sc.pp.neighbors(..., knn=True, n_neighbors=k) does not threshold the adjacency

[mkarikom]

Please make sure these conditions are met

• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of scanpy.
• (optional) I have confirmed this bug exists on the main branch of scanpy.

What happened?

According to the pp.neighbors() docs we have:

    knn
        If `True`, use a hard threshold to restrict the number of neighbors to
        `n_neighbors`, that is, consider a knn graph. Otherwise, use a Gaussian
        Kernel to assign low weights to neighbors more distant than the
        `n_neighbors` nearest neighbor.

However, the adjacency represented by adata.uns['neighbors']['connectivities_key'] shows many more neighbors than n_neighbors when knn=True

Minimal code sample

import urllib.request
import scanpy as sc

# load the data
h5_data = "https://datasets.cellxgene.cziscience.com/6ff309fa-e9f6-405d-b24e-3c35528f154e.h5ad"
urllib.request.urlretrieve(h5_data, "/tmp/data.h5ad")    
adata = sc.read_h5ad("/tmp/data.h5ad")

# compute the adjacency thresholded at k=10
k=10
sc.pp.neighbors(adata, n_neighbors=k, n_pcs=40, random_state=42,knn=True)
adjacency = (adata.obsp[adata.uns['neighbors']['connectivities_key']].todense() > 0).astype(np.int32)
print(f"adjacency matrix (k={k}) shape: {adjacency.shape}")

# check to see if we got a threshold
max_neighbors = np.max(adjacency.sum(axis=0))
print(f"Max neighbors={max_neighbors}")

Error output

adjacency matrix (k=10) shape: (1011, 1011)
Max neighbors=91

Versions

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anndata     0.10.6
scanpy      1.9.8
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-----
IPython             8.22.2
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Python 3.10.12 (main, Nov 20 2023, 15:14:05) [GCC 11.4.0]
Linux-6.5.0-27-generic-x86_64-with-glibc2.35
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Session information updated at 2024-04-18 18:58