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[SUGGESTION] Add uncorrected UMAP/tSNE when using batch effect correction (e.g. Harmony/BBKNN) #337

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cbravo93 opened this issue Apr 28, 2021 · 0 comments
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enhancement New feature or request

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@cbravo93
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cbravo93 commented Apr 28, 2021

Is your feature request related to a problem? Please describe.
When running batch effect correction methods, the final loom will contain the corrected UMAP in the 'HVG UMAP' tab, while the uncorrected UMAP coordinates will not be included (idem for tSNE). In some data sets it can be useful to have the uncorrected UMAP to check genes/regulons contributing to the batch effect,

Describe the solution you'd like
Would it be possible to keep uncorrected and corrected coordinates? E.g uncorrected coordinates could be kept on HVG UMAP, and corrected ones on Harmony HVG UMAP for example (making Harmony HVG UMAP the default embedding in this cases would be more useful)

Describe alternatives you've considered
Uncorrected coordinates can always be accessed in the intermediate files and added manually

@cbravo93 cbravo93 added the enhancement New feature or request label Apr 28, 2021
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