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UMAP interpretation in scRNA-seq analysis
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15 months ago
chipolino • 40

Hi,

If you analyze scRNA-seq data of some differentiation process (like stem cells) and use UMAP to visualize it, can you use the plot to retrieve the actual differentiation trajectory? I know that for example velocyto uses tSNE for this purpose, and UMAP was reported to be better in manifold capturing. I also know that there are specific tools for this, like Monocle or URD, but I just want to know, are we allowed to interpret UMAP (and tSNE) plots in this way.

Thanks

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14 months ago
rmf • 630

tSNE separates groups quite well, but does not preserve the global structure very well, therefore you cannot take three points and say two are closer than the other two. It does not preserve distance. Local structures may make sense. Therefore, it most likely doesn't show cell differentiation trajectory.

UMAP on the other hand does preserve global structure and since distances are preserved, it also tends to preserve continuity of cell states.

https://www.biorxiv.org/content/10.1101/298430v1.full

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