Seurat: moving over to R implementation of UMAP?
Looks like there is Rcpp implementation of UMAP available on CRAN: https://cran.r-project.org/web/packages/umap/index.html, or https://cran.r-project.org/web/packages/uwot/index.html per the umap doc's recommendation, I wonder if it makes sense to consider removing the dependency for the python implementation. Would be nice if user doesn't have to separately install python packages to be able to use RunUMAP. Admittedly the Rcpp implementation is probably less stable, but might be something to keep an eye on.
Yue-Jiang
All 2 comments
Hi,
It's a good suggestion. We're looking into this and will likely add this functionality in the near future as an option to RunUMAP.
andrewwbutler
on 14 Jun 2019
Update to this, we've added uwot support to the RunUMAP function. This is now available on the develop branch and will become the default option when we release 3.1 to CRAN (though will retain the umap python wrapper option for those wanting to reproduce old plots. To install the development version of Seurat, please see the instructions here.
andrewwbutler
on 1 Aug 2019
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Most helpful comment
Update to this, we've added
uwotsupport to theRunUMAPfunction. This is now available on the develop branch and will become the default option when we release 3.1 to CRAN (though will retain the umap python wrapper option for those wanting to reproduce old plots. To install the development version of Seurat, please see the instructions here.