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https://github.com/ismms-himc/clustergrammer2
"Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.
https://github.com/ismms-himc/clustergrammer2
binder binder-ready biology hacktoberfest heatmap javascript jupyter-widgets python regl visualization webgl
Last synced: 16 days ago
JSON representation
"Dimensionality-increasing" data visualization tool and interactive WebGL Jupyter widget built for single-cell data.
- Host: GitHub
- URL: https://github.com/ismms-himc/clustergrammer2
- Owner: ismms-himc
- License: mit
- Created: 2018-04-10T17:11:47.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2022-12-30T20:26:28.000Z (almost 2 years ago)
- Last Synced: 2024-10-15T18:00:25.672Z (about 1 month ago)
- Topics: binder, binder-ready, biology, hacktoberfest, heatmap, javascript, jupyter-widgets, python, regl, visualization, webgl
- Language: HTML
- Homepage: https://clustergrammer.readthedocs.io/case_studies.html
- Size: 70 MB
- Stars: 115
- Watchers: 4
- Forks: 20
- Open Issues: 57
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE.txt
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
- awesome-jupyter-widgets - clustergrammer2 - "Dimensionality-increasing" data visualization tool for single-cell data (Interactive Widgets / Interactive Jupyter Widget Ecosystem)
- awesome-single-cell - Clustergrammer2 - [Python, JavaScript] - Interative WebGL web-based heatmap for visualizing and analyzing single-cell high-dimensional and location-based biological data. Clustergrammer can be used within a Jupyter notebook as an interative widget that can be shared using GitHub and NBviewer, see [case studies](https://clustergrammer.readthedocs.io/case_studies.html). (Software packages / RNA-seq)
README
[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?urlpath=lab)
[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2_examples/master?filepath=notebooks%2F2.0_CCLE_Gene_Expression.ipynb)
Clustergrammer2 is an interactive heatmap Jupyter widget built using the [widget-ts-cookiecutter](https://github.com/jupyter-widgets/widget-ts-cookiecutter) library and the WebGL library [regl](https://github.com/regl-project/regl). Clustergrammer2 is built to help researchers interactively explore single cell data (e.g. scRNA-seq). Please see [Case Studies and Tutorials](https://clustergrammer.readthedocs.io/case_studies.html) for examples.
# Clustergrammer2 Examples
### Basic Example of Running Clustergrammer2 on MyBinder
[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F1.0_Running_Clustergrammer2.ipynb) [](https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/1.0_Running_Clustergrammer2.ipynb)
[](http://www.youtube.com/watch?v=UgO5LLvcfB0)
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](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2_examples/master?urlpath=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:
* [Case Studies and Tutorials](https://clustergrammer.readthedocs.io/case_studies.html)
* [Clustergrammer2-Notebooks](https://github.com/ismms-himc/clustergrammer2-notebooks) GitHub repository
### 2,700 PBMC scRNA-seq
[](https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F3.0_2700_PBMC_scRNA-seq.ipynb) [](https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/3.0_2700_PBMC_scRNA-seq.ipynb?flush_cache=true)
[](http://www.youtube.com/watch?v=BEPspcC7vIY)
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](https://www.10xgenomics.com/resources/datasets/). Bulk gene expression signatures of cell types from [CIBERSORT](https://cibersort.stanford.edu/) were used to obtain a tentative cell type for each cell. Please see the video tutorial above for more information.
# Clustergrammer2 Roadmap
Please see the project [Roadmap](https://github.com/ismms-himc/clustergrammer2/blob/master/ROADMAP.md) for information on where the project is heading.
# Installation
A typical installation requires the following commands to be run:
```bash
pip install clustergrammer2
jupyter nbextension install --py --sys-prefix clustergrammer2
jupyter nbextension enable --py --sys-prefix clustergrammer2
```
Optionally: --sys-prefix|--user|--system
Or, if you use jupyterlab:
```bash
pip install clustergrammer2
jupyter labextension install @jupyter-widgets/jupyterlab-manager
```
### Embedding the widget into static HTML Notebooks
```bash
jupyter nbconvert --to html notebook.ipynb
```
# Development
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).
#### Updating versions
Update the versions in the following files
##### JavaScript
* package.json
* widget.ts
#### Python
* _version.py
* example.py
* requirements.txt
* _frontend.py
#### Webpack
Run the following commands to build the JavaScript bundle:
```bash
npm run build
npm run build:nbextension
npm run build:labextension
```
Publish to npm using
```bash
npm publish
```
These instructions are based on the release instructions from the [jupyter-widgets/widget-ts-cookiecutterREADME](https://github.com/jupyter-widgets/widget-ts-cookiecutter).
### Bundling the Python Package
Next, bundle the python package using (optinally delete the old versions under `dist`)
```bash
python setup.py sdist bdist_wheel
```
Then, upload the PYPI:
```bash
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)
- https://pypi.org/project/clustergrammer2/
### Check HTML Embedding
- Run `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, like https://unpkg.com/[email protected]/dist/index.js)
- 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=True` in the URL to ensure that NBVIewer re-runs nbconvert.
### Check Cloud Services
- Check MyBinder
### Note for Sublime Development
Use this in the where section to restrict search
```
clustergrammer2/*.py,-*/build/*
```
# Contact
For issues and concerns please use the [issue tracker](https://github.com/ismms-himc/clustergrammer2/issues) or [gitter](https://gitter.im/clustergrammer2) discussion room.