scmagnify.tools.select_paga_path

scmagnify.tools.select_paga_path#

scmagnify.tools.select_paga_path(data, nodes, modal='RNA', groups_key='celltype', key_added='cell_state_masks')#

Select cells along specified nodes in a PAGA graph.

Parameters:

  • data (AnnData | MuData) – Single cell data object. Can be an anndata.AnnData, mudata.MuData, scmagnify.GRNMuData

  • modal (str (default: 'RNA')) – Modality key (e.g., ‘RNA’, ‘ATAC’) when using multi-modal data. mudata.MuData or scmagnify.GRNMuData must be provided.

  • nodes (list) – List of node names specifying the PAGA path.

  • groups_key (str (default: 'celltype')) – Key of the grouping used to run PAGA.

  • key_added (str (default: 'cell_state_masks')) – Key to add in adata.obsm to store the resulting mask.

Return type:

AnnData

Returns:

AnnData Annotated data with updated .obsm[key_added].

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