Overlay monocle3 on Seurat integrated object with wnn dimentionality reduction #9969
oliverabinader
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How can I overlay Monocle3 trajectory analysis on a Seurat-integrated object that uses WNN (weighted nearest neighbor) dimensionality reduction? I followed the tutorial here: https://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/monocle3.html, but when I tried to learn the graph, it failed with an error asking me to run dimensionality reduction using specific options. Since my Seurat object already includes WNN-based UMAP (wnn.umap), is there a way to directly use that embedding when creating the cell_data_set for Monocle3? Ay thoughts on that would be highly appreciated.
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