules_h().assay parameter in plot_modules_h() and plot_modules_v() now
must be specified explicitly (no default).prepare_WGCNA(): assay parameter must be specified explicitly
(no default).plot_trend(): ylab parameter renamed to ylabel, default changed from
"Abundance" to "Log2 abundance".plot_modules_v(): default ylabel changed from
"Log2 abundance normalised to Time 0" to "Log2 abundance".plot_cor_matrix(): default title changed from
"Correlation between samples" to NULL; the title is now auto-generated
as "Sample correlation (<Method>)" with the method capitalised (e.g.
"Sample correlation (Spearman)").plot_pca() and plot_umap(): when circle = TRUE, auto-computed axis
limits now use 0.35x padding around the data range (via coord_cartesian())
instead of 1.5x the min/max (via xlim()/ylim()).