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No warning when the manually specified table doesn't actually annotate the labels element #467
Description
Activity
Correct plot after setting it:
@timtreis I am having the same issue, could you explain how you are supposed to set the spatialdata_attrs to make this work? I've tried replacing the table.uns['spatialdata_attrs']['region_key'] with 'leiden', but it throws the error (Regions in the AnnData object and
leidendo not match.)Hey @VikramGanesanjs,
here you can find an example on how to manually set it: https://github.com/scverse/spatialdata-notebooks/blob/main/notebooks/examples/sdata_from_scratch.ipynb
the tl;dr is like this:
table.uns["spatialdata_attrs"] = { "region": "<name of the sdata element it annotates>", "region_key": "<column in adata.obs that will link a given obs to the elements it annotates, same entry as region>", "instance_key": "<column that matches a given obs in the table to a given circle by id>", }- linked a pull request that will close this issueUpdate CI/CD to use pixi and parallel testing; also moving to Python 3.11-3.13 #481
on Sep 11, 2025 - linked a pull request that will close this issueAdd warning if `table_name` and `color` are specified but the table doesn't annotate the element #490
on Sep 23, 2025
I forgot to set the spatialdata_attrs so the function was generating random colors for my labels - instead it should've failed and told me that the table doesn't annotate that labels object.