decoupler.pp.knn

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decoupler.pp.knn#

decoupler.pp.knn(adata, key='spatial', bw=100, max_nn=100, cutoff=0.1)#

Adds K-Nearest Neighbors similarities based on spatial distances.

Parameters:

  • adata (AnnData) – Annotated data matrix with observations (rows) and features (columns).

  • key (str (default: 'spatial')) – adata.obsm key to use.

  • bw (float (default: 100)) – Bandwith of kernel.

  • max_nn (int (default: 100)) – Maximum number of nearest neighbors to consider.

  • cutoff (float (default: 0.1)) – Values below this number are set to zero.

Return type:

None

Example

import decoupler as dc

adata = dc.ds.msvisium()
dc.pp.knn(adata, key="spatial", bw=100, cutoff=0.1)
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