I am using Louvain clustering (1,2) to cluster cells in scRNAseq data, as implemented by scanpy.
One of the parameter required for this kind of clustering is the number of neighbors used to construct the neighborhood graph of cells (docs).
Larger values result in a more global view of the manifold, leading to lower number of clusters, while reducing the number of neighbors goes in the opposite direction. However, it is unclear how to choose this parameter.
The resolution parameter seems to work in the opposite way.
Do you know of any methodology and/or rule-of-thumb to define these parameters? E.g. depending on the size of the dataset?
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