Python translation of the hybrid dynamicTreeCut method created by Peter Langfelder and Bin Zhang.

dynamicTreeCut was originally published by in Bioinformatics:

Langfelder P, Zhang B, Horvath S (2007) Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 2008 24(5):719-720

dynamicTreeCut R code is distributed under the GPL-3 License and original sources should be cited.

dynamicTreeCut contains methods for detection of clusters in hierarchical clustering dendrograms. NOTE: though the clusters match the R output, the cluster names are shuffled

Installing

To install, it's best to create an environment after installing and downloading the Anaconda Python Distribution

conda env create --file environment.yml

PyPI install, presuming you have all its requirements (numpy and scipy) installed:

pip install dynamicTreeCut

Importation

>>> from dynamicTreeCut import cutreeHybrid
>>> from scipy.spatial.distance import pdist
>>> import numpy as np
>>> from scipy.cluster.hierarchy import linkage
>>> d = np.transpose(np.arange(1,10001).reshape(100,100))
>>> distances = pdist(d, "euclidean")
>>> link = linkage(distances, "average")
>>> clusters = cutreeHybrid(link, distances)
..cutHeight not given, setting it to 495.1  ===>  99% of the (truncated) height range in dendro.
..done.
>>> clusters["labels"]
[2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3
 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 1 1 1 1 1 1 1 1 1 1
 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1]

Compared to R:

> library(dynamicTreeCut)
> d = matrix(1:10000, 100)
> distances <- dist(d, method="euclidean")
> dendro <- hclust(distances, method="average")
> clusters <- cutreeDynamic(dendro, distM=as.matrix(distances))
  ..cutHeight not given, setting it to 495  ===>  99% of the (truncated) height range in dendro.
  ..done.
> clusters
  [1] 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3
  [38] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 1 1 1 1 1 1 1 1 1 1
  [75] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

Installation

If you dont already have numpy and scipy installed, it is best to download Anaconda, a python distribution that has them included.

https://continuum.io/downloads

Dependencies can be installed by:

pip install -r requirements.txt

License

dynamicTreeCut is available under the GPL-3 License