libraries to plot topological data analysis persistence diagrams, complexes, and barcodes

Question

I am starting to do some Topological Data Analysis and am looking for a good plotting library to produce the diagrams of complexes, barcodes, and persistence diagrams. The most popular TDA libraries like DIPHA, GUDHI, and others can computer the information for barcodes and other summaries, but don't seem to have plotting capabilities to visualize these summaries. I think that the R TDA package has plotting capabilities, but I think this might be rather limited--especially if there are a large number of points. What packages have others been using to plot this info?

Answer 1

After doing some more searching and comparison, I figure that using a library such as plotly or bokeh are the proper choices. These tools are compatible with the jupyter notebooks and can generate interactive 3D figures within jupyter notebooks. Both websites have a good setof examples/models to emulate.

Using these libraries, I should be able to take results computed in DIPHA and Gudhi and then generate plots within python.

UPDATED:

One big improvement in the last few months is that Gudhi has a set of python bindings. So the python Gudhi package will plot results using Matplotlib.

Answer 2

Javaplex can be used to plot these diagrams, as witnessed in its documentation (it's from Matlab I think).

Maybe someone finds these notebooks useful. They utilize javaplex from Scala, a JVM functional language.