35 #ifndef OPENMS_COMPARISON_CLUSTERING_CLUSTERANALYZER_H 36 #define OPENMS_COMPARISON_CLUSTERING_CLUSTERANALYZER_H 74 std::vector<float> averageSilhouetteWidth(
const std::vector<BinaryTreeNode> & tree,
const DistanceMatrix<float> & original);
84 std::vector<float> dunnIndices(
const std::vector<BinaryTreeNode> & tree,
const DistanceMatrix<float> & original,
const bool tree_from_singlelinkage =
false);
93 std::vector<float> cohesion(
const std::vector<std::vector<Size> > & clusters,
const DistanceMatrix<float> & original);
104 float averagePopulationAberration(
Size cluster_quantity, std::vector<BinaryTreeNode> & tree);
121 void cut(
const Size cluster_quantity,
const std::vector<BinaryTreeNode> & tree, std::vector<std::vector<Size> > & clusters);
134 void cut(
const Size cluster_quantity,
const std::vector<BinaryTreeNode> & tree, std::vector<std::vector<BinaryTreeNode> > & subtrees);
144 String newickTree(
const std::vector<BinaryTreeNode> & tree,
const bool include_distance =
false);
155 #endif //OPENMS_COMPARISON_CLUSTERING_CLUSTERANALYZER_H A more convenient string class.
Definition: String.h:57
Bundles analyzing tools for a clustering (given as sequence of BinaryTreeNode's)
Definition: ClusterAnalyzer.h:52
A two-dimensional distance matrix, similar to OpenMS::Matrix.
Definition: DistanceMatrix.h:68
bool compareBinaryTreeNode(const BinaryTreeNode &x, const BinaryTreeNode &y)
returns the value of (x.distance < y.distance) for use with sort
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
Elements of a binary tree used to represent a hierarchical clustering process.
Definition: BinaryTreeNode.h:49