scmagnify.tools.get_network_score

scmagnify.tools.get_network_score#

scmagnify.tools.get_network_score(gdata, modal='GRN', attri='score', key_added='network_score', source_only=True)#

Calculate centrality measures for all nodes in a directed graph.

Parameters:
Return type:

DataFrame | dict

:param Single cell data object. Can be an anndata.AnnData: :param mudata.MuData: :param scmagnify.GRNMuData: :type modal: Literal['GRN', 'RNA', 'ATAC'] (default: 'GRN') :param modal: :param Modality key (e.g.: :param ‘RNA’: :param ‘ATAC’) when using multi-modal data. mudata.MuData or scmagnify.GRNMuData must be provided.: :type attri: str (default: 'score') :param attri: Edge attribute to filter the graph. Only edges with this attribute greater than 0.0 are considered. Default is “score”. :type key_added: str (default: 'network_score') :param key_added: Key in varm to store the results. Default is “network_score”. :type source_only: bool (default: True) :param source_only: If True, only nodes with outgoing edges are considered. Default is True.

Return type:

DataFrame | dict

Returns:

Union[pd.DataFrame, dict] If modal is “GRN”, returns a DataFrame with centrality measures for all nodes. If modal is “RNA” or “ATAC”, returns a dictionary with DataFrames for each modality.

Parameters:
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