Lost UMAP information in downloaded .RDS object

Dear there. The website is amazing to use. One issue i have is UMAP showed very good integration in the website. However, when i download the .RDS file and try to explore the data in R, all those UMAP information are lost. Can i get those information in the .RDS file as well?

Hi James,
thanks for posting your question and welcome to the Cellenics community forum!

Indeed, currently the UMAP information as well as the cluster information is not part of the .RDS export functionality. We are planning to add this to this export functionality in the future, but I cannot give you an exact timing at this stage.

I’ll keep you posted on this!

Hi James,
I am happy to inform you that we added important functionality to the download RDS object feature!

Namely, if you now download the RDS object the UMAP and clustering information are all part of the object.
Please note that the download now takes more time than before, because of this added functionality.

I hope this new feature is useful for you!

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Hello Jildou,
This function is exactly what I was looking for - I was wondering if you could tell me how to download the RDS project (with the clustering and UMAP) from the Cellenics page? I can’t seem to find this function easily.

Many Thanks, Katie

Hi Katie,

You can download the RDS object from the Data Management. You first need to select the project of interest, and then click on the “Download” button next to the “Share” and “Go to Data Processing” buttons. Then click on "Processed Seurat object (.rds). This will download the RDS object with the clustering and UMAP information included.

I hope this helps. Let me know if you have any questions.

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