dynamicTreeCut 0.1.1

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