Plot categorical color when colors are provided via .uns

[ArneDefauw]

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:

spatialdata-plot/src/spatialdata_plot/pl/utils.py

Line 758 in 478ab27

adata=sdata.table,

This PR fixes this;
#413

Minimal example to reproduce the issue:

import numpy as np
import pandas as pd
from anndata import AnnData
from spatialdata import get_element_instances
from spatialdata.datasets import blobs
from spatialdata.models import TableModel

import spatialdata_plot

RNG = np.random.default_rng(seed=42)

labels_name = "blobs_labels"

sdata_blobs = blobs()

instances = get_element_instances(sdata_blobs[labels_name])
n_obs = len(instances)
adata = AnnData(
    RNG.normal(size=(n_obs, 10)),
    obs=pd.DataFrame(RNG.normal(size=(n_obs, 3)), columns=["a", "b", "c"]),
)
adata.obs["instance_id"] = instances.values
adata.obs["category"] = RNG.choice(["a", "b", "c"], size=adata.n_obs)
adata.obs["category"][:3] = ["a", "b", "c"]
adata.obs["region"] = labels_name
table = TableModel.parse(
    adata=adata,
    region_key="region",
    instance_key="instance_id",
    region=labels_name,
)
sdata_blobs["other_table"] = table
sdata_blobs["other_table"].obs["category"] = sdata_blobs["other_table"].obs["category"].astype("category")

sdata_blobs["other_table"].uns["category_colors"] = ["#800080", "#008000", "#FFFF00"] #purple, green ,yellow
# placeholder, otherwise "category_colors" will be ignored
sdata_blobs["other_table"].uns["category"] = "__value__"
sdata_blobs.pl.render_labels("blobs_labels", color="category").pl.show()

With the small fix this gives

I've added a unit test which reproduces the issue in the PR https://github.com/ArneDefauw/spatialdata-plot/blob/5af65aa118f7abf87e47470038ecdbddb27ef1ca/tests/pl/test_render_labels.py#L217

As explained in the PR, I've stumbled upon an issue when trying to plot a subset of the data, trying to maintain the same colors, see https://github.com/ArneDefauw/spatialdata-plot/blob/5af65aa118f7abf87e47470038ecdbddb27ef1ca/tests/pl/test_render_labels.py#L225.

Starting from the code above, if we do:

sdata_blobs = bounding_box_query(
    sdata_blobs,
    axes=("y", "x"),
    min_coordinate=[0, 0],
    max_coordinate=[100, 100],
    target_coordinate_system="global",
)
sdata_blobs.pl.render_labels("blobs_labels", color="category").pl.show()

we get:

while we expect

This issue is caused by https://github.com/scverse/spatialdata/blob/03d3be80fad69ff54097e90a9e80ad02e9e0e242/src/spatialdata/_utils.py#L203.

There is a workaround for this:

 sdata_blobs["other_table"].obs["category"] = (
            sdata_blobs["other_table"].obs["category"].cat.remove_unused_categories()
        )

as documented here https://github.com/ArneDefauw/spatialdata-plot/blob/5af65aa118f7abf87e47470038ecdbddb27ef1ca/tests/pl/test_render_labels.py#L250, but this should probably be documented somewhere public.

[christophechu]

Really helpful