Updated render_shapes doc (#199)

* Updated render_shapes doc

* Updated render_shapes

* halfway points

* Updated type hints and handling

* Fixed color behaviour

* Changed source of logger; fixed type in test

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fixed typos in documentation; minor correction to type checks

* Fixed test

* Added tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: timtreis

src/spatialdata_plot/pl/basic.py

@@ -82,7 +82,7 @@ def _render_shapes(
 
     for e in elements:
         shapes = sdata.shapes[e]
-        n_shapes = sum([len(s) for s in shapes])
+        n_shapes = sum(len(s) for s in shapes)
 
         if sdata.table is None:
             table = AnnData(None, obs=pd.DataFrame(index=pd.Index(np.arange(n_shapes), dtype=str)))
@@ -94,11 +94,11 @@ def _render_shapes(
             sdata=sdata_filt,
             element=sdata_filt.shapes[e],
             element_name=e,
-            value_to_plot=render_params.color,
+            value_to_plot=render_params.col_for_color,
             layer=render_params.layer,
             groups=render_params.groups,
             palette=render_params.palette,
-            na_color=render_params.cmap_params.na_color,
+            na_color=render_params.color or render_params.cmap_params.na_color,
             alpha=render_params.fill_alpha,
             cmap_params=render_params.cmap_params,
         )
@@ -162,14 +162,18 @@ def _render_shapes(
             len(set(color_vector)) == 1 and list(set(color_vector))[0] == to_hex(render_params.cmap_params.na_color)
         ):
             # necessary in case different shapes elements are annotated with one table
-            if color_source_vector is not None:
+            if color_source_vector is not None and render_params.col_for_color is not None:
                 color_source_vector = color_source_vector.remove_unused_categories()
+
+            # False if user specified color-like with 'color' parameter
+            colorbar = False if render_params.col_for_color is None else legend_params.colorbar
+
             _ = _decorate_axs(
                 ax=ax,
                 cax=cax,
                 fig_params=fig_params,
                 adata=table,
-                value_to_plot=render_params.color,
+                value_to_plot=render_params.col_for_color,
                 color_source_vector=color_source_vector,
                 palette=palette,
                 alpha=render_params.fill_alpha,
@@ -179,7 +183,7 @@ def _render_shapes(
                 legend_loc=legend_params.legend_loc,
                 legend_fontoutline=legend_params.legend_fontoutline,
                 na_in_legend=legend_params.na_in_legend,
-                colorbar=legend_params.colorbar,
+                colorbar=colorbar,
                 scalebar_dx=scalebar_params.scalebar_dx,
                 scalebar_units=scalebar_params.scalebar_units,
             )
@@ -194,12 +198,6 @@ def _render_points(
     scalebar_params: ScalebarParams,
     legend_params: LegendParams,
 ) -> None:
-    if render_params.groups is not None:
-        if isinstance(render_params.groups, str):
-            render_params.groups = [render_params.groups]
-        if not all(isinstance(g, str) for g in render_params.groups):
-            raise TypeError("All groups must be strings.")
-
     elements = render_params.elements
 
     sdata_filt = sdata.filter_by_coordinate_system(
@@ -214,43 +212,56 @@ def _render_points(
 
     for e in elements:
         points = sdata.points[e]
+        col_for_color = render_params.col_for_color
+
         coords = ["x", "y"]
-        if render_params.color is not None:
-            color = [render_params.color] if isinstance(render_params.color, str) else render_params.color
-            coords.extend(color)
+        if col_for_color is not None:
+            if col_for_color not in points.columns:
+                # no error in case there are multiple elements, but onyl some have color key
+                msg = f"Color key '{col_for_color}' for element '{e}' not been found, using default colors."
+                logger.warning(msg)
+            else:
+                coords += [col_for_color]
 
         points = points[coords].compute()
-        if render_params.groups is not None:
-            points = points[points[color].isin(render_params.groups).values]
-            points[color[0]] = points[color[0]].cat.set_categories(render_params.groups)
-        points = dask.dataframe.from_pandas(points, npartitions=1)
-        sdata_filt.points[e] = PointsModel.parse(points, coordinates={"x": "x", "y": "y"})
-
-        point_df = points[coords].compute()
+        if render_params.groups is not None and col_for_color is not None:
+            points = points[points[col_for_color].isin(render_params.groups)]
 
         # we construct an anndata to hack the plotting functions
         adata = AnnData(
-            X=point_df[["x", "y"]].values, obs=point_df[coords].reset_index(), dtype=point_df[["x", "y"]].values.dtype
+            X=points[["x", "y"]].values, obs=points[coords].reset_index(), dtype=points[["x", "y"]].values.dtype
         )
-        if render_params.color is not None:
-            cols = sc.get.obs_df(adata, render_params.color)
+
+        # Convert back to dask dataframe to modify sdata
+        points = dask.dataframe.from_pandas(points, npartitions=1)
+        sdata_filt.points[e] = PointsModel.parse(points, coordinates={"x": "x", "y": "y"})
+
+        if render_params.col_for_color is not None:
+            cols = sc.get.obs_df(adata, render_params.col_for_color)
             # maybe set color based on type
             if is_categorical_dtype(cols):
                 _maybe_set_colors(
                     source=adata,
                     target=adata,
-                    key=render_params.color,
+                    key=render_params.col_for_color,
                     palette=render_params.palette,
                 )
 
+        # when user specified a single color, we overwrite na with it
+        default_color = (
+            render_params.color
+            if render_params.col_for_color is None and render_params.color is not None
+            else render_params.cmap_params.na_color
+        )
+
         color_source_vector, color_vector, _ = _set_color_source_vec(
             sdata=sdata_filt,
             element=points,
             element_name=e,
-            value_to_plot=render_params.color,
+            value_to_plot=render_params.col_for_color,
             groups=render_params.groups,
             palette=render_params.palette,
-            na_color=render_params.cmap_params.na_color,
+            na_color=default_color,
             alpha=render_params.alpha,
             cmap_params=render_params.cmap_params,
         )
@@ -278,9 +289,7 @@ def _render_points(
         )
         cax = ax.add_collection(_cax)
 
-        if not (
-            len(set(color_vector)) == 1 and list(set(color_vector))[0] == to_hex(render_params.cmap_params.na_color)
-        ):
+        if len(set(color_vector)) != 1 or list(set(color_vector))[0] != to_hex(render_params.cmap_params.na_color):
             if color_source_vector is None:
                 palette = ListedColormap(dict.fromkeys(color_vector))
             else:
@@ -291,7 +300,7 @@ def _render_points(
                 cax=cax,
                 fig_params=fig_params,
                 adata=adata,
-                value_to_plot=render_params.color,
+                value_to_plot=render_params.col_for_color,
                 color_source_vector=color_source_vector,
                 palette=palette,
                 alpha=render_params.alpha,
@@ -629,8 +638,8 @@ def _render_labels(
             _cax = ax.imshow(
                 labels_infill,
                 rasterized=True,
-                cmap=render_params.cmap_params.cmap if not categorical else None,
-                norm=render_params.cmap_params.norm if not categorical else None,
+                cmap=None if categorical else render_params.cmap_params.cmap,
+                norm=None if categorical else render_params.cmap_params.norm,
                 alpha=render_params.fill_alpha,
                 origin="lower",
             )
@@ -652,14 +661,11 @@ def _render_labels(
             _cax = ax.imshow(
                 labels_contour,
                 rasterized=True,
-                cmap=render_params.cmap_params.cmap if not categorical else None,
-                norm=render_params.cmap_params.norm if not categorical else None,
+                cmap=None if categorical else render_params.cmap_params.cmap,
+                norm=None if categorical else render_params.cmap_params.norm,
                 alpha=render_params.outline_alpha,
                 origin="lower",
             )
-            _cax.set_transform(trans_data)
-            cax = ax.add_image(_cax)
-
         else:
             # Default: no alpha, contour = infill
             label = _map_color_seg(
@@ -676,13 +682,13 @@ def _render_labels(
             _cax = ax.imshow(
                 label,
                 rasterized=True,
-                cmap=render_params.cmap_params.cmap if not categorical else None,
-                norm=render_params.cmap_params.norm if not categorical else None,
+                cmap=None if categorical else render_params.cmap_params.cmap,
+                norm=None if categorical else render_params.cmap_params.norm,
                 alpha=render_params.fill_alpha,
                 origin="lower",
             )
-            _cax.set_transform(trans_data)
-            cax = ax.add_image(_cax)
+        _cax.set_transform(trans_data)
+        cax = ax.add_image(_cax)
 
         _ = _decorate_axs(
             ax=ax,

src/spatialdata_plot/pl/render.py

@@ -72,6 +72,7 @@ class ShapesRenderParams:
     outline_params: OutlineParams
     elements: str | Sequence[str] | None = None
     color: str | None = None
+    col_for_color: str | None = None
     groups: str | Sequence[str] | None = None
     contour_px: int | None = None
     layer: str | None = None
@@ -89,6 +90,7 @@ class PointsRenderParams:
     cmap_params: CmapParams
     elements: str | Sequence[str] | None = None
     color: str | None = None
+    col_for_color: str | None = None
     groups: str | Sequence[str] | None = None
     palette: ListedColormap | str | None = None
     alpha: float = 1.0

src/spatialdata_plot/pl/render_params.py

@@ -52,10 +52,10 @@
 from spatial_image import SpatialImage
 from spatialdata._core.operations.rasterize import rasterize
 from spatialdata._core.query.relational_query import _locate_value, get_values
-from spatialdata._logging import logger as logging
 from spatialdata._types import ArrayLike
 from spatialdata.models import Image2DModel, Labels2DModel, SpatialElement
 
+from spatialdata_plot._logging import logger
 from spatialdata_plot.pl.render_params import (
     CmapParams,
     FigParams,
@@ -379,7 +379,7 @@ def _set_outline(
     if outline_width == 0.0:
         outline = False
     if outline_width < 0.0:
-        logging.warning(f"Negative line widths are not allowed, changing {outline_width} to {(-1)*outline_width}")
+        logger.warning(f"Negative line widths are not allowed, changing {outline_width} to {(-1)*outline_width}")
         outline_width *= -1
 
     # the default black and white colors can be changed using the contour_config parameter
@@ -561,7 +561,7 @@ def _get_colors_for_categorical_obs(
             palette = default_102
         else:
             palette = ["grey" for _ in range(len_cat)]
-            logging.info("input has more than 103 categories. Uniform " "'grey' color will be used for all categories.")
+            logger.info("input has more than 103 categories. Uniform " "'grey' color will be used for all categories.")
     else:
         # raise error when user didn't provide the right number of colors in palette
         if isinstance(palette, list) and len(palette) != len(categories):
@@ -623,7 +623,7 @@ def _set_color_source_vec(
         # numerical case, return early
         if not is_categorical_dtype(color_source_vector):
             if palette is not None:
-                logging.warning(
+                logger.warning(
                     "Ignoring categorical palette which is given for a continuous variable. "
                     "Consider using `cmap` to pass a ColorMap."
                 )
@@ -651,7 +651,7 @@ def _set_color_source_vec(
 
         return color_source_vector, color_vector, True
 
-    logging.warning(f"Color key '{value_to_plot}' for element '{element_name}' not been found, using default colors.")
+    logger.warning(f"Color key '{value_to_plot}' for element '{element_name}' not been found, using default colors.")
     color = np.full(sdata.table.n_obs, to_hex(na_color))
     return color, color, False
 
@@ -723,7 +723,7 @@ def _get_palette(
                 )
             return {cat: to_hex(to_rgba(col)[:3]) for cat, col in zip(categories, palette)}
         except KeyError as e:
-            logging.warning(e)
+            logger.warning(e)
             return None
 
     len_cat = len(categories)
@@ -737,7 +737,7 @@ def _get_palette(
             palette = default_102
         else:
             palette = ["grey" for _ in range(len_cat)]
-            logging.info("input has more than 103 categories. Uniform " "'grey' color will be used for all categories.")
+            logger.info("input has more than 103 categories. Uniform " "'grey' color will be used for all categories.")
         return {cat: to_hex(to_rgba(col)[:3]) for cat, col in zip(categories, palette[:len_cat])}
 
     if isinstance(palette, str):
@@ -904,9 +904,9 @@ def save_fig(fig: Figure, path: str | Path, make_dir: bool = True, ext: str = "p
         try:
             path.parent.mkdir(parents=True, exist_ok=True)
         except OSError as e:
-            logging.debug(f"Unable to create directory `{path.parent}`. Reason: `{e}`")
+            logger.debug(f"Unable to create directory `{path.parent}`. Reason: `{e}`")
 
-    logging.debug(f"Saving figure to `{path!r}`")
+    logger.debug(f"Saving figure to `{path!r}`")
 
     kwargs.setdefault("bbox_inches", "tight")
     kwargs.setdefault("transparent", True)
@@ -1070,13 +1070,13 @@ def _mpl_ax_contains_elements(ax: Axes) -> bool:
 
 def _get_valid_cs(
     sdata: sd.SpatialData,
-    coordinate_systems: Sequence[str],
+    coordinate_systems: list[str],
     render_images: bool,
     render_labels: bool,
     render_points: bool,
     render_shapes: bool,
     elements: list[str],
-) -> Sequence[str]:
+) -> list[str]:
     """Get names of the valid coordinate systems.
 
     Valid cs are cs that contain elements to be rendered:
@@ -1090,8 +1090,10 @@ def _get_valid_cs(
     cs_mapping = _get_coordinate_system_mapping(sdata)
     valid_cs = []
     for cs in coordinate_systems:
-        if (len(elements) > 0 and any(e in elements for e in cs_mapping[cs])) or (
-            len(elements) == 0
+        if (
+            elements
+            and any(e in elements for e in cs_mapping[cs])
+            or not elements
             and (
                 (len(sdata.images.keys()) > 0 and render_images)
                 or (len(sdata.labels.keys()) > 0 and render_labels)
@@ -1101,7 +1103,7 @@ def _get_valid_cs(
         ):  # not nice, but ruff wants it (SIM114)
             valid_cs.append(cs)
         else:
-            logging.info(f"Dropping coordinate system '{cs}' since it doesn't have relevant elements.")
+            logger.info(f"Dropping coordinate system '{cs}' since it doesn't have relevant elements.")
     return valid_cs
 
 

src/spatialdata_plot/pl/utils.py

@@ -37,3 +37,6 @@ def test_plot_can_stack_render_points(self, sdata_blobs: SpatialData):
             .pl.render_points(elements="blobs_points", na_color="blue", size=10)
             .pl.show()
         )
+
+    def test_plot_color_recognises_actual_color_as_color(self, sdata_blobs: SpatialData):
+        sdata_blobs.pl.render_points(elements="blobs_points", color="red").pl.show()

tests/_images/Points_color_recognises_actual_color_as_color.png

@@ -261,3 +261,6 @@ def test_plot_can_stack_render_shapes(self, sdata_blobs: SpatialData):
             .pl.render_shapes(elements="blobs_polygons", na_color="blue", fill_alpha=0.5)
             .pl.show()
         )
+
+    def test_plot_color_recognises_actual_color_as_color(self, sdata_blobs: SpatialData):
+        (sdata_blobs.pl.render_shapes(elements="blobs_circles", color="red").pl.show())