liana.utils.spatial_neighbors

liana.utils.spatial_neighbors(adata: AnnData, bandwidth=None, cutoff=0.1, max_neighbours=100, kernel='gaussian', set_diag=False, zoi=0, standardize=False, reference=None, spatial_key='spatial', key_added='spatial', inplace=True)

Generate spatial connectivity weights using Euclidean distance.

Parameters:
adata

Annotated data object.

bandwidth

Denotes signaling length (l) and controls the maximum distance at which two spots are considered. Corresponds to the units in which spatial coordinates are expressed.

cutoff

Values below this cutoff will be set to 0.

max_neighbours

Maximum nearest neighbours to be considered when generating spatial connectivity weights. Essentially, the maximum number of edges in the spatial connectivity graph.

kernel

Kernel function used to generate connectivity weights. It controls the shape of the connectivity weights. The following options are available: [‘gaussian’, ‘exponential’, ‘linear’, ‘misty_rbf’]

set_diag

Logical, sets connectivity diagonal to 0 if False. Default is True.

zoi

Zone of indifference. Values below this cutoff will be set to np.inf.

standardize

Whether to (l1) standardize spatial proximities (connectivities) so that they sum to 1. This plays a role when weighing border regions prior to downstream methods, as the number of spots in the border region (and hence the sum of proximities) is smaller than the number of spots in the center. Relevant for methods with unstandardized scores (e.g. product). Default is False.

reference

Reference coordinates to use when generating spatial connectivity weights. If None, uses the spatial coordinates in adata.obsm[spatial_key]. This is only relevant if you want to use a different set of coordinates to generate spatial connectivity weights.

spatial_key

Key in adata.obsm that contains the spatial coordinates. Default is ‘spatial’.

key_added

Key to add to adata.obsp if inplace = True. If reference is not None, key will be added to adata.obsm.

inplace

Whether to store results in place, or else to return them.

Returns:
If inplace = False, returns an np.array with spatial connectivity weights.
Otherwise, modifies the adata object with the following key:

  • anndata.AnnData.obsp ['{key_added}_connectivities'] with the aforementioned array

Notes

This function is adapted from mistyR, and is set to be consistent with the squidpy.gr.spatial_neighbors function in the squidpy package.