scmagnify.chromatin_constraint

scmagnify.chromatin_constraint#

scmagnify.chromatin_constraint(data, modal='RNA', layer='counts', gene_selected=None, tf_list=None, save=True, verbose=True)#

Build chromatin constraints and import them into the analysis.

Parameters:

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

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

  • layer (str (default: 'counts')) – Layer in layers. If None, defaults to X.

  • gene_selected (Optional[Index] (default: None)) – Genes to include; defaults to intersection with basal GRN genes.

  • tf_list (Optional[list[str]] (default: None)) – List of TFs. If None, uses the default TF list from settings.

  • save (bool (default: True)) – Whether to save filtered basal GRN into adata.uns.

  • verbose (bool (default: True)) – Whether to print summary statistics.

Return type:

tuple[AnnData, DataFrame]

Returns:

  • adata_filAnnData

    Filtered and normalized annotated data matrix.

  • basal_grnpd.DataFrame

    Basal gene regulatory network (GRN) matrix.

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