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gao-lab / SLAT

Spatial-Linked Alignment Tool
https://slat.readthedocs.io/en/latest/
MIT License
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Question about 'kidney_align.draw_3D' #3

Closed Changzhanhe closed 1 year ago

Changzhanhe commented 1 year ago

What a great tool for spatial slides alignment! :-)

I have met an error when I used draw_3D function to plot cell type alignment between two slides, an error occurred:

_"TypeError: drawlines() takes from 4 to 6 positional arguments but 7 were given."

Hope for your reply. Thanks!

xiachenrui commented 1 year ago

Thanks for your interest and feedback !

I can not reproduce your error in my computer (with latest version of SLAT). Could you update to the latest version (0.2.1) following our tutorial. If updating can not solve your error, counld you please provide your codes?

Best! Chen-Rui

xiachenrui commented 1 year ago

We close this issue because key information is missing. If you need more help, please open it again.

Starlitnightly commented 7 months ago

Hi, @xiachenrui

After testing, this bug is caused by a function parameter error in version 0.2.1 on pypi, which is not reported if installed version 0.2.2 using the github repository.

Also, scslat 0.2.2 requires scipy<1.9,>1.3 seems to be an unnecessary limitation, I run scslat on scipy==1.11.4 and everything works fine.

Also, some of the arguments to the functions in the tutorial don't seem to work correctly when the version of scslat is 0.2.2. For example:

kidney_align = match_3D_celltype(adata1_df, adata2_df, matching, meta='celltype', highlight_celltype = [[''],['']],
                                 subsample_size=300, highlight_line = ['blue'], scale_coordinate = True )
ValueError: ['blue'] is not a valid value for colour

Sincerely,

Zehua