'SpatialData' object has no attribute 'pl'

[chrismahony]

Hi Spatildata team,

I am running the following:

xenium_path = "/my_path/"
sdata = xenium(xenium_path)
sdata

SpatialData object
├── Images
│ ├── 'morphology_focus': DataTree[cyx] (1, 40826, 34055), (1, 20413, 17027), (1, 10206, 8513), (1, 5103, 4256), (1, 2551, 2128)
│ └── 'morphology_mip': DataTree[cyx] (1, 40826, 34055), (1, 20413, 17027), (1, 10206, 8513), (1, 5103, 4256), (1, 2551, 2128)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (40826, 34055), (20413, 17027), (10206, 8513), (5103, 4256), (2551, 2128)
│ └── 'nucleus_labels': DataTree[yx] (40826, 34055), (20413, 17027), (10206, 8513), (5103, 4256), (2551, 2128)
├── Points
│ └── 'transcripts': DataFrame with shape: (, 10) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (36812, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (36812, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (36812, 1) (2D shapes)
└── Tables
└── 'table': AnnData (34435, 377)
with coordinate systems:
▸ 'global', with elements:
morphology_focus (Images), morphology_mip (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)

sdata.pl.render_labels("cell_boundaries").pl.show(ax=axes[2], title="Cell labels", coordinate_systems="global")

---

AttributeError Traceback (most recent call last)
Cell In [22], line 1
----> 1 sdata.pl.render_labels("cell_boundaries").pl.show(ax=axes[2], title="Cell labels", coordinate_systems="global")

AttributeError: 'SpatialData' object has no attribute 'pl'

Do you have any idea as to why my object does not have pl? This is from a xenium v1 run, could this be the problem?

Thanks for your help
Chris

[chrismahony]

sorry, this can be ignored, i did not have spatial data plot installed, works fine now
Chris