Issues with converting SPATA objects to seurat objects

[mattli7]

Hello,

I have been trying to convert SPATA objects from the SPATA data using downloadSpataObjects function. I am able to download the data/RDS files fine. When I load them in with and try to convert them to a seurat object using the function asSeurat(), I get this error:
Error in validObject(.Object) :
invalid class “VisiumV1” object: 1: invalid object for slot "scale.factors" in class "VisiumV1": got class "NULL", should be or extend class "scalefactors"
invalid class “VisiumV1” object: 2: invalid object for slot "spot.radius" in class "VisiumV1": got class "NULL", should be or extend class "numeric"
I was wondering if anyone could help with this.

Thank you.

[simonmfr]

Hi @mattli7, sorry for the late reply. Please re-install SPATA2 and try again.

Alternatively, to transfer barcode metadata from SPATA2 to Seurat, an easy solution is:

meta_col <- as.data.frame(SPATA2::getMetaDf(spata_object)[c("barcodes","column_to_transfer")])
seurat_object <- Seurat::AddMetaData(seurat_object, meta_col)`

Hope that helps!