--- a
+++ b/man/runLeiden.Rd
@@ -0,0 +1,42 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/scAI_model.R
+\name{runLeiden}
+\alias{runLeiden}
+\title{Run Leiden clustering algorithm
+This code is modified from Tom Kelly (https://github.com/TomKellyGenetics/leiden), where we added more parameters (seed.use and n.iter) to run the Python version. In addition, we also take care of the singleton issue after running leiden algorithm.}
+\usage{
+runLeiden(SNN = matrix(), resolution = 1,
+  partition_type = c("RBConfigurationVertexPartition",
+  "ModularityVertexPartition", "RBERVertexPartition", "CPMVertexPartition",
+  "MutableVertexPartition", "SignificanceVertexPartition",
+  "SurpriseVertexPartition"), seed.use = 42L, n.iter = 10L,
+  initial.membership = NULL, weights = NULL, node.sizes = NULL)
+}
+\arguments{
+\item{SNN}{An adjacency matrix compatible with \code{\link[igraph]{igraph}} object.}
+
+\item{resolution}{A parameter controlling the coarseness of the clusters}
+
+\item{partition_type}{Type of partition to use. Defaults to RBConfigurationVertexPartition. Options include: ModularityVertexPartition, RBERVertexPartition, CPMVertexPartition, MutableVertexPartition, SignificanceVertexPartition, SurpriseVertexPartition (see the Leiden python module documentation for more details)}
+
+\item{seed.use}{set seed}
+
+\item{n.iter}{number of iteration}
+
+\item{initial.membership}{arameters to pass to the Python leidenalg function defaults initial_membership=None}
+
+\item{weights}{defaults weights=None}
+
+\item{node.sizes}{Parameters to pass to the Python leidenalg function}
+}
+\value{
+A parition of clusters as a vector of integers
+}
+\description{
+Implements the Leiden clustering algorithm in R using reticulate to run the Python version. Requires the python "leidenalg" and "igraph" modules to be installed. Returns a vector of partition indices.
+}
+\keyword{graph}
+\keyword{igraph}
+\keyword{mvtnorm}
+\keyword{network}
+\keyword{simulation}