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Samples missing spatial image information #4

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kangjiajinlong opened this issue Feb 20, 2023 · 1 comment
Open

Samples missing spatial image information #4

kangjiajinlong opened this issue Feb 20, 2023 · 1 comment

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

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