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Cannot pass layer selection of anndata #326

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wangjiawen2013 opened this issue Aug 16, 2024 · 2 comments · May be fixed by #402
Open

Cannot pass layer selection of anndata #326

wangjiawen2013 opened this issue Aug 16, 2024 · 2 comments · May be fixed by #402
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@Sonja-Stockhaus
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enhancement New feature or request priority: high tables 🗓️ Anything related to Tables

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@wangjiawen2013
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wangjiawen2013 commented Aug 16, 2024 •
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Hi,
There maybe many data layers in the annotation table such as scaled data, normalized data and raw counts. spatialdata-plot use adata.X as default, how to plot using the raw.X and data in adata.layers ? We can set the data by use_raw=True or layer = ... in scanpy/squidpy, however, it seems that we cannot set these parameters in spatialdata.
@LucaMarconato
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With napari-spatialdata you can find a dropdown menu for choosing the layer. I'll loop in @timtreis for info on the current support (or plan to support) within the spaitaldata-plot package.

@giovp giovp transferred this issue from scverse/spatialdata Aug 19, 2024
@timtreis
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Very valid point @wangjiawen2013, we should 100 % support that!

@timtreis timtreis added enhancement New feature or request priority: high tables 🗓️ Anything related to Tables labels Sep 11, 2024
@timtreis timtreis self-assigned this Sep 11, 2024
@timtreis timtreis removed their assignment Sep 30, 2024
@timtreis timtreis changed the title scaled data, normalized data and raw counts Cannot pass layer selection of anndata Oct 2, 2024
@Sonja-Stockhaus Sonja-Stockhaus mentioned this issue Jan 5, 2025
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@LucaMarconato LucaMarconato mentioned this issue Jan 6, 2025
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@Sonja-Stockhaus Sonja-Stockhaus linked a pull request Jan 7, 2025 that will close this issue
layer selection when coloring by values in a table #402
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@Sonja-Stockhaus Sonja-Stockhaus linked a pull request Jan 7, 2025 that will close this issue
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enhancement New feature or request priority: high tables 🗓️ Anything related to Tables
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layer selection when coloring by values in a table scverse/spatialdata-plot
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@LucaMarconato @timtreis @wangjiawen2013 @Sonja-Stockhaus