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Calculate cell type average silhouette width

calculate_cell_type_asw_sc.Rd

Average silhouette width on cell type labels in the embedding, rescaled to [0, 1] via (s + 1) / 2 as in scIB. Higher values mean cell types stay separated after correction. Counterpart to calculate_batch_asw_sc() on the biology side.

Usage

calculate_cell_type_asw_sc(
  object,
  cell_type_column,
  embd_to_use = "pca",
  max_cells = 5000L,
  seed = 42L,
  .verbose = TRUE
)

Arguments

object

SingleCells or SingleCellsSubset class.

cell_type_column

String. The column with the cell type labels in the obs data of the class.

embd_to_use

String. Which embedding to compute the ASW on. Defaults to "pca".

max_cells

Integer or NULL. If not NULL, subsample to this many cells for performance. Defaults to 5000L.

seed

Integer. Seed for subsampling reproducibility.

.verbose

Boolean. Controls verbosity of the function.

Value

A CellTypeAswScores object with the following elements

  • per_cell - Per-cell rescaled silhouette scores in [0, 1].

  • mean_asw - Mean rescaled silhouette width.

  • median_asw - Median rescaled silhouette width.

  • n_cell_types - Number of cell types.

  • embedding_used - Which embedding the ASW was computed on.

References

Luecken, et al., Nat. Methods, 2022

Examples

# cell type silhouette width on the PCA embedding
sc <- demo_single_cells(
  syn_data_params = params_sc_synthetic_data(
    n_cells = 600L, n_genes = 50L, n_batches = 3L
  )
)
calculate_cell_type_asw_sc(
  sc,
  cell_type_column = "cell_grp",
  .verbose = FALSE
)
#> Cell Type Silhouette Width (rescaled)
#>   Cells: 600 | Cell types: 3 | Embedding: pca
#>   Mean ASW:    0.5309 (0.5 = no structure, 1 = separated)
#>   Median ASW:  0.5313

unlink(sc@dir_data, recursive = TRUE, force = TRUE)