Add Xenium tutorial using spatialdata #125
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Thanks for the notebooks, asking for some (minor) changes:
- please write
adata = sdata.tables['table']and then useadata. It is less verbose and it has the same effect becauseadatais then a reference tosdata.tables['table'] - please explain that:
- Squidpy looks for the cell coordinates in
obsm['spatial']and that this is automatically set for Xenium data by the function inspatialdata-io. - for more complex data this needs to be done manually (the user can find more details in this notebook: https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/squidpy_integration.html)
- Squidpy looks for the cell coordinates in
- please keep the last plot, but also remake it using
spatialdata-plot, to show the user that they have also this possibility. - Also I would add (commented), the code to fire up napari (
from napari import Interactivefollowed byInteractive(sdata))
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Extra thing: @giovp after the code that you wrote in the latest hackathon on graph support for |
yes I think we could be using the new gr.spatial_neighbors that support directly spatialdata, but for that I think we'd first need to merge the PR/do release |
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super nice! I just reviewed it and there are few aesthetics that should be modified, for the rest it looks great! I would merge after the points in the review have been addressed |
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View / edit / reply to this conversation on ReviewNB giovp commented on 2024-08-23T15:38:30Z Line above I would remove, it appears elsewhere in the nb |
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View / edit / reply to this conversation on ReviewNB giovp commented on 2024-08-23T15:38:30Z also here and above LLehner commented on 2024-08-27T08:07:22Z Shouldn't some titles remain so people find certain sections more easily? giovp commented on 2024-08-30T21:10:37Z yeah but it doesn't look like they are rendered as title right? or you mean that the rendering here is incorrect with respect to how it will be render for in RTD? The lines are not about not having titles, but having titles rendered correctly, here I think the problem is that both --- and # are used. Does it make sense? |
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View / edit / reply to this conversation on ReviewNB giovp commented on 2024-08-23T15:38:31Z would be nice maybe a screenshot to add here of the napari plugin open? |
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Shouldn't some titles remain so people find certain sections more easily? View entire conversation on ReviewNB |
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yeah but it doesn't look like they are rendered as title right? or you mean that the rendering here is incorrect with respect to how it will be render for in RTD? The lines are not about not having titles, but having titles rendered correctly, here I think the problem is that both --- and # are used. Does it make sense? View entire conversation on ReviewNB |
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see the diffs here regarding the misunderstanding between lines and titles or
please re-add the titles, but make sure that they are rendered correctly, before there was the title AND the --- which were extra |
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e.g. see what I mean here, the title is in both, and the text should stay, but there is the line
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in the current read the docs latest they are not present
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An updated Xenium tutorial for analysis using Squidpy, but instead of only working with
anndata,spatialdatais used.@LucaMarconato please let me know if things should be added. So far I just reproduced the original Xenium tutorial with
spatialdata.