doRandomWalkCluster#

Last Updated: Sep 07, 2023

Description#

Cluster cells using a random walk approach.

Usage#

doRandomWalkCluster(
  gobject,
  name = "random_walk_clus",
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  walk_steps = 4,
  walk_clusters = 10,
  walk_weights = NA,
  return_gobject = TRUE,
  set_seed = FALSE,
  seed_number = 1234
)

Arguments#

`gobject`	giotto object
`name`	name for cluster, default to “random_walk_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”
`walk_steps`	number of walking steps, default = 4
`walk_clusters`	number of final clusters, default = 10
`walk_weights`	cluster column defining the walk weights
`return_gobject`	boolean: return giotto object (default = TRUE)
`set_seed`	set seed (default = FALSE)
`seed_number`	number for seed

Details#

See cluster_walktrap function from the igraph package in R for more information.

Value#

giotto object with new clusters appended to cell metadata