doLouvainCluster_community

Source: R/clustering.R

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
)

Arguments

gobject

giotto object
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

specify specific path to python if required
resolution

resolution
weight_col

weight column to use for edges
louv_random

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

Value

giotto object with new clusters appended to cell metadata

Details

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.