co occurance score

Calculate co-occurance scoring between original spatial coordinates. It can be defined as \(\frac{p(exp|cond)}{p(exp)}\).

Parameters

cluster_key: str Key by which to compute neighbouhood enrichment scores.

clusters: str Cluster annotation to use in co-occurance scoring.

Web view

Python equivalent

import squidpy as sq

sq.gr.co_occurrence(adata, cluster_key="celltype_mapped_refined")
sq.pl.co_occurrence(adata, cluster_key="celltype_mapped_refined", clusters="Lateral plate mesoderm", figsize=(10, 5))