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Documentation: Spatial mouse anterior vignette subset error #9715

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GCAT01 opened this issue Mar 1, 2025 · 0 comments
Open

Documentation: Spatial mouse anterior vignette subset error #9715

GCAT01 opened this issue Mar 1, 2025 · 0 comments
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documentation Error in documentation

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@GCAT01
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GCAT01 commented Mar 1, 2025

Issue Description

I am following this vignette: https://satijalab.org/seurat/articles/spatial_vignette.html and ran into an error when running

cortex <- subset(cortex, anterior1_imagerow > 400 | anterior1_imagecol < 150, invert = TRUE)

This is the same issue as #3704 and #2432 . I tried the solutions in both looking for the key

> Key(cortex)
 meta.data    Spatial        SCT        pca       umap     slice1 
     "md_" "spatial_"     "sct_"      "PC_"    "umap_"  "slice1_" 

> cortex@images
$slice1
Spatial coordinates for 2174 cells
Default segmentation boundary: centroids 
Associated assay: Spatial 
Key: slice1_ 

So my key is slice1 so I used that:

> cortex <- subset(cortex, slice1_imagerow > 400 | slice1_imagecol < 150, invert = TRUE)
Error in `FetchData()`:
! Spatial coordinates are no longer fetchable with FetchData
Run `rlang::last_trace()` to see where the error occurred.

What do I need to do to get this to work and finish the vignette?

@GCAT01 GCAT01 added the documentation Error in documentation label Mar 1, 2025
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