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scverse / squidpy

Spatial Single Cell Analysis in Python
https://squidpy.readthedocs.io/en/stable/
BSD 3-Clause "New" or "Revised" License
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spatial neighbors and datasets integration #543

Closed wangjiawen2013 closed 2 years ago

wangjiawen2013 commented 2 years ago

Hi, I don't quite understand about the "library_key" parameter in sq.gr.spatial_neighbors. I have integrated several datasets in an anndata object, the datasets are from different 10xvisium samples. In this case, how the neighbors are computed ? The spatial coordinates of the spots will be the same among different samples, so I wanna the ways that squidpy process this kind of object. In fact, all the downstream analysis, such moranI, ripleyL, co occurrence are related to this kind of problems and this is a question about spatial transcriptome data integration.

giovp commented 2 years ago

hey @wangjiawen2013 library_key is the key in adata.obs that soters the various library_ids I think we have tutorials for now in multiple places around the docs, will close but please feel free to reopen