cassiopeia.sp.get_spatial_graph_from_anndata#
- cassiopeia.sp.get_spatial_graph_from_anndata(adata, neighborhood_radius=30.0, neighborhood_size=None, connect_key='spatial')[source]#
Get a spatial graph structure from an spatial anndata
Construct a spatial graph connecting each node to its nearest neighbors in space. Assumes that the specified adata has spatial coordinates specified in the .obsm key.
- Parameters:
- adata
AnnData Anndata of spatially-resolved data. Only the spatial coordinates need to be stored, and this is used to construct a graph.
- neighborhood_size
float|None(default:None) If a connectivitity graph is being constructed, this is the number of nearest neighbors to connect to a node.
- neighborhood_radius
int(default:30.0) Intead of passing in neighborhood_size, this is the radius of the connectivity graph.
- connect_key
str(default:'spatial') Key used to store spatial connectivities in adata.obsp. This will be passed into the key_added argument of sq.gr.spatial_neighbors and an etnry in adata.obsp will be added of the form {connect_key}_connectivities.
- adata
- Return type:
DiGraph- Returns:
A networkx object storing the spatial graph.