added Suerat compatibility (return object)

yanwu2014 / swne

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

BSD 3-Clause "New" or "Revised" License

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added Suerat compatibility (return object) #15

Closed TomKellyGenetics closed 5 years ago

TomKellyGenetics commented 5 years ago

Specifically:

run SWNE on dimension reductions (in a similar manner to RunTSNE and RunUMAP in the Suerat package)
return an updated Suerat object (optional)

Defaults to returning a raw embedding to retain compatibility with existing workflows.

TomKellyGenetics commented 5 years ago

This version successfully returns Seurat objects for test cases. Compatible with inputs for Seurat::RunTSNE such as reduction.use (including CCA corrected data). This should enable seamless integration into a Seurat analysis: load the package, run SWNE, return a Seurat object, and continue with plotting, clustering, and so on.