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https://github.com/dev-ev/ms-interactive-viz
Customizable and informative mass spectra with Bokeh
https://github.com/dev-ev/ms-interactive-viz
bokeh interactive-visualizations mass-spectrometry proteomics visualization
Last synced: about 4 hours ago
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Customizable and informative mass spectra with Bokeh
- Host: GitHub
- URL: https://github.com/dev-ev/ms-interactive-viz
- Owner: dev-ev
- License: mit
- Created: 2021-05-02T19:43:59.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2022-03-19T19:57:00.000Z (over 2 years ago)
- Last Synced: 2023-10-20T06:36:15.461Z (about 1 year ago)
- Topics: bokeh, interactive-visualizations, mass-spectrometry, proteomics, visualization
- Language: Jupyter Notebook
- Homepage:
- Size: 416 KB
- Stars: 5
- Watchers: 1
- Forks: 2
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# ms-interactive-viz
### Customizable and informative mass spectra with Bokeh
The notebook was created on Ubuntu 20.04 with Python 3.8.5, Bokeh 2.3.1 and JupyterLab 3.0.14.
Standalone Bokeh visualizations can be saved as html files and displayed in a web browser. To display the plots in the notebook, we need to install the extension first:
pip install jupyter_bokeh
or
conda install jupyter_bokeh
With the extension in place, call the Bokeh function output_notebook(), and the plots should become embedded. Note that installing the extension via pip is a relatively new feature as of May 2021, so make sure that your versions of Bokeh and JupyterLab are at least not older than 2.3.1 and 3.0.14, respectively.
Download the notebook and run on your machine to display the plots. All of the code from the notebook is also saved in a text script file for convenience. If you just want to check out how a resulting visualization looks, an annotated interactive mass spectrum has been saved as a standalone html file, feel free to download it and open with Firefox, Google Chrome or new Microsoft Edge (Chromium-based).