scverse / squidpy

Spatial Single Cell Analysis in Python
https://squidpy.readthedocs.io/en/stable/
BSD 3-Clause "New" or "Revised" License
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sq.pl.spatial_scatter return_ax = True not working #791

Open parser-algebra-0m opened 6 months ago

parser-algebra-0m commented 6 months ago

Hi squidpy team,

Thank you for a great tool!

I think the sq.pl.spatial_scatter function might not be working as expected. Setting return_ax = True, should return Axes object, but it's still returning None.

Am I doing this right?

here's my code

p=sq.pl.nhood_enrichment(
    adata_mine,
    cluster_key="celltype_final",
    figsize=(6, 6),
    title="Neighborhood enrichment adata",
    return_ax = True,
#     ax=ax[0],
)

type(p)

Heatmap is plotted + this:

/diskmnt/Projects/Users/i.strunilin/Tools/miniforge3/envs/squidpy/lib/python3.11/site-packages/anndata/_core/anndata.py:522: FutureWarning: The dtype argument is deprecated and will be removed in late 2024.
  warnings.warn(
/diskmnt/Projects/Users/i.strunilin/Tools/miniforge3/envs/squidpy/lib/python3.11/site-packages/squidpy/pl/_utils.py:556: FutureWarning: Series.__getitem__ treating keys as positions is deprecated. In a future version, integer keys will always be treated as labels (consistent with DataFrame behavior). To access a value by position, use `ser.iloc[pos]`
  row_labels = adata.obs[key][row_order]
Out[380]:
NoneType

Package versions

from importlib.metadata import version
print(version('squidpy'))
print(version("scanpy"))
print(version("anndata"))

output

1.3.1
1.9.6
0.10.4

...