spatialdata-plot

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Certain issues noticed: - Geometry type not validated from QuPath (i.e Polygons are sometimes just multi polygons. So analysis only considered first array of coords) - MultiPolygons are not being...

rushin682

Performance issue when plotting spatialdata object with many samples

2

I have a spatialdata object with 49 Visium samples. It looks like this: sdata ``` SpatialData object, with associated Zarr store: /cfs//02_nfcore_spatialvi/output/aggregation/data/merged_sdata.zarr ├── Images │ ├── 'study1_sample1_hires_image': DataArray[cyx] (3, 2000,...

grst

render_labels plots can not show any legend

3

I am using below script: ``` sdata.pl.render_labels('cell_labels', color=ct_name).pl.show(title="Cell labels", coordinate_systems="global", legend_loc="right margin") ``` I check the documents, but my script can not show legend: 

liuyang2006

Hi there, I'm trying to show a leiden clustering in space for an `sdata` object with many coordinate systems. I'm calling ```python ( sdata .pl.render_shapes(fill_alpha=1, method="matplotlib", color="leiden") .pl.show(colorbar=False) ) ```...

Marius1311

Simplify affine matrix calculation for datashader

1

I simplified the code from https://github.com/scverse/spatialdata-plot/pull/378 (taking https://github.com/scverse/spatialdata-plot/issues/381 into account), now the test pass using a simpler construction of the matrix. CC @Sonja-Stockhaus

LucaMarconato

Wip for - https://github.com/scverse/spatialdata-plot/issues/414 - https://github.com/scverse/spatialdata-plot/issues/391 - https://github.com/scverse/spatialdata-plot/issues/409 I will not work for this for 1+ week, feel free to take over meanwhile.

LucaMarconato

Plot categorical color when colors are provided via .uns

1

When trying to plot a categorical column (say `key`) of `sdata.tables[table_name].obs` using spatialdata-plot, colors specified in `sdata.tables[table_name].uns[ "{key}_colors" ]` are ignored due to this line: https://github.com/scverse/spatialdata-plot/blob/478ab27f9e8a6e06fc28c411e7721f1332b34b66/src/spatialdata_plot/pl/utils.py#L758 This PR fixes this;...

ArneDefauw

pl.render_shapes do not support normal hex color

5

Hi, An normal hex color is a string include seven chars, such as "#DD4958", but pl.render_shapes uses nine chars when using datashader, which is not compatible with palette in stored...

wangjiawen2013

Plotting cluster sometimes results in coordinate system not being found, even if set correctly

1

Hi, reporting an issue with plotting. ``` SpatialData object, with associated Zarr store: ... ├── Images │ ├── 'wt1_cytassist_image': DataArray[cyx] (3, 3000, 3200) │ ├── 'wt1_hires_image': DataArray[cyx] (3, 4818, 6000)...

marcouderzo

```python from matplotlib.colors import Normalize from matplotlib import rcParams import spatialdata_plot from spatialdata.datasets import blobs blob=blobs() cmap = matplotlib.colormaps[rcParams["image.cmap"]] cmap.set_under("black") cmap.set_over("grey") norm = Normalize(vmin=0.3, vmax=0.7, clip=False) blob.pl.render_images(element="blobs_image", channel=0, norm=norm, cmap=cmap).pl.show()...

Sonja-Stockhaus