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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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Add a wrapper function RunSWNE #7

Closed TomKellyGenetics closed 6 years ago

TomKellyGenetics commented 6 years ago

Adds a wrapper function to run SWNE analysis (derive a SWNE embedding from Seurat object). For more convenient usage (mainly with default parameters) as demonstrated in vignette examples. Allows for passing pre-computed k values for performance or consistency.

TomKellyGenetics commented 6 years ago

The FindNumFactors function has also be amended for compatibility with previously expected behaviour (as described in Issue #8).

TomKellyGenetics commented 6 years ago

Additional handling of dist.use inputs and error messages has also been added (as described in Issue #9).

yanwu2014 commented 6 years ago

Thanks! This looks really useful!

TomKellyGenetics commented 6 years ago

No problem, I've tweaked it mostly to work for my own pipeline but hopefully others find it beneficial too. Sorry to pester again but I've added Methods to RunSWNE (PR #10).

yanwu2014 commented 6 years ago

Looks great!

I was actually meaning to add a wrapper function but I've been a little busy recently. I'll update the vignettes with RunSWNE when I get some time.

Thanks again!