Dependencies

• cellmaps_utils

• tqdm

• pandas

• numpy

• ndex2

• HiDeF

Compatibility

• Python 3.8 - 3.11

Installation

git clone https://github.com/idekerlab/cellmaps_generate_hierarchy
cd cellmaps_generate_hierarchy
pip install -r requirements_dev.txt
make dist
pip install dist/cellmaps_generate_hierarchy*whl

Run make command with no arguments to see other build/deploy options including creation of Docker image

make

Output:

clean                remove all build, test, coverage and Python artifacts
clean-build          remove build artifacts
clean-pyc            remove Python file artifacts
clean-test           remove test and coverage artifacts
lint                 check style with flake8
test                 run tests quickly with the default Python
test-all             run tests on every Python version with tox
coverage             check code coverage quickly with the default Python
docs                 generate Sphinx HTML documentation, including API docs
servedocs            compile the docs watching for changes
testrelease          package and upload a TEST release
release              package and upload a release
dist                 builds source and wheel package
install              install the package to the active Python's site-packages
dockerbuild          build docker image and store in local repository
dockerpush           push image to dockerhub

Before running tests, please install: pip install -r requirements_dev.txt.

For developers

# From base directory of this repo cellmaps_generate_hierarchy
pip uninstall cellmaps_generate_hierarchy -y ; make clean dist; pip install dist/cellmaps_generate_hierarchy*whl

Needed files

The output directory for co-embedding is required (see Cell Maps Coembedding).

Usage

For information invoke cellmaps_generate_hierarchycmd.py -h

Example usage

cellmaps_generate_hierarchycmd.py ./cellmaps_generate_hierarchy --coembedding_dirs ./cellmaps_coembedding_outdir

Coming soon...

Cite

If you find this tool useful, please cite:

Lenkiewicz, J., Churas, C., Hu, M., Qian, G., Jain, M., Levinson, M. A., … & Schaffer, L. V. (2025). Cell Mapping Toolkit: An end-to-end pipeline for mapping subcellular organization. Bioinformatics, 41(6), btaf205.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

0.3.0 (2026-07-15)

• Added --weighted_edgelist flag to enable generation of a single weighted edge list with cosine similarity values as a third column, instead of multiple cutoff-based edge lists. When this flag is set, only the first cutoff value from --ppi_cutoffs is used (defaults to parent cutoff if not specified), and the resulting edge list includes edge weights that can be utilized by HiDeF for hierarchy generation.

  • Added test suite for verifying weighted edgelist behavior.

0.2.5 (2025-10-08)

• Remove leading spaces from name of hierarchy.

0.2.4 (2025-05-15)

• Updated to PEP 517 compliant build system

0.2.3 (2025-03-19)

• Update requirements versions

• Increase timeout for cmd run

• Fix ‘k’ argument type

0.2.2 (2024-11-25)

• Added default argument for password.

0.2.1 (2024-11-08)

• Fixed types of arguments.

0.2.0 (2024-10-16)

• Added the --bootstrap_edges flag, which allows specifying the percentage of edges to be randomly removed from each PPI network (across networks at different PPI cutoffs).

• Added a style for proteins specified as bait.

• Refactored code and expose more methods for hierarchy generation from edgelists.

0.1.0 (2024-09-06)

• First release on PyPI.