doLouvainCluster#

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Last Updated: Mar 11, 2023

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 = FALSE,
  return_gobject = TRUE,
  set_seed = FALSE,
  seed_number = 1234,
  ...
)

Arguments#

`gobject`	giotto object
`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