ClusterAnalyzer Class Reference

Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's) More...

#include <OpenMS/COMPARISON/CLUSTERING/ClusterAnalyzer.h>

Public Member Functions
	ClusterAnalyzer ()
	default constructor More...
	ClusterAnalyzer (const ClusterAnalyzer &source)
	copy constructor More...
virtual	~ClusterAnalyzer ()
	destructor More...
std::vector< float >	averageSilhouetteWidth (const std::vector< BinaryTreeNode > &tree, const DistanceMatrix< float > &original)
	Method to calculate the average silhouette widths for a clustering. More...
std::vector< float >	dunnIndices (const std::vector< BinaryTreeNode > &tree, const DistanceMatrix< float > &original, const bool tree_from_singlelinkage=false)
	Method to calculate Dunns indices for a clustering. More...
std::vector< float >	cohesion (const std::vector< std::vector< Size > > &clusters, const DistanceMatrix< float > &original)
	Method to calculate the cohesions of a certain partition. More...
float	averagePopulationAberration (Size cluster_quantity, std::vector< BinaryTreeNode > &tree)
	Method to calculate the average aberration from average population in partition resulting from a certain step in clustering. More...
void	cut (const Size cluster_quantity, const std::vector< BinaryTreeNode > &tree, std::vector< std::vector< Size > > &clusters)
	Method to calculate a partition resulting from a certain step in clustering given by the number of clusters. More...
void	cut (const Size cluster_quantity, const std::vector< BinaryTreeNode > &tree, std::vector< std::vector< BinaryTreeNode > > &subtrees)
	Method to calculate subtrees from a given tree resulting from a certain step in clustering given by the number of clusters. More...
String	newickTree (const std::vector< BinaryTreeNode > &tree, const bool include_distance=false)
	Returns the hierarchy described by a clustering tree as Newick-String. More...

Private Member Functions
ClusterAnalyzer &	operator= (const ClusterAnalyzer &source)
	assignment operator More...

Detailed Description

Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's)

Constructor & Destructor Documentation

ClusterAnalyzer() [1/2]

ClusterAnalyzer

(

)

default constructor

ClusterAnalyzer() [2/2]

ClusterAnalyzer

(

const ClusterAnalyzer &

source

)

copy constructor

~ClusterAnalyzer()

virtual ~ClusterAnalyzer ( )

virtual

destructor

Member Function Documentation

averagePopulationAberration()

float averagePopulationAberration	(	Size	cluster_quantity,
		std::vector< BinaryTreeNode > &	tree
	)

Method to calculate the average aberration from average population in partition resulting from a certain step in clustering.

Parameters

cluster_quantity	desired partition Size analogue to ClusterAnalyzer::cut
tree	vector of BinaryTreeNode's representing the clustering

Exceptions

invalid_parameter

if desired clustering is invalid

Returns

the average aberration from the average cluster population (number of elements/cluster_quantity) at cluster_quantity

See also

BinaryTreeNode

averageSilhouetteWidth()

std::vector<float> averageSilhouetteWidth	(	const std::vector< BinaryTreeNode > &	tree,
		const DistanceMatrix< float > &	original
	)

Method to calculate the average silhouette widths for a clustering.

Parameters

tree	vector of BinaryTreeNode's representing the clustering
original	DistanceMatrix for all clustered elements started from

Returns

a vector filled with the average silhouette widths for each cluster step

The average silhouette width will be calculated for each clustering step beginning with the first step(n-1 cluster) ending with the last (1 cluster, average silhouette width is 0 by definition).

See also

BinaryTreeNode

cohesion()

std::vector<float> cohesion	(	const std::vector< std::vector< Size > > &	clusters,
		const DistanceMatrix< float > &	original
	)

Method to calculate the cohesions of a certain partition.

Parameters

clusters	vector of vectors holding the clusters (with indices to the actual elements)
original	DistanceMatrix for all clustered elements started from

Returns

a vector that holds the cohesions of each cluster given with clusters (order corresponds to clusters)

cut() [1/2]

void cut	(	const Size	cluster_quantity,
		const std::vector< BinaryTreeNode > &	tree,
		std::vector< std::vector< BinaryTreeNode > > &	subtrees
	)

Method to calculate subtrees from a given tree resulting from a certain step in clustering given by the number of clusters.

Parameters

cluster_quantity	Size giving the number of clusters (i.e. starting elements - cluster_quantity = cluster step)
tree	vector of BinaryTreeNode's representing the clustering
subtrees	vector of trees holding the trees, tree is composed of cut at given size

Exceptions

invalid_parameter

if desired clusterstep is invalid

See also

BinaryTreeNode

after call of this method the argument clusters is filled corresponding to the given cluster_quantity with the indices of the elements clustered

cut() [2/2]

void cut	(	const Size	cluster_quantity,
		const std::vector< BinaryTreeNode > &	tree,
		std::vector< std::vector< Size > > &	clusters
	)

Method to calculate a partition resulting from a certain step in clustering given by the number of clusters.

If you want to fetch all clusters which were created with a threshold, you simply count the number of tree-nodes which are not -1, and subtract that from the number of leaves, to get the number of clusters formed , i.e. cluster_quantity = data.size() - real_leaf_count;

Parameters

cluster_quantity	Size giving the number of clusters (i.e. starting elements - cluster_quantity = cluster step)
tree	vector of BinaryTreeNode's representing the clustering
clusters	vector of vectors holding the clusters (with indices to the actual elements)

Exceptions

invalid_parameter

if desired clusterstep is invalid

See also

BinaryTreeNode

after call of this method the argument clusters is filled corresponding to the given cluster_quantity with the indices of the elements clustered

Referenced by SpectraMerger::mergeSpectraPrecursors().

dunnIndices()

std::vector<float> dunnIndices	(	const std::vector< BinaryTreeNode > &	tree,
		const DistanceMatrix< float > &	original,
		const bool	tree_from_singlelinkage = false
	)

Method to calculate Dunns indices for a clustering.

Parameters

tree	vector of BinaryTreeNode's representing the clustering
original	DistanceMatrix for all clustered elements started from
tree_from_singlelinkage	true if tree was created by SingleLinkage, i.e. the distances are the minimal distances in increasing order and can be used to speed up the calculation

See also

BinaryTreeNode

newickTree()

String newickTree	(	const std::vector< BinaryTreeNode > &	tree,
		const bool	include_distance = false
	)

Returns the hierarchy described by a clustering tree as Newick-String.

Parameters

tree	vector of BinaryTreeNode's representing the clustering
include_distance	bool value indicating whether the distance shall be included to the string

See also

BinaryTreeNode

operator=()

ClusterAnalyzer& operator= ( const ClusterAnalyzer &  source )

private

assignment operator