MDS 2D scatter per method — nm_plot_mds • NADIA

Classical MDS on Euclidean distances of scaled, complete-case data. Faceted by method, colored by condition.

Usage

nm_plot_mds(
  se,
  assay_names = NULL,
  condition_col = "Condition",
  mds_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.
mds_scales: Facet scaling: "free" (default) allows independent axes per panel; "fixed" forces shared axes for easier cross-method comparison.
...: 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_mds(se)