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theMILOlab / SPATAData

The database for spatially resolved transcriptomics
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Samples missing spatial image information #4

Open kangjiajinlong opened 1 year ago

kangjiajinlong commented 1 year ago

Hi SPATA team,

I am learning how to use SPATA and specifically how to plot variables over the sample image. I tried with loading spata object, converting to seurat object and using SpatialDimPlot as follows.

library(SPATAData) library(SPATA2) library(Seurat)

spata_obj <- loadSpataObject("./objects/217_T.RDS") seurat_obj <- transformSpataToSeurat(object = spata_obj) SpatialDimPlot(object = seurat_obj,group.by="seurat_clusters")

But I got the error "Error in SpatialPlot(object = object, group.by = group.by, images = images, : Could not find any spatial image information". This also happens to a few other samples. Would you mind checking which part of the code I did wrong? If the image is indeed missing, could you kindly point out where I can download the corresponding images?

Thanks, Jack

kangjiajinlong commented 1 year ago

OK I saw that there is an image folder in the repo. Seems that only a few samples got corresponding image.