doLouvainCluster | R Documentation |
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,
...
)
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 |
Louvain clustering using the community or multinet implementation of the louvain clustering algorithm.
giotto object with new clusters appended to cell metadata
doLouvainCluster_community
and doLouvainCluster_multinet
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