doLouvainCluster#
Last Updated: Oct 02, 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#
|
giotto object |
|
implemented version of Louvain clustering to use |
|
name for cluster, default to “louvain_clus” |
|
type of NN network to use (kNN vs sNN), default to “sNN” |
|
name of NN network to use, default to “sNN.pca” |
|
[community] specify specific path to python if required |
|
[community] resolution, default = 1 |
|
weight column name |
|
[multinet] Resolution parameter for modularity in the generalized louvain method, default = 1 |
|
[multinet] Inter-layer weight parameter in the generalized louvain method, default = 1 |
|
[community] Will randomize the node evaluation order and the community evaluation order to get different partitions at each call (default = FALSE) |
|
boolean: return giotto object (default = TRUE) |
|
set seed (default = FALSE) |
|
number for seed |
|
arguments passed to
|
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