Visualize global properties of large RNAs using force-directed layout from GraphViz.
- Hannah Wayment-Steele
- Credit to utils from Rhiju Das' ToyFold-1D code. Above: MS2 bacteriophage genome structure, colored by prob(unpaired), calculated in EternaFold.
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
pip install, as noted here.
examples.ipynb for example usage.