Top loadings

[hyeonjin-cho]

Hi,

I'm wondering how Seurat is finding it's top loading genes. So for PC1, I think it's

head(sort((Loadings(seurat_obj)[,1])), n=30)

Because the list of genes that came out from the above code matched to the VizDimLoadings() function.
However, for PC2 this didn't match.

Also, where can I find the equation for loading calculations? I want to know how Seurat came up with the number assigned to each gene/PCs.

Thank you!

[timoast]

We use the TopFeatures() function to return genes for each PC to display in VizDimLoadings().

The loadings are the left singular vectors, by default multiplied by the singular values: https://github.com/satijalab/seurat/blob/master/R/dimensional_reduction.R#L866