omicverse.single.MetaCell

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omicverse.single.MetaCell#

omicverse.single.MetaCell(adata, method: str = 'seacells', use_rep: str = 'X_pca', n_metacells: int | None = None, layer: str | None = None, device: str = 'cpu', random_state: int = 0, **kwargs)[source]#

Unified metacell wrapper with dispatchable backends.

Parameters:

  • adata – Input single-cell AnnData.

  • method (default: 'seacells') – Backend key. One of 'seacells' (default, backward-compatible), 'metaq', 'mc2', 'supercell', 'kmeans', 'random', 'geosketch'.

  • use_rep (default: 'X_pca') – Embedding key in adata.obsm. Used by graph-based backends (seacells/supercell/kmeans/geosketch). MetaQ and MC2 derive their own representations and ignore this.

  • n_metacells (default: None) – Target number of metacells. Default adata.n_obs // 75.

  • layer (default: None) – Counts layer for backends that need raw counts (MetaQ, MC2).

  • device (default: 'cpu') – 'cpu', 'cuda', or 'mps' for GPU-capable backends.

  • random_state (default: 0) – Seed forwarded to all backends.

  • **kwargs – Forwarded to the backend constructor. See each backend’s docstring for valid kwargs.

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