RunLeiden: Run Leiden clustering algorithm

In satijalab/seurat: Tools for Single Cell Genomics

Run Leiden clustering algorithm

Description

Returns a vector of partition indices.

Usage

RunLeiden(
  object,
  method = deprecated(),
  partition.type = c("RBConfigurationVertexPartition", "ModularityVertexPartition",
    "RBERVertexPartition", "CPMVertexPartition", "MutableVertexPartition",
    "SignificanceVertexPartition", "SurpriseVertexPartition"),
  initial.membership = NULL,
  node.sizes = NULL,
  resolution.parameter = 1,
  random.seed = 1,
  n.iter = 10
)

Arguments

object	An adjacency matrix or adjacency list.
method	DEPRECATED.
partition.type	Type of partition to use for Leiden algorithm. Defaults to "RBConfigurationVertexPartition", see https://cran.rstudio.com/web/packages/leidenbase/leidenbase.pdf for more options.
initial.membership	Passed to the 'initial_membership' parameter of 'leidenbase::leiden_find_partition'.
node.sizes	Passed to the 'node_sizes' parameter of 'leidenbase::leiden_find_partition'.
resolution.parameter	A parameter controlling the coarseness of the clusters for Leiden algorithm. Higher values lead to more clusters. (defaults to 1.0 for partition types that accept a resolution parameter)
random.seed	Seed of the random number generator, must be greater than 0.
n.iter	Maximal number of iterations per random start

satijalab/seurat documentation built on Jan. 14, 2025, 8:48 p.m.