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A package for automatic clustering hyperparameter optmization

Project description

Hypercluster

A package for clustering optimization with sklearn.

Requirements:

pandas
numpy
scipy
matplotlib
seaborn
scikit-learn
hdbscan

Optional: snakemake

Install

With pip:

pip install hypercluster

or with conda:

conda install hypercluster
# or
conda install -c conda-forge -c bioconda hypercluster

If you are having problems installing with conda, try changing your channel priority. Priority of conda-forge > bioconda > defaults is recommended. To check channel priority: conda config --get channels It should look like:

--add channels 'defaults'   # lowest priority
--add channels 'bioconda'
--add channels 'conda-forge'   # highest priority

If it doesn't look like that, try:

conda config --add channels bioconda
conda config --add channels conda-forge

Docs

https://hypercluster.readthedocs.io/en/latest/index.html

It will also be useful to check out sklearn's page on clustering and evaluation metrics

Examples

https://github.com/liliblu/hypercluster/tree/dev/examples

Quickstart with SnakeMake

Default config.yml and hypercluster.smk are in the snakemake repo above.
Edit the config.yml file or arguments.

snakemake -s hypercluster.smk --configfile config.yml --config input_data_files=test_data input_data_folder=. 

Example editing with python:

import yaml

with open('config.yml', 'r') as fh:
    config = yaml.load(fh)

input_data_prefix = 'test_data'
config['input_data_folder'] = os.path.abspath('.')
config['input_data_files'] = [input_data_prefix]
config['read_csv_kwargs'] = {input_data_prefix:{'index_col': [0]}}

with open('config.yml', 'w') as fh:
    yaml.dump(config, stream=fh)

Then call snakemake.

snakemake -s hypercluster.smk

Or submit the snakemake scheduler as an sbatch job e.g. with BigPurple Slurm:

module add slurm
sbatch snakemake_submit.sh

Examples for snakemake_submit.sh and cluster.json is in the scRNA-seq example.

Quickstart with python

import pandas as pd
from sklearn.datasets import make_blobs
import hypercluster

data, labels = make_blobs()
data = pd.DataFrame(data)
labels = pd.Series(labels, index=data.index, name='labels')

# With a single clustering algorithm
clusterer = hypercluster.AutoClusterer()
clusterer.fit(data).evaluate(
  methods = hypercluster.constants.need_ground_truth+hypercluster.constants.inherent_metrics, 
  gold_standard = labels
  )

clusterer.visualize_evaluations()

# With a range of algorithms

clusterer = hypercluster.MultiAutoClusterer()
clusterer.fit(data).evaluate(
  methods = hypercluster.constants.need_ground_truth+hypercluster.constants.inherent_metrics, 
  gold_standard = labels
  )

clusterer.visualize_evaluations()

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