Table 1.

Overview of the methods' functionality.

Object	Method	H1	H2	H3	H4	Toolbox
Single	Ripley's function	yes	no	no	no	Squidpy, PySpacell, CytoMap
	Newman's assortativity	yes	no	no	no	PySpacell
	Centrality scores	no	yes	no	no	Squidpy
Two	Cluster co-occurrence ratio	no	no	yes	no	Squidpy
	Neighborhood enrichment test	no	no	yes	no	Giotto, Matisse, Squidpy, histoCAT
	Object-Object Correlation Analysis	no	no	yes	no	CytoMap
Multiple	Spatial co-expression patterns	no	no	yes	yes	Giotto
	Spage2vec	no	no	no	yes	Spage2vec
	SSAM	no	no	no	yes	SSAM
	Vector approach	no	no	no	yes	CytoMap, ClusterMap, Matisse