lmcinnes/hypertools

A python toolbox for gaining geometric insights into high-dimensional data

"To deal with hyper-planes in a 14 dimensional space, visualize a 3D space and say 'fourteen' very loudly. Everyone does it." - Geoff Hinton

Overview

HyperTools is designed to facilitate dimensionality reduction-based visual explorations of high-dimensional data. The basic pipeline is to feed in a high-dimensional dataset (or a series of high-dimensional datasets) and, in a single function call, reduce the dimensionality of the dataset(s) and create a plot. The package is built atop many familiar friends, including matplotlib, scikit-learn and seaborn. Our package was recently featured on Kaggle's No Free Hunch blog.

Try it!

Click the badge to launch a binder instance with example uses:

or

Check the repo of Jupyter notebooks from the HyperTools paper.

Installation

To install the latest stable version run:

pip install hypertools

To install the latest unstable version directly from GitHub, run:

pip install -U git+https://github.com/ContextLab/hypertools.git

Or alternatively, clone the repository to your local machine:

git clone https://github.com/ContextLab/hypertools.git

Then, navigate to the folder and type:

pip install -e .

(These instructions assume that you have pip installed on your system)

Requirements

• python 2.7, 3.4+
• PPCA>=0.0.2
• scikit-learn>=0.18.1
• pandas>=0.18.0
• seaborn>=0.8.1
• matplotlib>=1.5.1
• scipy>=0.17.1
• numpy>=1.10.4
• future
• requests
• deepdish
• pytest (for development)
• ffmpeg (for saving animations)

If installing from github (instead of pip), you must also install the requirements: pip install -r requirements.txt

Documentation

Check out our readthedocs page for further documentation, complete API details, and additional examples.

Citing

We wrote a paper about HyperTools, which you can read here. We also have a repo with example notebooks from the paper here.

Please cite as:

Heusser AC, Ziman K, Owen LLW, Manning JR (2017) HyperTools: A Python toolbox for visualizing and manipulating high-dimensional data. arXiv: 1701.08290

Here is a bibtex formatted reference:

@ARTICLE {,
    author  = "A C Heusser and K Ziman and L L W Owen and J R Manning",
    title   = "HyperTools: A Python toolbox for visualizing and manipulating high-dimensional data",
    journal = "arXiv",
    year    = "2017",
    volume  = "1701",
    number  = "08290",
    month   = "jan"
}

Contributing

If you'd like to contribute, please first read our Code of Conduct.

For specific information on how to contribute to the project, please see our Contributing page.

Testing

To test HyperTools, install pytest (pip install pytest) and run pytest in the HyperTools folder

Examples

See here for more examples.

Plot

import hypertools as hyp
hyp.plot(list_of_arrays, '.', group=list_of_labels)

Align

import hypertools as hyp
hyp.plot(list_of_arrays, align='hyper')

BEFORE

AFTER

Cluster

import hypertools as hyp
hyp.plot(array, '.', n_clusters=10)

Describe

import hypertools as hyp
hyp.tools.describe(list_of_arrays, reduce='PCA', max_dims=14)