NOTE: This repository is no longer actively maintained. To get the latest version or report issues please go to the fork at https://github.com/dpeerlab/phenograph.
PhenoGraph is a clustering method designed for high-dimensional single-cell data. It works by creating a graph ("network") representing phenotypic similarities between cells and then identifying communities in this graph.
This implementation is written in Python3 and depends only on scikit-learn (>= 0.17) and its dependencies.
This software package includes compiled binaries that run community detection based on C++ code written by E. Lefebvre and J.-L. Guillaume in 2008 ("Louvain method"). The code has been altered to interface more efficiently with the Python code here. It should work on reasonably current Linux, Mac and Windows machines.
To install PhenoGraph, simply run the setup script:
python3 setup.py installOr use:
pip3 install git+https://github.com/jacoblevine/phenograph.gitExpected use is within a script or interactive kernel running Python 3.x. Data are expected to be passed as a numpy.ndarray.
When applicable, the code uses CPU multicore parallelism via multiprocessing.
To run basic clustering:
import phenograph
communities, graph, Q = phenograph.cluster(data)For a dataset of N rows, communities will be a length N vector of integers specifying a community assignment for each row
in the data. Any rows assigned -1 were identified as outliers and should not be considered as a member of any community.
graph is a N x N scipy.sparse matrix representing the weighted graph used for community detection.
Q is the modularity score for communities as applied to graph.
If you use PhenoGraph in work you publish, please cite our publication:
@article{Levine_PhenoGraph_2015,
doi = {10.1016/j.cell.2015.05.047},
url = {http://dx.doi.org/10.1016/j.cell.2015.05.047},
year = {2015},
month = {jul},
publisher = {Elsevier {BV}},
volume = {162},
number = {1},
pages = {184--197},
author = {Jacob H. Levine and Erin F. Simonds and Sean C. Bendall and Kara L. Davis and El-ad D. Amir and Michelle D. Tadmor and Oren Litvin and Harris G. Fienberg and Astraea Jager and Eli R. Zunder and Rachel Finck and Amanda L. Gedman and Ina Radtke and James R. Downing and Dana Pe'er and Garry P. Nolan},
title = {Data-Driven Phenotypic Dissection of {AML} Reveals Progenitor-like Cells that Correlate with Prognosis},
journal = {Cell}
}cdist and multiprocessing. This may be more efficient than kdtree on very large high-dimensional data sets
and avoids memory issues that arise in sklearn's implementation.parallel_jaccard_kernel to remove unnecessary use of ctypes and multiprocessing.Array.louvain_time_limit a parameter to phenograph.cluster.phenograph.cluster can now take as input a square sparse matrix, which will be interpreted as a k-nearest neighbor graph.
Note that this graph must have uniform degree (i.e. the same value of k at every point).time_limit for Louvain iterations has been increased to a more generous 2000 seconds (~half hour).multiprocessing package is used.