Analysis reporting with Vuegen

Analysis reporting with Vuegen#

VueGen is a Python package that automates the creation of scientific reports.

With VueGen, users can produce reports by simply specifying a directory containing output files, such as plots, tables, networks, Markdown text, HTML components, and API calls, along with the report format. Supported formats include documents (PDF, HTML, DOCX, ODT), presentations (PPTX, Reveal.js), Jupyter notebooks, and Streamlit web applications.

In the GitHub workspace, we will use the base conda environment which you can activate with the following command:

Create a new virtual environment called vuegen and activate it:

python3 -m venv vuegen
source vuegen/bin/activate

Install the required packages#

  • vuegen for the report generation (developed by Henry Webel from DSP and Sebastian Ayala and Alberto Santos from MoNA at DTU Biosustain)

pip install vuegen

VueGen Report#

We saved some of the analyses (plots and tables) from the R markdown to results/report folder.

You can use the following command to generate a VueGen report from them:

vuegen -dir scripts/Tutorial/results/report

This will create a streamlit app in the streamlit_report folder. Check the options availble for the command line tool vuegen with the following command:

vuegen -h

Create and start the streamlit app with the following command:

vuegen -dir scripts/Tutorial/results/report -st_autorun

Further information about VueGen#

If you are interested to know more about VueGen and use it for your own research projects, check out some tutorials in youtube tutorials on youtube, and also our biorxiv paper

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