Leiden clustering of Region data — cluster_leiden.region • SpatialMap

Takes Region object, extracts a NN graph by name, and performs modularity optimization using leiden from the igraph package.

Usage

cluster_leiden.region(
  object,
  nn.name = "umap",
  col.name = ".clusters",
  cluster.resolution = 1,
  objective.function = "modularity",
  ...
)

Arguments

object: A Region object
nn.name: The name of the NN object to cluster from
col.name: The name of the column containing cluster assignments to add to Regions' cellMetadata
cluster.resolution: The resolution parameter.
objective.function: Must be either "modularity" or "CPM" (Constant Potts Model). Defaults to modularity.
...: Additional parameters passed to clustering functions