scran::ClusterSnnGraphMultiLevel Class Reference

Multi-level clustering on a shared nearest-neighbor graph. More...

#include <ClusterSnnGraph.hpp>

Classes
struct	Defaults
	Default parameter settings. More...
struct	Results
	Result of the igraph multi-level community detection algorithm. More...

Public Member Functions
ClusterSnnGraphMultiLevel &	set_seed (int s=Defaults::seed)
ClusterSnnGraphMultiLevel &	set_resolution (double r=Defaults::resolution)
Results	run (const BuildSnnGraph::Results &store) const
Results	run (const igraph::Graph &graph, const igraph_real_t *weights) const

Detailed Description

Multi-level clustering on a shared nearest-neighbor graph.

This applies multi-level (i.e., "Louvain") clustering on a shared nearest neighbor graph. See here for more details on the multi-level algorithm.

Member Function Documentation

set_seed()

ClusterSnnGraphMultiLevel & scran::ClusterSnnGraphMultiLevel::set_seed ( int  s = Defaults::seed )

inline

Parameters

s	Seed for the default igraph random number generator.

Returns

A reference to this ClusterSnnGraphMultiLevel object.

set_resolution()

ClusterSnnGraphMultiLevel & scran::ClusterSnnGraphMultiLevel::set_resolution ( double  r = Defaults::resolution )

inline

Parameters

r	Resolution of the clustering, must be non-negative. Lower values favor fewer, larger communities; higher values favor more, smaller communities.

Returns

A reference to this ClusterSnnGraphMultiLevel object.

run() [1/2]

Results scran::ClusterSnnGraphMultiLevel::run ( const BuildSnnGraph::Results &  store ) const

inline

Run the multi-level community detection algorithm on a shared nearest-neighbor graph constructed from knncolle::Base object.

Parameters

store

SNN graph built by BuildSnnGraph::run().

Returns

A Results object containing the clustering results for all cells.

run() [2/2]

Results scran::ClusterSnnGraphMultiLevel::run ( const igraph::Graph &  graph, const igraph_real_t *  weights  ) const

inline

Run the multi-level community detection algorithm on a pre-constructed shared nearest-neighbor graph as a Graph object.

Parameters

graph	An existing igraph::Graph object, typically built by BuildSnnGraph::Results::to_igraph().
weights	Pointer to an array of weights of length equal to the number of edges in graph.

Returns

A Results object containing the clustering results for all cells.

---

The documentation for this class was generated from the following file:

• scran/clustering/ClusterSnnGraph.hpp