spatialtis.find_neighbors

class spatialtis.find_neighbors(data, method='kdtree', r=None, k=None, scale=None, export_key=None, **kwargs)[source]

To find the neighbors of each cell

KD-tree and Delaunay triangulation are used when cells are points

R-tree is used when cells are polygons

Note

When method="kdtree", you can search neighbors within radius and/or by nearest-neighbors. If you specific r=30, k=5, this will search within 30 while limited the number of neighbors to 5;

Parameters

  • data (anndata._core.anndata.AnnData) – AnnData object to perform analysis

  • method (Optional[str]) – “kdtree”, “rtree” and “delaunay”, Default: “kdtree”

  • r (Optional[float]) – The search radius

  • k (Optional[int]) – The (minimum) number of nearest-neighbors

  • scale (Optional[Union[int, float]]) – How much to scale each cell, only if cell has shape

  • export_key (str) – The key used to store result

  • **kwargs – Pass to spatialtis.abc.AnalysisBase

spatial_weights()[source]

A generator that return spatial weight in CSR matrix (roi_name, spatial_weight_matrix)

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