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Categorical color obs column crashes the plotting #355
Description
Hi,
When the "color" is categorical, it crashes and returns ValueError in version 0.2.6. The categorial "test" column contains NaN values. There are 11 possible categories.
This code was working perfectly in version 0.2.4.
Cheers,
sdata_small.pl.render_images("queried_cytassist",alpha=1).pl.render_shapes(
f"{sample_id}_square_00{bin_size}um", color="test",method="matplotlib"
).pl.show(coordinate_systems="global", title="Test clusters", legend_fontsize=8,figsize=(10,10),dpi=200,save=None)
[359](https://file+.vscode-resource.vscode-cdn.net/Users/sium/projects/visiumhd/testing/notebooks/~/miniconda/envs/testing/lib/python3.11/site-packages/spatialdata_plot/pl/utils.py:359) "Could not convert values in the `color` column to float, if `color` column represents"
[360](https://file+.vscode-resource.vscode-cdn.net/Users/sium/projects/visiumhd/testing/notebooks/~/miniconda/envs/testing/lib/python3.11/site-packages/spatialdata_plot/pl/utils.py:360) " categories, set the column to categorical dtype."
[361](https://file+.vscode-resource.vscode-cdn.net/Users/sium/projects/visiumhd/testing/notebooks/~/miniconda/envs/testing/lib/python3.11/site-packages/spatialdata_plot/pl/utils.py:361) ) from e
TypeError: '<' not supported between instances of 'str' and 'float'
Activity
LucaMarconato commentedon Oct 3, 2024
I tried to reproduce with Visium HD data and I report the following:
np.nanworksnp.nanvalues gives an error. I have tried both when the column is in atable.obsand when the column is directly in theGeoDataFrame.nanvalue is intable.obsI get your errornanvalue is in a column of theGeoDataFrame, the plot fails with a different error.nanvalue in a continuous column. I report the following:nanvalue is intable.obs, no exception is raised but the plot looks all gray (while it should not). So it still fails.nanvalue is in a column of theGeoDataFrame, the plot fails (with the same error for the categorical case for dataframe columns).Actionable for @sinanugur. I suggest to remove the rows with
nanvalues for the moment.Actionable for us. I suggest to support the handing of
nanvalues and add the following tests:nanvalues intable.obscolumns (both categorical and continous).nanvalues intable.Xnanvalues in the dataframe column (both categorical and continous)timtreis commentedon Oct 3, 2024
Thank you so much for the triage @LucaMarconato! ❤️
Handle NaN values in continuous and categorical coloring (#355)