search

scverse / scanpy

Single-cell analysis in Python. Scales to >1M cells.
https://scanpy.readthedocs.io
BSD 3-Clause "New" or "Revised" License
1.86k stars 595 forks source link

deprecate/remove read spatial and plotting spatial from scanpy. #2331

Open giovp opened 1 year ago

giovp commented 1 year ago

I think it makes sense to deprecate and then remove sc.read_visium. and sc.pl.spatial since I don't plan to maintain it here anymore and updated versions are present in Squidpy. What do you think @ivirshup ?

Zethson commented 1 year ago

I would like to second this. I think that it makes sense that we don't duplicate functionality and responsibility of our core tools. People shouldn't be looking for spatial stuff in scanpy nor be confused if they suddenly see spatial tooling in the scanpy docs. We should always point them to the awesome squidpy.

linhuawang commented 1 year ago

I just had issues using sc.pl.spatial after reading spaceranger2.0.0 outputs using sc.read_visium. Although the issue is resolved. I am wondering if these functions are not maintained anymore. I am not familiar with Squidpy. But it seems to use these functions in its package. I would very much appreciate any clarification here.

giovp commented 1 year ago

hi @linhuawang ,

yes I'd suggest you to use squidpy for plotting, unfortunately the spaceranger 2.0 reading is not in main yet (will be by end of the week).