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.
