spatialdata-plot

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Remove `pp` accessor as its functionality is now in `spatialdata`

3

timtreis

### Report https://github.com/scverse/spatialdata-plot/blob/582c8379f2478d0e7bc0a7d4733d3cb6fa9af061/src/spatialdata_plot/pl/basic.py#L81 copying the entire spatialdata object can be expensive if elements are on memory. Consider change logic to avoid this. ### Version information _No response_

giovp

Feature request: remove need for intermediate pl calls when chaining renderers

2

### Description of feature Thanks for the super nice work, @timtreis and @sagar87 ! I think it would be nice if we didn't have to add intermediate calls to `pl`...

kevinyamauchi

Plotting multiple elements in the same `ax` seems to work only when `show()` is not called.

2

I refer to the code mentioned in this other issue: https://github.com/scverse/spatialdata-plot/issues/68 This code here: ``` ax = plt.gca() sdata.pl.render_shapes(element='s', na_color=(0.5, 0.5, 0.5, 0.5)).pl.render_points().pl.show(ax=ax) sdata.pl.render_shapes(element='c', na_color=(0.7, 0.7, 0.7, 0.5)).pl.show(ax=ax) plt.show() ```...

LucaMarconato

updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.6 → v0.6.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.5.6...v0.6.1)

pre-commit-ci[bot]

Unable to set vmin vmax when plotting vector data

3

Hi, I want set the vmin and vmax of the color, but failed. This is the first method: ``` norm = matplotlib.colors.Normalize(vmin=-1.0, vmax=0.4) sdata.pl.render_shapes("cell_circles", norm=norm, color="NOTCH2", method="matplotlib").pl.show(coordinate_systems= "physical", figsize=(10,4)) ```...

wangjiawen2013

Cannot pass `layer ` selection of anndata

2

Hi, There maybe many data layers in the annotation table such as scaled data, normalized data and raw counts. spatialdata-plot use adata.X as default, how to plot using the raw.X...

wangjiawen2013

Bug in the MERFISH Technology tutorial

1

**Describe the bug** Hi there, I'm running the public MERFISH tutorial using spatialdata `0.2.2` and spatialdata_plot `0.2.4` (https://spatialdata.scverse.org/en/stable/tutorials/notebooks/notebooks/examples/technology_merfish.html) and when I execute the final cell containing ```Python import matplotlib.pyplot as...

Marius1311

Successor of https://github.com/scverse/spatialdata-plot/pull/262 to avoid solving unneccecary merge conflicts due to age

timtreis

Plotting multiple genes

2

Hi, Scanpy/squidpy can plot mutliple genes at once and save as a image file. such as `sc.pl.umap(adata, color=["genes1", "genes2", "genes3"], save="a.pdf")` This is very convinient. while spatialdata_plot can plot only...

wangjiawen2013