Clustergrammer2 is an interactive heatmap Jupyter widget built using the widget-ts-cookiecutter library and the WebGL library regl. Clustergrammer2 is built to help researchers interactively explore single cell data (e.g. scRNA-seq). Please see Case Studies and Tutorials for examples.
Basic Example of Running Clustergrammer2 on MyBinder
The above notebook shows how Clustergrammer2 can be used to load a small dataset and visualize a large random DataFrame. By running the notebook on MyBinder using Jupyter Lab it can also be used to visualize a user uploaded dataset. Please see the video tutorial above for more information.
For additional examples and tutorials please see:
2,700 PBMC scRNA-seq
Single cell RNA-seq (scRNA-seq) is a powerful method to interrogate gene expression across thousands of single cells. This method produces thousands of measurements (single cells) across thousands of dimensions (genes). This notebook uses Clustergrammer2 to interactively explore an example dataset measuring the gene expression of 2,700 PBMCs obtained from 10X Genomics. Bulk gene expression signatures of cell types from CIBERSORT were used to obtain a tentative cell type for each cell. Please see the video tutorial above for more information.
A typical installation requires the following commands to be run:
pip install clustergrammer2 jupyter nbextension enable --py --sys-prefix clustergrammer2
Or, if you use jupyterlab:
pip install clustergrammer2 jupyter labextension install @jupyter-widgets/jupyterlab-manager
Embedding the widget into static HTML Notebooks
jupyter nbconvert --to html notebook.ipynb
During development run
npm run watch for real time updates. When releasing a new version, first confirm that latest version of the front and back ends are working locally (check console logs, etc).
Update the versions in the following files
npm run build npm run build:nbextension npm run build:labextension
Publish to npm using
These instructions are based on the release instructions from the jupyter-widgets/widget-ts-cookiecutterREADME.
Bundling the Python Package
Next, bundle the python package using
python setup.py sdist bdist_wheel
Then, upload the PYPI:
twine upload dist/*
Checklist after release
After releasing a new version several things need to be checked to ensure proper widget functioning.
Check Package Managers
- https://www.npmjs.com/package/clustergrammer2 (can be slow to update)
Check HTML Embedding
jupyter nbconvert --to html introduction_nb.ipynb(from the examples directory) to generate a static HTML and check that the latest widget is working (uses unpkg.com)
- Check NBViewer using link to notebook on GitHub (e.g. https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2/blob/master/examples/introduction_nb.ipynb?flush_cache=true). Make sure to use the querystring
flush_cache=Truein the URL to ensure that NBVIewer re-runs nbconvert.
Check Cloud Services
- Check MyBinder
- Check Kaggle (re-install clustergrammer2)