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labsyspharm / scimap

Spatial Single-Cell Analysis Toolkit
https://scimap.xyz/
MIT License
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Implicit change in matplotlib parameters while importing scimap #111

Closed ConstensouxAlexis closed 3 months ago

ConstensouxAlexis commented 3 months ago

Hello, I use SCIMAP package with Xenium spatial transcriptomics data. Before importing SCIMAP, I have no issues with plotting the Xenium data: before_scimap

But, when I import SCIMAP package and do the same plot, plotting parameters are changed so I cannot properly vizualise the Xenium data: after_scimap

It also raises the error message: findfont: Generic family 'sans serif' not found because none of the following families were found: Arial

So I guess SCIMAP changes matplotlib parameters but don't know where in the code, and why. Do you know if it is possible to bypass this behaviour ? Thanks ! I run scimap 2.1.1

ajitjohnson commented 3 months ago

hi @ConstensouxAlexis Thank you for raising the bug. Could you update the package pip install scimap --upgrade and check if the issue persists? Thank you.

ConstensouxAlexis commented 3 months ago

Hi @ajitjohnson , I saw that you changed matplotlib default params, so this should fix my issue. I just have an incompatibility with the new scimap version: scimap 2.1.2 requires dask[array]<2024.0.0,>=2023.11.0, but you have dask 2024.4.1 which is incompatible. spatialdata 0.2.2 requires dask>=2024.4.1, but you have dask 2023.12.1 which is incompatible.

I work on spatial transcriptomics data, so spatialdata library is necessary. I know scimap is not designed to work on spatial transcriptomics, but it provides a lot of useful features for spatial transcriptomics data analysis. It could be nice if scimap could support a more recent version of dask ! Thanks a lot

ajitjohnson commented 3 months ago

No problem. I have released a new version with the requirements relaxed. Hope it helps.