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Calculate cell type silhouette width from an embedding

rs_cell_type_asw.Rd

[Experimental] Average silhouette width on cell type labels, rescaled to [0, 1] via (s + 1) / 2. Higher values mean cell types stay separated.

Usage

rs_cell_type_asw(embedding, labels, max_cells, verbose, seed)

Arguments

embedding

Numeric matrix. Cells x dimensions.

labels

Integer vector. The cell type per cell. The codes need not be 0-based or contiguous.

max_cells

Integer or NULL. If not NULL, subsample to this many cells for performance. If NULL, all cells are used.

verbose

Boolean. Controls verbosity of the function.

seed

Integer. Seed for subsampling reproducibility.

Value

A list with the following items

  • per_cell - Per-cell rescaled silhouette scores

  • mean_asw - Mean rescaled silhouette width

  • median_asw - Median rescaled silhouette width

References

Luecken, et al., Nat Methods, 2022