doLouvainCluster_multinet

Source: R/clustering.R

cluster cells using a NN-network and the Louvain algorithm from the multinet package in R.

doLouvainCluster_multinet(
  gobject,
  name = "louvain_clus",
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  gamma = 1,
  omega = 1,
  return_gobject = TRUE,
  set_seed = F,
  seed_number = 1234
)

Arguments

gobject

giotto object
name

name for cluster
nn_network_to_use

type of NN network to use (kNN vs sNN)
network_name

name of NN network to use
gamma

Resolution parameter for modularity in the generalized louvain method.
omega

Inter-layer weight parameter in the generalized louvain method.
return_gobject

boolean: return giotto object (default = TRUE)
set_seed

set seed
seed_number

number for seed

Value

giotto object with new clusters appended to cell metadata

Details

See glouvain_ml from the multinet package in R for more information.