The Cell Maps CoEmbedding is part of the Cell Mapping Toolkit
Creates Coembedding from Cell Maps ImmunoFluorscent Image Embedder and Cell Maps PPI Embedder using an implementation of MUSE
- Free software: MIT license
- Documentation: https://cellmaps-coembedding.readthedocs.io.
- Python 3.8+
git clone https://github.com/idekerlab/cellmaps_coembedding cd cellmaps_coembedding make dist pip install dist/cellmaps_coembedding*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.
Below are steps to make changes to this code base, deploy, and then run against those changes.
Make changes
Modify code in this repo as desired
Build and deploy
# From base directory of this repo cellmaps_coembedding pip uninstall cellmaps_coembedding -y ; make clean dist; pip install dist/cellmaps_coembedding*whl
The output directories for the image embeddings (see Cell Maps Image Embedding) and protein-protein interaction network embeddings (see Cell Maps PPI Embedding) are required.
For information invoke cellmaps_coembeddingcmd.py -h
Example usage
cellmaps_coembeddingcmd.py ./cellmaps_coembedding_outdir --embeddings ./cellmaps_image_embedding_outdir ./cellmaps_ppi_embedding_outdir
Example usage
Coming soon...
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.