Subset error in vignette

[GCAT01]

I am following the "Analysis, visualization, and integration of spatial datasets with Seurat" vignette. I am at the section "Subset out anatomical regions" when I run the first subset command, I get the following:

> cortex <- subset(brain, idents = c(1, 2, 3, 4, 6, 7))
Warning messages:
1: Not validating Centroids objects 
2: Not validating Centroids objects 
3: Not validating FOV objects 
4: Not validating FOV objects 
5: Not validating FOV objects 
6: Not validating FOV objects 
7: Not validating FOV objects 
8: Not validating FOV objects 
9: Not validating Seurat objects 

Then, when running a further subset, it throws an error:

> cortex <- subset(cortex, anterior1_imagerow > 400 | anterior1_imagecol < 150, invert = TRUE)
Error in `FetchData()`:
! None of the requested variables were found: 

I have seen a few other people having issues with subset although I can't seem to find a solution that works for me in this situation.

[suanzaoren]

Hi , I have the same absolutely error! I also hope someone could give me a help. If you have resolved this issue, please tell me, thanks.

[suanzaoren]

I am following the "Analysis, visualization, and integration of spatial datasets with Seurat" vignette. I am at the section "Subset out anatomical regions" when I run the first subset command, I get the following:

> cortex <- subset(brain, idents = c(1, 2, 3, 4, 6, 7))
Warning messages:
1: Not validating Centroids objects 
2: Not validating Centroids objects 
3: Not validating FOV objects 
4: Not validating FOV objects 
5: Not validating FOV objects 
6: Not validating FOV objects 
7: Not validating FOV objects 
8: Not validating FOV objects 
9: Not validating Seurat objects 

Then, when running a further subset, it throws an error:

> cortex <- subset(cortex, anterior1_imagerow > 400 | anterior1_imagecol < 150, invert = TRUE)
Error in `FetchData()`:
! None of the requested variables were found: 

I have seen a few other people having issues with subset although I can't seem to find a solution that works for me in this situation.

Hi, Now I have a possible solution:

Extract coordinates (assuming the image name is "anterior1")

spatial_coords <- GetTissueCoordinates(cortex, image = "anterior1")

Rename a column (optional: Make sure the column name matches the subset condition)
colnames(spatial_coords) <- c("anterior1_imagerow", "anterior1_imagecol")

Adds coordinates to metadata

cortex <- AddMetaData(cortex, metadata = spatial_coords[,-3])

Check the column names of the metadata to make sure they are correct

colnames(cortex@meta.data)