hclust

hclust

Package for performing agglomerative hierarchical clustering in Golang.

Methods

Distance matrices can be calculated using the binary, Canberra, Euclidean, Jaccard, Manhattan or maximum metrics. The linkage methods available are: average, centroid, complete, McQuitty, median, single and Ward. The linkage method algorithms used are as recommended in Müllner. Briefly, the single method is implemented using MST, the average, complete, McQuitty and Ward methods are implemented using the nearest-neighbor chain algorithm and the centroid and median methods are implemented using the generic algorithm. Leaf optimization is performed using the improved optimization approach of Bar-Jospeh, et al.

Installation

go get github.com/knightjdr/hclust

Usage

import "github.com/knightjdr/hclust"

Distance

Setting the transpose argument to true will calculate distances between columns as apposed to rows. Euclidean distances will be calculated if an invalid metric is supplied. Valid metric values are: binary, canberra, euclidean, jaccard, manhattan or maximum.

hclust.Distance(matrix [][]float64, metric string, transpose bool) (dist [][]float64)

Cluster

Cluster requires a symmetric distance matrix and a linkage method. It will return a dendrogram with each element in the dendrogram corresponding to a node containing the leafs/subnodes and the length of the branches to the leafs/subnodes. Valid linkage values are: average, centroid, complete, mcquitty, median, single and ward.

type SubCluster struct {
	Leafa   int
	Leafb   int
	Lengtha float64
	Lengthb float64
	Node    int
}

hclust.Cluster(matrix [][]float64, method string) (dendrogram Dendrogram, err error)

Optimize

Optimize takes the dendrogram produced by hclust.Cluster and the distance matrix produced by hclust.Distance and optimizes the leaf ordering. The dendrogram from hclust.Cluster should be input as produced by that method without any modifications.

The running time will be at worst O(n⁴) with the optimzation approach of Bar-Jospeh. Certain (typically very large) datasets, and particular combinations of distance metric and linkage method can produce balanced nodes that require a huge number of comparisons to determine the optimal order. At these nodes the benefit of optimization is low and you can use the ignore argument to skip optimization for them.

To optimize every node in the tree, set the ignore argument to 0. Otherwise set the argument to the number of comparisons beyond which you wish to skip optimization. For example, nodes with 500 leaves on each side could require up to 250 000 test comparisons, so setting the ignore argument to 250 000 will skip these and larger nodes. The ordering that will be used at skipped nodes is the best ordering generated thus far.

The best practice is to run the optimization algorithm optimizing every node and if the run time is too long, adjust this value until an acceptable run time is reached.

hclust.Optimize(dendrogram Dendrogram, dist [][]float64, ignore int) (optimized Dendrogram)

Tree

Tree takes the dendrogram produced by hclust.Cluster or hclust.Optimize and a list of names for the leaves and generates a newick tree. It also returns the names vector sorted based on the clustering order. The input names vector should be in the same order as the rows/columns of the starting matrix/table used for generating the distance matrix. For example, if you are generating a distance matrix between rows of a matrix and those rows are ordered as:

then the names vector should be []string{"rowA", "rowB", "rowC"}.

The dendrogram from hclust.Cluster or hclust.Optimize should be input as produced by those methods without any modifications.

type TreeLayout struct {
	Newick     string
	Order      []string
}

hclust.Tree(dendrogram Dendrogram, names []string) (tree TreeLayout, err error)

Sort

The hclust.Sort method can be used to sort the original data matrix that was input to hclust.Distance based on the clustering order. The method requires a vector containing the names of the rows/columns in their original order and a vector with the sorted order. The sorted order can be obtained from the hclust.Tree method. The dim argument must be one of "column" or "row". To sort a matrix by both column and row, simply call this method twice (once for columns and once for rows).

hclust.Sort(matrix [][]float64, names, sortOrder []string, dim string) (sorted [][]float64, err error)

Benchmarks

Benchmarking tests were performed using a single core on a 3.7 GHz Quad-Core Intel Xeon E5 processor with 32 GB RAM.

Distance matrix benchmarks were measured using an input table with 4157 rows and 199 columns, with the distances calculated between rows.

Clustering benchmarks were measured using a symmetric distance matrix with dimensions 4157×4157.

The Leaf optimization benchmark was measured using a dendrogram with 4157 leafs (4156 internal nodes).

Tests

go test

© 2018 James Knight.