scverse
colormap is not considered using napari squidpy plugin
Description
I can not change the color map of the spatial transcriptomic data in Napari
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Minimal reproducible example
viewer = napari.Viewer() viewer.add_image( img1, colormap='plasma', name="test", metadata={"adata": adata, "library_id": "test"}, )
colormap='plasma' is not considered
Many thanks Sophie
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Traceback
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Version
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hi @sophieRAIBAUD , which napari implementation are you using? the one in squidpy or the napari-spatialdata?
I am using napari with your plugin https://github.com/scverse/napari-spatialdata
great, I moved the issue in the appropriate repository. Will keep it open, we'll take a look!
hi @sophieRAIBAUD , one quick question, the colormap you want to change is the one used for plotting the continuos values on the circles overlaying the image right? which should be the same as the one for the colorbar on the bottom left pasrt of the GUI ?
I would prefer 'magma' or 'plasma' or whatever
I am also strugglingwith the scale:
normally 1 spot = 55µm
distance between spots = 100µm
in napari I get:
depite typing viewer.scale_bar.visible = True viewer.scale_bar.unit = "µm" Thanks again for the greatfull help !!
