Hi! I am working with a CosMx dataset where spatial coordinates are originally defined per FOV. CosMx also provides coordinates transformed into a global coordinate system, which I use to visualize all FOVs belonging to a TMA core together.
I am plotting the cells with:
sq.pl.spatial_scatter(
sdata,
spatial_key="global",
shape=None,
connectivity_key="global_connectivities",
)
This produces the warning:
WARNING: Please specify a valid `library_id` or set it permanently in `adata.uns['spatial']`
I am having trouble understanding why a library_id is needed in this case. I am using shape=None and only want to make a scatter plot in my custom global coordinate system, without plotting a tissue image, is library_id actually necessary here? How do I silence the warning?
Thanks!