geneGATer.pp.pre_clustering#

geneGATer.pp.pre_clustering(adata, n_rings=2, n_neighs=6, alpha=0.2, resolution=1, connectivities='connectivities', spatial_connectivities='spatial_connectivities', library_key='sample_name', cluster_key='cluster')#

Create a basic leiden-pre-clustering and spatial graph.

Parameters

  • adata (AnnData) – The AnnData object to preprocess.

  • n_rings (default: 2) – Number of rings to use for the spatial graph.

  • n_neighs (default: 6) – Number of neighbours to use for the spatial graph. (6 Standard for Visium data)

  • alpha (default: 0.2) – Alpha parameter for the joint graph.

  • resolution (default: 1) – Resolution parameter for the leiden clustering.

  • connectivities (default: 'connectivities') – Key for the gene connectivities.

  • spatial_connectivities (default: 'spatial_connectivities') – Key for the spatial connectivities.

  • library_key (default: 'sample_name') – Key for donor names.

  • cluster_key (default: 'cluster') – Key in which clustering is getting saved in adata.obs.

Returns

Raw pre-clustering.