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VPetukhov avatar VPetukhov commented on June 3, 2024

Hm, it's very weird. embedGraph has nothing to do with Seurat objects: it calls embedGraphUmap, which calls embedKnnGraph, which inside calls uwot::umap and returns the embedding. So, after the message "15:34:41 Optimization finished" from the uwot package and "Done" from embedGraphUmap it simply sets obj$embedding field to the Nx2 matrix with the embedding and returns it. There is nothing, which could produce the last 6 lines:

Merging 25 samples
Adding pairwise alignments to 'conos.pairs' in miscellaneous data
Adding graph as 'SCT_mnn'
Adding graph embedding as largeVis
Adding clustering information
^M |======================================================================| 100%

Are you sure you didn't miss some code?

And what do you mean by "it is done in LargeVis format"? Both embedding has the same format, which is Nx2 matrix with 2d coordinates.

from conos.

evanbiederstedt avatar evanbiederstedt commented on June 3, 2024

There's been no follow-up on this issue for some time.

I'll close for now.

from conos.

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