doLouvainCluster#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/clustering.R#L452

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#

Argument

Description

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_communi ty <#dolouvainclustercommunity>`__ or `doLouvainCluster_multi net <#dolouvainclustermultinet>`__

Details#

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

Value#

giotto object with new clusters appended to cell metadata

Seealso#

`doLouvainCluster_community <#dolouvainclustercommunity>`__ and `doLouvainCluster_multinet <#dolouvainclustermultinet>`__