svgbit.find_combinations

svgbit.find_combinations(dataset: svgbit.core.STDataset.STDataset, center_spots: Union[int, list], selected_genes: Optional[list] = None, use_neighbor: bool = True) → pandas.core.frame.DataFrame

Find gene pairs in certain SVG cluster.

Parameters

datasetSTDataset

A STDataset with all steps finished.

center_spotsint or list

If a int is given, find gene pairs for this SVG cluster. If a list of spots is given, find gene pairs within those spots. selected_genes should be given if center_cluster is a list.

selected_geneslist or None, default None

If a list of genes is given, find gene pairs within given genes.

use_neighborbool, default True

Whether to find gene pairs with neighbor SVG clusters.

Returns

gene_pairs_dfpd.DataFrame

A pd.DataFrame for gene pairs in center_cluster with weights.