cellspec.pp.filter_cells

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cellspec.pp.filter_cells#

cellspec.pp.filter_cells(adata, min_variants=None, max_variants=None, inplace=True)#

Filter cells/samples based on number of variants detected.

Parameters:

  • adata (ad.AnnData) – AnnData object with variants

  • min_variants (int, optional) – Minimum number of variants a cell must have

  • max_variants (int, optional) – Maximum number of variants a cell must have

  • inplace (bool, default True) – Modify adata in place or return copy

Return type:

AnnData | None

Returns:

ad.AnnData or None Filtered AnnData (if inplace=False), otherwise None

Examples

>>> import cellspec as spc
>>> # Keep cells with at least 10 variants
>>> spc.pp.filter_cells(adata, min_variants=10)

>>> # Remove cells with too many variants (potential doublets)
>>> spc.pp.filter_cells(adata, min_variants=10, max_variants=1000)

Notes

Variant counts are from .X (binary presence/absence matrix).

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