How to interpret a tSNE or UMAP plot to get biological conclusions ?

Question

[Chris]

Hello all,

Would you please tell me how to interpret a tSNE or UMAP plot to get biological conclusions? I read some scRNA-Seq analysis but still haven't gotten the biological meaning of these plots. Thank you so much!

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6937596/ Figure 6 of this paper is a sample.

[zbidav]

In general, tSNE or uMAP are just methods to cluster the data to diffrent clusters. Afterwarwds you can check which genes/markers each cluster are consist of, and then devide the general cell vluster to smaller vlusters, which each defined by unique markers (gene expression/etc.)

[dsull]

That is not technically correct. Community detection algorithms are used to generate clusters. tSNE and UMAP are dimensionality reduction algorithms.

[Chris]

Would you please clarify which not technically correct is?

[dsull]

"tSNE or uMAP are just methods to cluster the data" is not correct. They are dimensionality reduction algorithms.

[Chris]

Thank you for your reply!

Answer 1

[dsull]

Here's one take on them:

https://www.biorxiv.org/content/10.1101/2021.08.25.457696v3

[Chris]

Thank you for your reply!