A Cytoscape widget for Jupyter
A widget enabling interactive graph visualization with cytoscape.js in JupyterLab and the Jupyter notebook.
Try it out using binder: or install and try out the examples.
- Conversion from NetworkX see example1, example2
- Conversion from Pandas DataFrame see example
- Conversion from neo4j see example
mamba install -c conda-forge ipycytoscape
conda install -c conda-forge ipycytoscape
pip install ipycytoscape
You can install the Pandas dependencies for
ipycytoscape with pip:
pip install pandas
mamba install pandas
You can install the neo4j dependencies for
ipycytoscape with pip:
pip install -e ".[neo4j]"
mamba install py2neo neotime
For jupyterlab 1.x or 2.x:
If you are using JupyterLab 1.x or 2.x then you will also need to install
nodejs and the
jupyterlab-manager extension. You can do this like so:
# installing nodejs conda install -c conda-forge nodejs # install jupyterlab-manager extension jupyter labextension install @firstname.lastname@example.org --no-build # if you have previously installed the manager you still to run jupyter lab build jupyter lab build
For Jupyter Notebook 5.2 and earlier
You may also need to manually enable the nbextension:
jupyter nbextension enable --py [--sys-prefix|--user|--system] ipycytoscape
For a development installation:
While not required, we recommend creating a conda environment to work in:
conda create -n ipycytoscape -c conda-forge jupyterlab nodejs conda activate ipycytoscape # clone repo git clone https://github.com/cytoscape/ipycytoscape.git cd ipycytoscape
Install python package for development
run npm install and
npm run build.
This command will also install the test suite and the docs locally:
pip install jupyter_packaging==0.7.9 pip install -e ".[test, docs]" jupyter labextension develop . --overwrite
optionally install the pre-commit hooks with:
Or for classic notebook, you can run:
jupyter nbextension install --sys-prefix --symlink --overwrite --py ipycytoscape jupyter nbextension enable --sys-prefix --py ipycytoscape
Note that the
--symlink flag doesn't work on Windows, so you will here have to run
install command every time that you rebuild your extension. For certain installations
you might also need another flag instead of
--sys-prefix, but we won't cover the meaning
of those flags here.
How to see your changes
To continuously monitor the project for changes and automatically trigger a rebuild, start watching the ipycytoscape code:
npm run watch
And in a separate terminal start JupyterLab normally:
once the webpack rebuild finishes refresh the JupyterLab page to have your changes take effect.
If you make a change to the python code then you need to restart the notebook kernel to have it take effect.
How to run tests locally
Install necessary dependencies with pip:
pip install -e ".[test]"
Or with conda/mamba:
mamba -c conda-forge install networkx pandas nbval pytest
And to run it:
How to build the docs
conda env update --file doc_environment.yml
And build them:
The ipycytoscape project was started by Mariana Meireles at QuantStack. This initial development was funded as part of the PLASMA project, which is led by Claire Vandiedonck, Pierre Poulain, and Sandrine Caburet.
We use a shared copyright model that enables all contributors to maintain the copyright on their contributions.
This software is licensed under the BSD-3-Clause license. See the LICENSE file for details.
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