Cluster cells using a NN-network and the Louvain algorithm. This utilizes the generalized Louvain implementation from multinet.
gamma | numeric (default = 1). Resolution parameter for modularity in the generalized louvain method, |
omega | numeric (default = 1). Inter-layer weight parameter in the generalized louvain method |
g <- GiottoData::loadGiottoMini("visium")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 3.1 read Giotto spatial shape information
#> 3.2 read Giotto spatial centroid information
#> 3.3 read Giotto spatial overlap information
#> 4. read Giotto image information
#> python already initialized in this session
#> active environment : '/usr/bin/python3'
#> python version : 3.12
clusterData(g, clusterParam("louvain_multinet"))
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'param' in selecting a method for function 'clusterData': package 'multinet' is not yet installed
#>
#> To install:
#> install.packages(c("multinet"))