Visualisation for hierarchically clustered graph on map in python

Question

I am starting a new project in python (to be used through jupyter-notebooks), where I'll need to visualise some hierarchically clustered graphs.

I have looked for existing packages, but so far I am not convinced by what I have seen. I am not interested in the clustering process in itself, because this will be another part of the project and I know (roughly) how the graphs will be built up progressivelly. What I am looking for are:

1. an appropriate data structure for storing hierarchically clustered graphs,
2. visualisation tools that would allow to represent the graph on a map (based on X and Y coordinates of the nodes) and either represent the subparts of the clusters, or simplify the clusters depending on their type or depth in the graph structure,
3. ideally, bring some interactivity, for example the ability to zoom-in or-out, or click on some clustered nodes to expand the nodes that were hidden in the cluster.

It looks pretty specific and despite some cool packages I have seen I am not sure which one would help without having too much to reimplement. So far, NetworkX looks like a cool starting point, especially with some D3.js (as shown here ), but it is still far from what I have in mind.

Any advice about where to start digging?

Thanks a lot.

Gautier

Answer 1

For Python, Seaborn's clustermaps are nice. Seaborn is mainly meant to be used with Pandas dataframes; however, the documentation for clustermap says it can be rectangular data, and so I think it means other arrays will wor.

See also:

• Dendrogram with heat map

• SciPy Hierarchical Clustering and Dendrogram Tutorial

• Hierarchical Clustering in Python