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KrishnaswamyLab / PHATE

PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
http://phate.readthedocs.io
GNU General Public License v2.0
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color phate plot by local intrinsic dimension #72

Open kevinafra opened 4 years ago

kevinafra commented 4 years ago

In the PHATE paper and in Smita's talks, she mentions coloring a phate plot by local intrinsic dimension so as to show branch points. This would be very useful. Is it implemented? It would be great to just make 'lid' an attribute of the phate object, so that after fit_transform() one can plot the data with LID coloring with a command like:

phate.plot.scatter3d(phate_data, c=ph.lid)

I'm actually using PHATE in a chemical application, for data that also shows trajectory structure, and as I think about it, it seems like quite a few fields could benefit from a dimensionality reduction algorithm that does not assume that the data is cleanly separable into discrete clusters. I hope that PHATE will continue to be developed. Best wishes!

scottgigante commented 4 years ago

Thanks @kevinafra for raising this. We have experimental code to compute intrinsic dimension and branch points which you can access here: https://github.com/KrishnaswamyLab/PHATE/blob/branch-pred/Python/tutorial/brach_prediction.py#L79

There is ongoing work developing this to a point where it can be integrated into the main package.