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[BUG] GET http://localhost:5005/api/v0.2/colors: 404 (NOT FOUND) #2598
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does work though. Could it have to do with this warning?
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A little more digging:
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Removing all my colors from
They display properly when I make UMAPs in scanpy.. |
Oh that's interesting -- they're all hex rgbA... |
Hey Alex - am I correct in understanding that you have resolved your own issue? |
yes, but I think there's still an issue with cellxgene, when it loads adatas written by modern versions of scanpy. When I set the palette in a scanpy UMAP, it will save the palette under Since scanpy will be doing this for many users, perhaps cellxgene should be able to handle these 8-digit hex colors (and parse them as RGBA? In the meantime, here's my workaround (call this function right before writing your h5ad to read into cellxgene): def rgba_hex_colors_to_rgb(adata):
for key in adata.uns.keys():
if key.endswith('colors'):
adata.uns[key] = np.array([(c if len(c)<=7 else c[:-2]) for c in adata.uns[key]]) |
Got it - thanks, for the explanation Alex - following up on this internally! |
ps which version of scanpy did you generate your dataset with? |
scanpy==1.9.1, python 3.9.13, macOS 12.5.1 |
perfect, thanks! |
Describe the bug
Just installed cellxgene, and tried to load a dataset of mine, got this error and fails to load.
Version (please complete the following information):
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