doLouvainCluster: doLouvainCluster

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

doLouvainCluster

Description

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

Usage

doLouvainCluster(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  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 = FALSE,
  return_gobject = TRUE,
  set_seed = FALSE,
  seed_number = 1234,
  ...
)

Arguments

gobject	giotto object
spat_unit	spatial unit (e.g. "cell")
feat_type	feature type (e.g. "rna", "dna", "protein")
version	implemented version of Louvain clustering to use
name	name for cluster, default to "louvain_clus"
nn_network_to_use	type of NN network to use (kNN vs sNN), default to "sNN"
network_name	name of NN network to use, default to "sNN.pca"
python_path	[community] specify specific path to python if required
resolution	[community] resolution, default = 1
weight_col	weight column name
gamma	[multinet] Resolution parameter for modularity in the generalized louvain method, default = 1
omega	[multinet] Inter-layer weight parameter in the generalized louvain method, default = 1
louv_random	[community] Will randomize the node evaluation order and the community evaluation order to get different partitions at each call (default = FALSE)
return_gobject	boolean: return giotto object (default = TRUE)
set_seed	set seed (default = FALSE)
seed_number	number for seed
...	arguments passed to doLouvainCluster_community or doLouvainCluster_multinet

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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.