Fix palette and groups

src/spatialdata_plot/pl/basic.py

@@ -1,6 +1,7 @@
 from __future__ import annotations
 
 import sys
+import warnings
 from collections import OrderedDict
 from copy import deepcopy
 from pathlib import Path
@@ -762,7 +763,9 @@ def show(
         # go through tree
 
         for i, cs in enumerate(coordinate_systems):
-            sdata = self._copy()
+            with warnings.catch_warnings():
+                warnings.filterwarnings("ignore", category=UserWarning)
+                sdata = self._copy()
             _, has_images, has_labels, has_points, has_shapes = (
                 cs_contents.query(f"cs == '{cs}'").iloc[0, :].values.tolist()
             )
@@ -851,7 +854,7 @@ def show(
                                     source=sdata[table],
                                     target=sdata[table],
                                     key=params_copy.color[index],
-                                    palette=params_copy.palette,
+                                    palette=params_copy.palette[index],
                                 )
 
                     rasterize = (params_copy.scale is None) or (

src/spatialdata_plot/pl/render.py

@@ -604,8 +604,8 @@ def _render_labels(
             element_index=i,
             element_name=e,
             value_to_plot=cast(list[str], render_params.color)[i],
-            groups=render_params.groups,
-            palette=render_params.palette,
+            groups=render_params.groups[i],
+            palette=render_params.palette[i],
             na_color=render_params.cmap_params.na_color,
             cmap_params=render_params.cmap_params,
             table_name=cast(str, table_name),
@@ -686,7 +686,7 @@ def _render_labels(
             adata=table,
             value_to_plot=cast(list[str], render_params.color)[i],
             color_source_vector=color_source_vector,
-            palette=render_params.palette,
+            palette=render_params.palette[i],
             alpha=render_params.fill_alpha,
             na_color=render_params.cmap_params.na_color,
             legend_fontsize=legend_params.legend_fontsize,

src/spatialdata_plot/pl/utils.py

@@ -628,11 +628,11 @@ def _set_color_source_vec(
         color_source_vector = pd.Categorical(color_source_vector)  # convert, e.g., `pd.Series`
         categories = color_source_vector.categories
 
-        if groups is not None:
+        if groups is not None and groups[0] is not None:
             color_source_vector = color_source_vector.remove_categories(categories.difference(groups))
             categories = groups
 
-        if groups is not None:
+        if groups is not None and groups[0] is not None:
             if isinstance(palette, list):
                 palette_input = palette[0] if palette[0] is None else palette
         elif palette is not None and isinstance(palette, list):
@@ -717,6 +717,7 @@ def _get_palette(
     palette: ListedColormap | str | list[str] | None = None,
     alpha: float = 1.0,
 ) -> Mapping[str, str] | None:
+    palette = None if isinstance(palette, list) and palette[0] is None else palette
     if adata is not None and palette is None:
         try:
             palette = adata.uns[f"{cluster_key}_colors"]  # type: ignore[arg-type]
@@ -772,6 +773,7 @@ def _maybe_set_colors(
             palette = ListedColormap([palette])
         if isinstance(palette, ListedColormap):  # `scanpy` requires it
             palette = cycler(color=palette.colors)
+        palette = None
         add_colors_for_categorical_sample_annotation(target, key=key, force_update_colors=True, palette=palette)
 
 
@@ -809,6 +811,7 @@ def _decorate_axs(
             # order of clusters should agree to palette order
             clusters = color_source_vector.unique()
             clusters = clusters[~clusters.isnull()]
+            palette = None if isinstance(palette, list) and palette[0] else palette
             palette = _get_palette(
                 adata=adata, cluster_key=value_to_plot, categories=clusters, palette=palette, alpha=alpha
             )