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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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Catch-all: XYZ doesn't work with `SpatialData` #875

Open timtreis opened 3 months ago

timtreis commented 3 months ago

Please just post/link functions here that do not work with SpatialData - we will then gradually port those over.

timtreis commented 2 months ago

Essentially tried following the Squidpy Xenium tutorial but using a spatialdata object. Failed when I tried to color my plot by Leiden colors.

giovp commented 2 months ago

Essentially tried following the Squidpy Xenium tutorial but using a spatialdata object. Failed when I tried to color my plot by Leiden colors.

with this?

https://github.com/scverse/squidpy_notebooks/pull/125

timtreis commented 2 months ago

No, this one seems to basically just extract the adata and then does normal things that were possible before. I think the goal should be to directly pass either the sdata.tables[...] or sdata and table_name (if the latter cannot be inferred), wdyt? 🤔

LLehner commented 2 months ago

No, this one seems to basically just extract the adata and then does normal things that were possible before. I think the goal should be to directly pass either the sdata.tables[...] or sdata and table_name (if the latter cannot be inferred), wdyt? 🤔

We did that initially, but to keep verbosity low, chose the adata approach.