doRandomWalkCluster: doRandomWalkCluster

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

doRandomWalkCluster

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

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.