PCA scatter plot per method — nm_plot_pca • NADIA

PC1 vs PC2 scatter, colored by condition, faceted by method. Percentage of variance explained shown on each axis.

Usage

nm_plot_pca(
  se,
  assay_names = NULL,
  condition_col = "Condition",
  pca_scales = c("free", "fixed"),
  ...
)

Arguments

se: SummarizedExperiment from import_norm_matrices().
assay_names: Character vector of assay names to include. NULL = all.
condition_col: Column in colData with condition labels.
pca_scales: Facet scaling: "free" (default) allows independent axes per method; "fixed" uses shared axes to compare separation magnitude.
...: Additional arguments (unused).

Value

ggplot object.

Examples

data(nadia_dia)
se <- nm_prepare_se(nadia_dia, verbose = FALSE)
se <- nm_run_normalizations(se, methods = c("cycloess", "quantile", "MAD"),
                            verbose = FALSE)

nm_plot_pca(se, pca_scales = "fixed")