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theMILOlab / SPATA2

A Toolbox for Spatial Gene Expression Analysis
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QC filter SPATA2 object / SPATA2 to Seurat #113

Open BaluPai opened 2 months ago

BaluPai commented 2 months ago

Hi, I have been trying to use SPATA2 with Seurat and I have been trying to convert/transform one to the other (initiateSPATA > SPATA2 object > Seurat) and also (initial process and filtering in Seurat > SPATA2). Especially since I like how SPATA2 can be used to perform CNV analysis.

1) I am not able to switch the object back to Seurat using asSeurat!

G4Sp2Seu<- asSeurat(G4seu2sp, process = TRUE) _"Error in process_seurat_object(seurat_object = seurat_object, assay_name = assayname, : Invalid input for argument 'SCTransform'. Must either be TRUE, FALSE or a named list "

I tried to do this is since I noticed object that I initiated in SPATA2 keeps some low quality spots that I can remove when I process the data initially using Seurat.

2) Another issue is I am not able to use "subset" function on my Seurat object (generated like this = initiateSPATA > SPATA2 object > Seurat)

GSp2Seufilt<- subset(GSp2Seu, percent.mt < 15)# & 12000 > GSp2Seu$nFeature_Spatial & GSp2Seu$nFeature_Spatial> 400 & GSp2Seu$nCount_Spatial > 1000)

Error in if (!DefaultAssay(object = value) %in% Assays(object = x)) { : argument is of length zero

Any suggestions to perhaps manually filter SPATA2 initiated object would be helpful to start with.

Thanks!

Best regards