--- a
+++ b/man/getClusters.Rd
@@ -0,0 +1,41 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/clustering.R
+\name{getClusters}
+\alias{getClusters}
+\title{getClusters}
+\usage{
+getClusters(
+  object,
+  resolution = 1,
+  nclus = integer(0),
+  assay = NULL,
+  method = "leiden",
+  label = "clusters",
+  graph = "kNN",
+  seed = 1,
+  abundance_limit = 2
+)
+}
+\arguments{
+\item{object}{a VoltRon object}
+
+\item{resolution}{the resolution parameter for leiden clustering.}
+
+\item{nclus}{The number of cluster centers for K-means clustering.}
+
+\item{assay}{assay name (exp: Assay1) or assay class (exp: Visium, Xenium), see \link{SampleMetadata}. 
+if NULL, the default assay will be used, see \link{vrMainAssay}.}
+
+\item{method}{The method of clustering. Use 'leiden' to perform graph clustering and 'kmeans' for K-means based clustering}
+
+\item{label}{the name for the newly created clustering column in the metadata}
+
+\item{graph}{the graph type to be used}
+
+\item{seed}{seed}
+
+\item{abundance_limit}{the minimum number of points for a cluster, hence clusters with abundance lower than this limit will be appointed to other nearby clusters}
+}
+\description{
+Get clustering of the VoltRon object
+}