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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
To install, it's best to create an environment after installing and downloading the
Anaconda Python Distribution <https://www.continuum.io/downloads>
__
conda env create --file environment.yml
PyPI install, presuming you have all its requirements (numpy and scipy) installed::
pip install dynamicTreeCut
::
>>> 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
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
dynamicTreeCut is available under the GPL-3 License