RiboGraphViz

Visualize global properties of large RNAs using force-directed layout from GraphViz.

Authors:

• Hannah Wayment-Steele
• Credit to utils from Rhiju Das' ToyFold-1D code. Above: MS2 bacteriophage genome structure, colored by prob(unpaired), calculated in EternaFold.

Below: Visualizing the MFE structure and p(unpaired) of an mRNA for eGFP at increasing temperatures in Vienna.

Note: Not intended for detailed layouts -- loops may switch orientation in z-axis.

To set up:

sudo pip install -r requirements.txt
sudo python setup.py install

You'll need to use Python3; Python2 won't work.

Tips for Mac users: if you're stuck with Python 2, setting up a virtual environment (e.g., with conda environment) to install Python3 might be a good choice. You may also need to install pygraphviz -- which does not work with conda, but does work with brew and pip install, as noted here.

See examples.ipynb for example usage.

Below: Vienna MFE structures of 20 randomly-generated RNAs.