slingshot analysis on PCA but visualization on UMAP

Question

[Tolga]

Hi Bio-community,

I am using slingshot for TI. I am wondering If I can use PCA as reducedDim argument in the slingshot function and for visualization the UMAP in embedCurves? Since I am getting biologically more reasonable results, if working in the PC space, because UMAP can distort data quit a lot.. Is this a reasonable approach?

Thanks!

Cheers, Tolga

Answer 1

[ATpoint]

Yes, you can. The developers even recommend it. I cannot find the precise timestamp in below video, but they're answering user questions in the last third of it, and someone asked about which dimRed to use, be it tSNE, UMAP, PCA, diffusion maps...and PCA was recommended. Just check out the video:

[Tolga]

Thank you! And the visuailzation with UMAP afterwards is also recommended?

[ATpoint]

It's a common way of doing so. I mean, after all it is just transferring data to a common manifold, that is fine.

There is a good section in https://bioconductor.org/books/release/OSCA.advanced/trajectory-analysis.html#principal-curves on using slingshot and embedding it onto UMAP (or other / any manifold).