Preventing Overlap Of Edges And Nodes With NetwrokX/Matplotlib

I am trying to plot numbers of a problem 'Collatz Conjecture' which forms a nice network between numbers(node labels). However, in the final plot of the solution using networkx nx.

Solution 1:

Picking up on the really helpful comment from DYZ about using graphviz_layout(), I thought I'd share my experience here, in case anyone else is having a similar issue, because getting this set up wasn't totally straightforward (for me, at least, on Ubuntu 16.04):

I found sudo pip install pygraphviz didn't work, because it couldn't find one of the files it needed. I then tried sudo apt-get install graphviz libgraphviz-dev pkg-config followed by sudo pip install pygraphviz (thanks to this suggestion), which looked like it worked (i.e. installation succeeded), but I still couldn't use graphviz_layout() through NetworkX. So, I uninstalled pygraphviz (sudo pip uninstall pygraphviz) and installed it again as follows (thanks to a tip on this thread):

sudo pip install pygraphviz --install-option="--include-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz/"

This did work, and visualisations with graphviz_layout() do seem to have less node overlap than using NetworkX's spring_layout(), as well as a more æsthetically pleasing approach to edge length and cluster spacing.