Repository navigation
Delegate plots to spatialdata-plot #912
Description
Cowritten with @timtreis.
Many functions in squidpy essentially generate similar plots like we do in spatialdata-plot (it precedes spatialdata-plot) and was the basis of it.
It’d reduce maintenance effort if we pivot those functions to delegate to spatialdata-plot.
We could establish convenience wrappers for “plot the same plot with 3 genes”: example notebook here.
See further discussion here.
Activity
LLehner commentedon Nov 13, 2024
I guess the main plots where it's useful to wrap
spatialdata-plotwould bespatial_scatterandspatial_segmentsince the others are about visualizing statistics.LLehner commentedon Nov 13, 2024
Is the idea to replace the current
spatial_scatterandspatial_segmentwithspatialdata-plotor also add different plotting capabilities?If one wants the "classic" 4 plots in a row graphic, should it just be a wrapper in the sense that the plots from
spatialdata-plotare captured in memory and then put on a new grid to visualize? @LucaMarconato @timtreisA current draft implementation of mine would yield something like this for labels (using MIBI-TOF example data set):
timtreis commentedon Nov 13, 2024
Basically yeah, the core idea is that
spatialdata-plotis akin tomatplotlib, basically just delivering the base plotting capability. And anything fancy is then a wrapper around that. So, as you said, in that case a squidpy function would keep it's old interface but then just callspatialdata-plotonce per gene and put that on the respectiveaxobject 👍timtreis commentedon Nov 13, 2024
The codebase of
spatialdata-plotstarted out as some chimera between Squidpy's plotting and a prototype from Harald, but has matured a lot since. So we're essentially maintaining duplicate code. Ideally, we can remove a lot of the spatial plotting code from Squidpy and fully delegate tospatialdata-plotso we only fix/advance that in one place.timtreis commentedon Apr 16, 2026
Related PR that unblocks feature-parity scverse/spatialdata-plot#592
Add spatialdata-plot delegation backend (gated by feature flag)