spatialdata-plot
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Plotting cluster sometimes results in coordinate system not being found, even if set correctly
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)
│ ├── 'wt1_lowres_image': DataArray[cyx] (3, 482, 600)
│ ├── 'wt5_cytassist_image': DataArray[cyx] (3, 3000, 3200)
│ ├── 'wt5_hires_image': DataArray[cyx] (3, 5013, 6000)
│ ├── 'wt5_lowres_image': DataArray[cyx] (3, 501, 600)
│ ├── 'wt8_cytassist_image': DataArray[cyx] (3, 3000, 3200)
│ ├── 'wt8_hires_image': DataArray[cyx] (3, 6000, 5907)
│ └── 'wt8_lowres_image': DataArray[cyx] (3, 600, 591)
├── Shapes
│ ├── 'wt1_square_002um': GeoDataFrame shape: (2919200, 1) (2D shapes)
│ ├── 'wt1_square_008um': GeoDataFrame shape: (182450, 1) (2D shapes)
│ ├── 'wt1_square_016um': GeoDataFrame shape: (46427, 1) (2D shapes)
│ ├── 'wt5_square_002um': GeoDataFrame shape: (1779504, 1) (2D shapes)
│ ├── 'wt5_square_008um': GeoDataFrame shape: (111219, 1) (2D shapes)
│ ├── 'wt5_square_016um': GeoDataFrame shape: (28148, 1) (2D shapes)
│ ├── 'wt8_square_002um': GeoDataFrame shape: (1498336, 1) (2D shapes)
│ ├── 'wt8_square_008um': GeoDataFrame shape: (93646, 1) (2D shapes)
│ └── 'wt8_square_016um': GeoDataFrame shape: (23643, 1) (2D shapes)
└── Tables
├── 'square_002um': AnnData (6197040, 19059)
├── 'square_008um': AnnData (381575, 19059)
└── 'square_016um': AnnData (98218, 19059)
with coordinate systems:
▸ 'downscaled_hires', with elements:
wt1_hires_image (Images), wt5_hires_image (Images), wt8_hires_image (Images), wt1_square_002um (Shapes), wt1_square_008um (Shapes), wt1_square_016um (Shapes), wt5_square_002um (Shapes), wt5_square_008um (Shapes), wt5_square_016um (Shapes), wt8_square_002um (Shapes), wt8_square_008um (Shapes), wt8_square_016um (Shapes)
▸ 'downscaled_lowres', with elements:
wt1_lowres_image (Images), wt5_lowres_image (Images), wt8_lowres_image (Images), wt1_square_002um (Shapes), wt1_square_008um (Shapes), wt1_square_016um (Shapes), wt5_square_002um (Shapes), wt5_square_008um (Shapes), wt5_square_016um (Shapes), wt8_square_002um (Shapes), wt8_square_008um (Shapes), wt8_square_016um (Shapes)
▸ 'global', with elements:
wt1_cytassist_image (Images), wt5_cytassist_image (Images), wt8_cytassist_image (Images), wt1_square_002um (Shapes), wt1_square_008um (Shapes), wt1_square_016um (Shapes), wt5_square_002um (Shapes), wt5_square_008um (Shapes), wt5_square_016um (Shapes), wt8_square_002um (Shapes), wt8_square_008um (Shapes), wt8_square_016um (Shapes)
and
sdata['wt1_hires_image'].transform
{'downscaled_hires': Identity }
When I try to plot some clusters with "group=", some of them are indeed plotted and others, without any apparent reason, yield this error:
clusters_list = sdata['square_008um'].obs['clusters'].unique()
for cluster in clusters_list:
try:
sdata.pl.render_images('wt1_hires_image').pl.render_shapes(
'wt1_square_008um',
color="clusters", # Color by the 'clusters' column
groups=[cluster],
size=0.3,
).pl.show(
coordinate_systems="downscaled_hires",
figsize=(10, 10)
)
except Exception as e:
print(f"Error while plotting cluster {cluster}: {e}")
INFO Rasterizing image for faster rendering.
[/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata/_core/_elements.py:105](https://192.33.153.24/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata/_core/_elements.py#line=104): UserWarning: Key wt1_square_008um already exists. Overwriting it in-memory.
self._check_key(key, self.keys(), self._shared_keys)
[/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata/_core/_elements.py:125](https://192.33.153.24/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata/_core/_elements.py#line=124): UserWarning: Key square_008um already exists. Overwriting it in-memory.
self._check_key(key, self.keys(), self._shared_keys)
INFO Using 'datashader' backend with 'None' as reduction method to speed up plotting. Depending on the
reduction method, the value range of the plot might change. Set method to 'matplotlib' do disable this
behaviour.
[/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata_plot/pl/utils.py:771](https://192.33.153.24/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata_plot/pl/utils.py#line=770): FutureWarning: The default value of 'ignore' for the na_action parameter in [pandas.Categorical.map](http://pandas.categorical.map/) is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
color_vector = color_source_vector.map(color_mapping)
Error while plotting cluster 0: The element does not contain any coordinate system named 'downscaled_hires', please pass a different coordinate system with the argument 'coordinate_system'.
INFO Rasterizing image for faster rendering.
[/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata/_core/_elements.py:105](https://192.33.153.24/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata/_core/_elements.py#line=104): UserWarning: Key wt1_square_008um already exists. Overwriting it in-memory.
self._check_key(key, self.keys(), self._shared_keys)
[/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata/_core/_elements.py:125](https://192.33.153.24/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata/_core/_elements.py#line=124): UserWarning: Key square_008um already exists. Overwriting it in-memory.
self._check_key(key, self.keys(), self._shared_keys)
[/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata_plot/pl/utils.py:771](https://192.33.153.24/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata_plot/pl/utils.py#line=770): FutureWarning: The default value of 'ignore' for the na_action parameter in [pandas.Categorical.map](http://pandas.categorical.map/) is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
color_vector = color_source_vector.map(color_mapping)
INFO Rasterizing image for faster rendering.
[/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata/_core/_elements.py:105](https://192.33.153.24/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata/_core/_elements.py#line=104): UserWarning: Key wt1_square_008um already exists. Overwriting it in-memory.
self._check_key(key, self.keys(), self._shared_keys)
[/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata/_core/_elements.py:125](https://192.33.153.24/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata/_core/_elements.py#line=124): UserWarning: Key square_008um already exists. Overwriting it in-memory.
self._check_key(key, self.keys(), self._shared_keys)
INFO Using 'datashader' backend with 'None' as reduction method to speed up plotting. Depending on the
reduction method, the value range of the plot might change. Set method to 'matplotlib' do disable this
behaviour.
[/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata_plot/pl/utils.py:771](https://192.33.153.24/opt/conda/envs/spatialdatahd/lib/python3.10/site-packages/spatialdata_plot/pl/utils.py#line=770): FutureWarning: The default value of 'ignore' for the na_action parameter in [pandas.Categorical.map](http://pandas.categorical.map/) is deprecated and will be changed to 'None' in a future version. Please set na_action to the desired value to avoid seeing this warning
color_vector = color_source_vector.map(color_mapping)
Error while plotting cluster 15: The element does not contain any coordinate system named 'downscaled_hires', please pass a different coordinate system with the argument 'coordinate_system'.
Though it seems that coordinate systems are set, as shown above.
Any ideas why?
Thanks!
Thanks for reporting 😊 I add also that the problem occurs only with the datashader backend.
