SpaGTL.regulons

SpaGTL.regulons(adata, tf_names=None, motif_annotations_fname=None, db_fnames=None, thresholds=(0.75, 0.9), top_n_targets=(50,), top_n_regulators=(5, 10, 50), min_genes=20, copy=False)

Regulon inference for spatial transcriptomics [Aibar17].

Parameters:

adata : AnnData

Annotated data matrix.

tf_names : Sequence[str] | NoneOptional[Sequence[str]] (default: None)

List of transcription factors (TFs).

motif_annotations_fname : str | NoneOptional[str] (default: None)

Path of motif annotation file.

db_fnames : Sequence[str] | NoneOptional[Sequence[str]] (default: None)

List of path of ranking database files.

thresholds : default: (0.75, 0.9)

The first method to create the TF-modules based on the best targets for each transcription factor.

top_n_targets : default: (50,)

The second method is to select the top targets for a given TF.

top_n_regulators : default: (5, 10, 50)

The alternative way to create the TF-modules is to select the best regulators for each gene.

min_genes : default: 20

The required minimum number of genes in a resulting module.

copy : bool (default: False)

Return a copy instead of writing to adata.

Return type:

Optional[AnnData]

Returns:

: Depending on copy, returns or updates adata with the following fields.

.uns[‘regulon’]

The inferred regulons.