sq.pl.spatial_scatter() for stereo-seq without .uns['spatial']

scverse / squidpy

Spatial Single Cell Analysis in Python

https://squidpy.readthedocs.io/en/stable/

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sq.pl.spatial_scatter() for stereo-seq without .uns['spatial'] #749

Closed YuchiQiu closed 2 days ago

YuchiQiu commented 9 months ago

Hi, I am using Squidpy to generate scatter plot for stereo-seq datasets. However, there is no .uns['spatial'] for the data.

I tried to force the plot without the image: sq.pl.spatial_scatter(adata,img=False,color=['Fgf9'])

But I still got the error "Spatial key 'spatial' not found in adata.uns."

As stated in the documentation: If no image is plotted, it defaults to a scatter plot, see matplotlib.axes.Axes.scatter() So what do I miss to plot the scatter without image?

Thank you. ...

giovp commented 2 days ago

you need to pass the argument shape=None