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use UMAP to project data to 1D for quick-and-dirty heatmap ordering #42

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cornhundred opened this issue Oct 3, 2019 · 2 comments
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@cornhundred
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Is your feature request related to a problem? Please describe.
I would like to try to use UMAP to project data down to one dimension, then rank the data points in this one dimensional space to use as an ordering for the points in a heatmap. I plan on doing this for rows and columns separately. My hope is that this will enable a faster way of arranging/clustering data points and dimensions in a heatmap (it will lack the hierarchical clustering information obtained via hierarchical clustering). But it may be useful as a quick and dirty way of producing a heatmap from a large dataset.

@lmcinnes, would you think this seems like a reasonable idea?

Describe the solution you'd like
I'll use UMAP with n_componenets=1 (see https://github.com/lmcinnes/umap/blob/3f6e92f0ece650423d52eb560fac31db7e3f7dc7/doc/parameters.rst#n_components) then proceed as described above.

@lmcinnes
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lmcinnes commented Oct 4, 2019

For large datasets I think this is not unreasonable. In principle I would think that hierarchical clustering with single linkage could be made almost as fast, but you would be stuck with single linkage which is not especially noise tolerant.

@cornhundred
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Thanks for the feedback @lmcinnes! I want to experiment with this for large datasets (~20,000 samples with ~200 dimensions) and see if the GPU implementation speeds things up further (https://medium.com/the-artificial-impostor/umap-on-rapids-15x-speedup-f4eabfbdd978).

@cornhundred cornhundred added the enhancement New feature or request label Nov 7, 2019
@cornhundred cornhundred self-assigned this Nov 7, 2019
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