update

Author: giovp

src/spatialdata_plot/pl/basic.py

@@ -611,15 +611,8 @@ def show(
                     )
 
                 elif cmd == "render_points":
-                    for idx, ax in enumerate(axs):
-                        key = list(sdata.points.keys())[idx]
-                        if params["color_key"] is not None:
-                            if params["color_key"] not in sdata.points[key].columns:
-                                raise ValueError(
-                                    f"The column '{params['color_key']}' is not present in the 'metadata' of the points."
-                                )
-
-                        _render_points(sdata=sdata, params=params, key=key, ax=ax, extent=extent)
+                    key = list(sdata.points.keys())[0]  # TODO: remove, hack
+                    _render_points(sdata=sdata, params=params, key=key, ax=fig_params.ax, extent=extent)
 
                 elif cmd == "render_labels":
                     if (

src/spatialdata_plot/pl/render.py

@@ -113,7 +113,6 @@ def _get_collection_shape(
             patches = [Circle(circ, radius=r * s) for circ, r in zip(shapes["geometry"], shapes["radius"])]
 
         collection = PatchCollection(patches, snap=False, **kwargs)
-        print(c)
         if isinstance(c, np.ndarray) and np.issubdtype(c.dtype, np.number):
             collection.set_array(np.ma.masked_invalid(c))
             collection.set_norm(norm)
@@ -153,6 +152,7 @@ def _get_collection_shape(
         rasterized=sc_settings._vector_friendly,
         cmap=render_params.cmap_params.cmap,
         norm=norm,
+        alpha=render_params.alpha,
         # **kwargs,
     )
     cax = ax.add_collection(_cax)

src/spatialdata_plot/pl/utils.py

@@ -34,6 +34,7 @@
 from matplotlib.collections import Collection, PatchCollection
 from scanpy._settings import settings as sc_settings
 from scanpy.plotting._tools.scatterplots import _add_categorical_legend
+from spatialdata._logging import logger as logging
 
 Palette_t = Optional[Union[str, ListedColormap]]
 _Normalize = Union[Normalize, Sequence[Normalize]]
@@ -517,7 +518,7 @@ def _get_palette(
                     )
                 return {cat: to_hex(to_rgba(col)[:3]) for cat, col in zip(categories, palette)}
             except KeyError as e:
-                print(e)
+                logging.warning(e)
                 return None
 
     len_cat = len(categories)