doLouvainCluster_multinet: doLouvainCluster_multinet

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

doLouvainCluster_multinet

Description

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

Usage

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

Details

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

Value

giotto object with new clusters appended to cell metadata

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.