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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[doc improvment] inconsistent usage of img_key and img_res_key in code base #884

Open TTTPOB opened 2 months ago

TTTPOB commented 2 months ago

I encountered a problem today using sq.pl.spatial_scatter, I have to use lowres image in my object, so I see the docstring said - Use ``img_key`` to display the image in the background. https://github.com/scverse/squidpy/blob/e6b5b0ccd2739aa50b55c7628e685a6750249d8f/src/squidpy/pl/_spatial.py#L392 but when I specified img_key in sq.pl.spatial_scatter, I encountered error saying that it is not a valid parameter. So I looked into the source code, and found sq.pl.spatial_scatter calls _spatial_plot https://github.com/scverse/squidpy/blob/e6b5b0ccd2739aa50b55c7628e685a6750249d8f/src/squidpy/pl/_spatial.py#L47

in which the real parameter is named img_res_key https://github.com/scverse/squidpy/blob/e6b5b0ccd2739aa50b55c7628e685a6750249d8f/src/squidpy/pl/_spatial.py#L57 but the docstring of _spatial_plot says img_key as well https://github.com/scverse/squidpy/blob/e6b5b0ccd2739aa50b55c7628e685a6750249d8f/src/squidpy/pl/_spatial.py#L143

I wanted to submit a pr because this seems a simple fix, just fix the docstring would be good, but when I grep the code base I found image image

There seem to be a major name inconsistency, and I don't know what is the intended name in opinion of your team, so I gave up and file an issue.

giovp commented 2 months ago

hi @TTTPOB , thank you for pointing it out. Feel free to submit a PR for fixing the docstrings. Thank you!