doRandomWalkCluster#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/clustering.R#L529

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#

Argument

Description

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 <#clusterwalktrap>`__ function from the igraph package in R for more information.

Value#

giotto object with new clusters appended to cell metadata