How to obtain an adjacency matrix for cluster.graph

[joonlee3]

Hi,

I was trying to use a wrapper function for the leiden algorithm, cluster.graph. It is not clear to me how to obtain an input adjacency matrix from a SCE/ACE object. I am currently using v3.0.2.

For older versions, Leiden.clustering seems to be used for the leiden clustering. The input was an SCE/ACE object instead of an adjacency matrix.

Best,
Joon

[sebastianpineda]

The wrapper that accepts ace objects is now called leiden.clustering. cluster.graph is a low-level generic function that accepts a sparse adjacency matrix.

[shmohammadi86]

You can either use the clusterCells() function, or directly call cluster.graph() with ace$ACTIONet object (adjacency matrix of ACTIONet).

[joonlee3]

@sebastianpineda leiden.clustering.cluster.graph does not seem to be available in v3.0.2.

@shmohammadi86 Thanks. It works.