doLouvainCluster multinet

Source: R/clustering.R

cluster cells using a NN-network and the Louvain algorithm from the multinet package in R.

.doLouvainCluster_multinet(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  name = "louvain_clus",
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  gamma = 1,
  omega = 1,
  return_gobject = TRUE,
  set_seed = FALSE,
  seed_number = 1234
)

Arguments

gobject

giotto object

spat_unit

spatial unit (e.g. "cell")

feat_type

feature type (e.g. "rna", "dna", "protein")

name

name for cluster, default to "louvain_clus"

nn_network_to_use

type of NN network to use (kNN vs sNN), default to "sNN"

network_name

name of NN network to use, default to "sNN.pca"

gamma

Resolution parameter for modularity in the generalized louvain method. default = 1

omega

Inter-layer weight parameter in the generalized louvain method. default = 1

return_gobject

boolean: return giotto object (default = TRUE)

set_seed

set seed (default = FALSE)

seed_number

number for seed

Value

giotto object with new clusters appended to cell metadata

Details

See glouvain_ml from the multinet package in R for more information.