Perform clustering — cluster • phenomenalist

Cluster similar cells based on their expression profiles.

Usage

cluster(
  x,
  method = c("leiden"),
  resolution = 1,
  n_neighbors = 50,
  out_dir = NULL
)

Arguments

x: A SpatialExperiment object.
method: Clustering method (only leiden is implemented currently).
resolution: Value of the parameter controlling the coarseness of the clusters (higher resolution yields more clusters).
n_neighbors: The maximum number of nearest neighbors to compute.
out_dir: Name of the output analysis directory. If specified, the object and the corresponding plots will be saved there.

Value

A SpatialExperiment object.