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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?

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  • $\begingroup$ This comes a bit late, but you can find MATLAB scripts to plot barcodes and persistence diagrams using the output files that you get from DIPHA, GUDHI, as well as other libraries for the computations of persistent homology here. $\endgroup$ – n.o. Sep 6 '17 at 18:11
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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.

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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.

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