Neighbourhood graph or embedding?

[YY-SONG0718]

Dear Alec,

I have a question regarding the outputs of SAMap. Is the final output of SAMap the neighbourhood information stored in sm.samap.adata.uns['neighbors'] and sm.samap.adata.obsp['connectivities'], or the embedding in sm.samap.adata.obsm['wPCA']? Can I use the weighted PCA embedding to calculate neighbourhoods of different sizes?

Thank you so much!

Kind regards,
Yuyao

[wubaosheng]

I think the wPCA is the weigh of different species, so it is right to use the wPCA for embeding.

[atarashansky]

Hi @wubaosheng

Please do not use wPCA as an embedding. wPCA is just an intermediate joint embedding used for calculating the stitched neighborhood graph. The correct output is sm.samap.adata.obsp['connectivities'].