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How to use Seurat Generated UMAP for Monocle3 pseudotime analyse? #388
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This issue has been brought up on the Seurat issues page as well, where a user there has posted a script that will work (although I personally had to make some modifications to get it to work for my purposes, namely changing the cluster source and carrying over the RNA assay matrix for differential analysis rather than the integrated one, as the UMAP is preserved either way). |
Hi Robert, I am also having some issues with the script Would you be able to share the modifications to it you made? Thanks for any help! |
So it would seem that there's a major issue with porting Seurat objects into Monocle, namely that the integration anchor data takes the place of PCA loadings, which causes issues downstream with pseudotime analysis as graphtest only has access to PCA loadings. Therefore I would suggest that you NOT use integration with monocle at this time. You might choose to try the Align function in Monocle which hypothetically serves a similar purpose, or to just cluster in seurat which, in my case gave me a cleaner result (although in my case I'm examining transcriptional change with the addition of certain chemicals-something align/integrate seemed to muddle somewhat). Here's what I ran with some personal inputs expunged, you're going to need to find the resolution variables and whatnot yourself. I've still used the first steps as I prefer seurat's filtering features, but I CAN NOT RECOMMEND using the partition onward. Frankly, I've forgotten what most of the changes I made are and why, so take caution when using this.)
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Great, thanks for the help! Best, Joshua |
Hello, This issue appears to be an issue about our new package, Monocle 3. Please post any issues for Monocle 3 to the monocle3 repository at https://github.com/cole-trapnell-lab/monocle3. Monocle 3 Development team |
Hello, Any idea how to solve this? It seems like it doesn't recognize the dimensionality reduction from Seurat in order to create trajectories..or this is what I understand. Thank you in advance! |
This has worked for me - good luck!
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Added a row/column name clean up so that you can run pseudo time... Apologies - it was strung across two scripts. |
Hi,
We want to use monocle3 for pseudotime analyze. But it generate a totally different UMAP than Seurat and it split into too many clusters. Monocle3 generates pseudotime based on UMAP. Can we use the UMAP of Seurat?
Thanks!
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