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JinmiaoChenLab / Rphenograph

Rphenograph: R implementation of the PhenoGraph algorithm
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Changing clustering resolution #2

Closed asmagen closed 4 years ago

asmagen commented 6 years ago

Hello

I'm currently changing the clustering resolution (increasing or decreasing the number of output clusters) by changing the KNN parameter. Is there a way to change the resolution by changing the Louvain parameters and not the KNN?

Thanks

SamGG commented 4 years ago

Hi, There seems to be no such parameter in the Louvain implementation available in the igraph package. https://igraph.org/r/doc/cluster_louvain.html

SamGG commented 4 years ago

Hi, jmlong has implemented the resolution parameter in the Louvain algorithm in igraph (C code) and rigraph (R functions depending on C). https://github.com/igraph/rigraph/issues/239#issuecomment-637152537 Changing the k does not properly achieve this feature IMHO. If you are still using Rphenograph, have a look at my current fork. https://github.com/i-cyto/Rphenograph Best.