omicverse.space.cellcharter

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omicverse.space.cellcharter#

omicverse.space.cellcharter(adata, n_clusters, *, use_rep='X_pca', spatial_key='spatial', n_layers=3, aggregations='mean', out_key='X_cellcharter', cluster_key='cellcharter', connectivity_key='spatial_connectivities', distances_key='spatial_distances', sample_key=None, build_spatial_graph=True, delaunay=True, n_neighs=6, radius=None, trim_long_links=True, distance_percentile=99.0, random_state=1024, covariance_type='full', backend='auto', batch_size=None, trainer_params=None)[source]#

Run a minimal CellCharter workflow on a spatial AnnData object.

Parameters:

  • adata (AnnData)

  • n_clusters (int)

  • use_rep (str (default: 'X_pca'))

  • spatial_key (str (default: 'spatial'))

  • n_layers (int (default: 3))

  • aggregations (str | list[str] (default: 'mean'))

  • out_key (str (default: 'X_cellcharter'))

  • cluster_key (str (default: 'cellcharter'))

  • connectivity_key (str (default: 'spatial_connectivities'))

  • distances_key (str (default: 'spatial_distances'))

  • sample_key (Optional[str] (default: None))

  • build_spatial_graph (bool (default: True))

  • delaunay (bool (default: True))

  • n_neighs (int (default: 6))

  • trim_long_links (bool (default: True))

  • distance_percentile (float (default: 99.0))

  • random_state (int (default: 1024))

  • covariance_type (str (default: 'full'))

  • backend (str (default: 'auto'))

  • batch_size (Optional[int] (default: None))

  • trainer_params (Optional[dict] (default: None))

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