doLouvainCluster: doLouvainCluster

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

cluster cells using a NN-network and the Louvain algorithm.

Usage

doLouvainCluster(
  gobject,
  version = c("community", "multinet"),
  name = "louvain_clus",
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  python_path = NULL,
  resolution = 1,
  weight_col = NULL,
  gamma = 1,
  omega = 1,
  louv_random = F,
  return_gobject = TRUE,
  set_seed = F,
  seed_number = 1234,
  ...
)

Arguments

gobject	giotto object
version	implemented version of Louvain clustering to use
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
python_path	[community] specify specific path to python if required
resolution	[community] resolution
weight_col	weight column name
gamma	[multinet] Resolution parameter for modularity in the generalized louvain method.
omega	[multinet] Inter-layer weight parameter in the generalized louvain method
louv_random	[community] Will randomize the node evaluation order and the community evaluation order to get different partitions at each call
return_gobject	boolean: return giotto object (default = TRUE)
set_seed	set seed
seed_number	number for seed
...	additional parameters

Details

Louvain clustering using the community or multinet implementation of the louvain clustering algorithm.

Value

giotto object with new clusters appended to cell metadata

See Also

doLouvainCluster_community and doLouvainCluster_multinet

Examples

    doLouvainCluster(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.