cluster cells using a NN-network and the Louvain algorithm from the community module in Python
doLouvainCluster_community(
gobject,
name = "louvain_clus",
nn_network_to_use = "sNN",
network_name = "sNN.pca",
python_path = NULL,
resolution = 1,
weight_col = NULL,
louv_random = F,
return_gobject = TRUE,
set_seed = F,
seed_number = 1234
)
giotto object
name for cluster
type of NN network to use (kNN vs sNN)
name of NN network to use
specify specific path to python if required
resolution
weight column to use for edges
Will randomize the node evaluation order and the community evaluation order to get different partitions at each call
boolean: return giotto object (default = TRUE)
set seed
number for seed
giotto object with new clusters appended to cell metadata
This function is a wrapper for the Louvain algorithm implemented in Python, which can detect communities in graphs of nodes (cells). See the https://python-louvain.readthedocs.io/en/latest/index.htmlreadthedocs page for more information.
Set weight_col = NULL to give equal weight (=1) to each edge.