Categorical data is now correctly colored in the legend when plotting

CHANGELOG.md

@@ -12,8 +12,10 @@ and this project adheres to [Semantic Versioning][].
 
 ### Fixed
 
--   Fix color assignment for NaN values (#257)
--   Fix channel str support #221
+-   Fixed channel str support (#221)
+-   Fixed color assignment for NaN values (#257)
+-   Updated incorrect link to documentation (#261)
+-   Fixed plotting of categorical data (#262)
 
 ## [0.2.2] - 2024-05-02
 

src/spatialdata_plot/pl/basic.py

@@ -503,16 +503,16 @@ def render_images(
     def render_labels(
         self,
         elements: list[str] | str | None = None,
-        color: list[str | None] | str | None = None,
-        groups: list[list[str | None]] | list[str | None] | str | None = None,
+        color: list[str] | str | None = None,
+        groups: list[str] | str | None = None,
         contour_px: int = 3,
         outline: bool = False,
-        palette: list[list[str | None]] | list[str | None] | str | None = None,
+        palette: list[ColorLike] | ColorLike | None = None,
         cmap: Colormap | str | None = None,
         norm: Normalize | None = None,
-        na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
+        na_color: ColorLike | None = "lightgrey",
         outline_alpha: float | int = 1.0,
-        fill_alpha: float | int = 0.3,
+        fill_alpha: float | int = 0.35,  # 0.3
         scale: list[str] | str | None = None,
         table_name: list[str] | str | None = None,
         **kwargs: Any,
@@ -554,8 +554,11 @@ def render_labels(
             Colormap for continuous annotations, see :class:`matplotlib.colors.Colormap`.
         norm : Normalize | None, optional
             Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
-        na_color : ColorLike | None, optional
-            Color to be used for NAs values, if present.
+        na_color : str | list[float] | None, default "lightgrey"
+            Color to be used for NAs values, if present. Can either be a named color
+            ("red"), a hex representation ("#000000ff") or a list of floats that
+            represent RGB/RGBA values (1.0, 0.0, 0.0, 1.0). When None, the values won't
+            be shown.
         outline_alpha : float | int, default 1.0
             Alpha value for the outline of the labels.
         fill_alpha : float | int, default 0.3

src/spatialdata_plot/pl/render.py

@@ -104,14 +104,25 @@ def _render_shapes(
             )
             sdata_filt[table_name].obs[col_for_color] = sdata_filt[table_name].obs[col_for_color].astype("category")
 
+        assert isinstance(groups, list), "groups must be a list"
+        if isinstance(groups[index], list) and groups[index][0] is None:
+            group = None
+        elif all(isinstance(g, str) for g in groups[index]):
+            group = groups[index]
+        else:
+            raise ValueError("groups must be a list of strings or a list of lists of strings")
+
+        if group is not None or (isinstance(group, list) and all(isinstance(g, str) for g in group)):
+            raise ValueError("groups must be a list of strings or a list of lists of strings")
+
         # get color vector (categorical or continuous)
         color_source_vector, color_vector, _ = _set_color_source_vec(
             sdata=sdata_filt,
             element=sdata_filt.shapes[e],
             element_index=index,
             element_name=e,
             value_to_plot=col_for_color,
-            groups=groups[index] if groups[index][0] is not None else None,
+            groups=group,
             palette=(
                 palettes[index] if palettes is not None else None
             ),  # and render_params.palette[index][0] is not None
@@ -192,6 +203,7 @@ def _render_shapes(
                 fig_params=fig_params,
                 adata=table,
                 value_to_plot=col_for_color,
+                color_vector=color_vector,
                 color_source_vector=color_source_vector,
                 palette=palette,
                 alpha=render_params.fill_alpha,
@@ -349,6 +361,7 @@ def _render_points(
                 fig_params=fig_params,
                 adata=adata,
                 value_to_plot=col_for_color,
+                color_vector=color_vector,
                 color_source_vector=color_source_vector,
                 palette=palette,
                 alpha=render_params.alpha,
@@ -596,6 +609,7 @@ def _render_labels(
     palettes = _return_list_list_str_none(render_params.palette)
     colors = _return_list_str_none(render_params.color)
     groups = _return_list_list_str_none(render_params.groups)
+    print(element_table_mapping)
 
     if render_params.outline is False:
         render_params.outline_alpha = 0
@@ -640,11 +654,11 @@ def _render_labels(
             instance_id = np.unique(label)
             table = None
         else:
-            regions, region_key, instance_key = get_table_keys(sdata[table_name])
+            _, region_key, instance_key = get_table_keys(sdata[table_name])
             table = sdata[table_name][sdata[table_name].obs[region_key].isin([e])]
 
             # get instance id based on subsetted table
-            instance_id = table.obs[instance_key].values
+            instance_id = np.unique(table.obs[instance_key].values)
 
         trans = get_transformation(label, get_all=True)[coordinate_system]
         affine_trans = trans.to_affine_matrix(input_axes=("x", "y"), output_axes=("x", "y"))
@@ -731,13 +745,17 @@ def _render_labels(
         _cax.set_transform(trans_data)
         cax = ax.add_image(_cax)
 
+        if groups[i][0] is not None and color_source_vector is not None:
+            color_source_vector = color_source_vector.set_categories(groups[i])
+
         _ = _decorate_axs(
             ax=ax,
             cax=cax,
             fig_params=fig_params,
             adata=table,
             value_to_plot=color,
             color_source_vector=color_source_vector,
+            color_vector=color_vector,
             palette=palettes[i],
             alpha=render_params.fill_alpha,
             na_color=render_params.cmap_params.na_color,