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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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MapQuery projection onto ForceAtlas2 embeddings #7233

Closed EspressoKris closed 1 year ago

EspressoKris commented 1 year ago

Dear Seurat team,

Thanks for the great tool. I would like to project a queried sample onto a force-atlas2 embedding computed on my reference (saved in a the reference seurat object in reductions). However, currently MapQuery seem to be restricted on umap embeddings.

Is there anyway I could perform such projection? As I can easily compute the transfer anchors, could i just copy the first two dimensions of the reduction in the metadata and transfer it using TransferData?

Thanks

AustinHartman commented 1 year ago

No familiar with force-atlas2, but it seems reasonable that you could copy to metadata and then use TransferData. Of course, this isn't a supported workflow in Seurat so I can't really speak on the validity of this approach.