Cluster Cells Using NN-Network and Louvain Algorithm¶

doLouvainCluster()

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

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

Value¶

Giotto object with new clusters appended to cell metadata

Details¶

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