doLouvainCluster

Source: R/clustering.R

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.