angelolab / angelolab/SpaceCat

Squidpy spatial neighbors row/col index mismatch in knn mode

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bug
Lenguaje dominante
Python
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19
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1
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Sin PR fusionados en 30 d

Descripción

**Describe the bug**
Older versions of the Squidpy spatial neighbors function improperly indexes rows and columns when using k-nearest neighbor graph. I obtained this error using squidpy v1.2.2, as required in the conda env. This is resolved in newer versions of squidpy. [https://github.com/scverse/squidpy/pull/792](https://github.com/scverse/squidpy/pull/792)

**Expected behavior**
Following graph construction, rows should sum to `n_neighbors`; however, the transpose is true.

**Solution**
Upgrade squidpy version >=1.6.1

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