cellmaps-coembedding 0.3.1

A tool to generate coembeddings from IF image embeddings and PPI network embeddings

Cell Maps CoEmbedder

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.

Dependencies

• cellmaps_utils

• phenograph

• numpy

• torch

• pandas

• matplotlib

• dill

• tqdm

Compatibility

• Python 3.8+

Installation

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.

For developers

To deploy development versions of this package

Below are steps to make changes to this code base, deploy, and then run against those changes.

1. Make changes

   Modify code in this repo as desired

2. 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

Needed files

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.

Usage

For information invoke cellmaps_coembeddingcmd.py -h

Example usage

cellmaps_coembeddingcmd.py ./cellmaps_coembedding_outdir --embeddings ./cellmaps_image_embedding_outdir ./cellmaps_ppi_embedding_outdir

Via Docker

Example usage

Coming soon...

Credits

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

History

0.3.1 (2024-09-13)

• Bug fix: raise more informative error when no embeddings overlap.

0.3.0 (2024-09-06)

• Added --provenance flag to pass a path to json file with provenance information. This removes the necessity of input directory to be an RO-Crate.

0.2.0 (2024-07-17)

• Added a new coembedding algorithm accessible via flag --algorithm auto. This algorithm utilizes neural networks to generate latent embeddings, optimizing both reconstruction and triplet losses to improve embedding accuracy by learning intra- and inter-modality relationships.

0.1.0 (2024-02-12)

• First release on PyPI.