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 install

Or use:

pip3 install git+https://github.com/jacoblevine/phenograph.git

Expected 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 paper:

@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}
}