Categorical data is now correctly colored in the legend when plotting v2

CHANGELOG.md

@@ -10,18 +10,28 @@ and this project adheres to [Semantic Versioning][].
 
 ## [0.2.x] - tbd
 
-## [0.2.4] - 2024-08-07
-
 ### Added
 
-- Added utils function for 0-transparent cmaps (#302)
+- Replaced `outline` parameter in `render_labels` with alpha-based logic (#323)
+- Lowered RMSE-threshold for plot-based tests from 60 to 45 (#323)
+- Minor fixes for several tests as a result of the threshold change (#323)
 
 ### Changed
 
 -
 
 ### Fixed
 
+-
+
+## [0.2.4] - 2024-08-07
+
+### Added
+
+- Added utils function for 0-transparent cmaps (#302)
+
+### Fixed
+
 - Took RNG out of categorical label test (#306)
 - Performance bug when plotting shapes (#298)
 - scale parameter was ignored for single-scale images (#301)

src/spatialdata_plot/pl/basic.py

@@ -59,6 +59,9 @@
 )
 from spatialdata_plot.pp.utils import _verify_plotting_tree
 
+# replace with
+# from spatialdata._types import ColorLike
+# once https://github.com/scverse/spatialdata/pull/689/ is in a release
 ColorLike = Union[tuple[float, ...], str]
 
 
@@ -158,11 +161,10 @@ def render_shapes(
  fill_alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
- outline: bool = False,
+ na_color: ColorLike | None = "default",
  outline_width: float | int = 1.5,
  outline_color: str | list[float] = "#000000ff",
- outline_alpha: float | int = 1.0,
+ outline_alpha: float | int = 0.0,
  cmap: Colormap | str | None = None,
  norm: bool | Normalize = False,
  scale: float | int = 1.0,
@@ -201,19 +203,17 @@ def render_shapes(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If element is None, broadcasting behaviour is attempted (use the same values for
  all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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 : bool, default False
- If `True`, a border around the shape elements is plotted.
  outline_width : float | int, default 1.5
  Width of the border.
  outline_color : str | list[float], default "#000000ff"
  Color of the border. 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).
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of shapes.
+ outline_alpha : float | int, default 0.0
+ Alpha value for the outline of shapes. Invisible by default.
  cmap : Colormap | str | None, optional
  Colormap for discrete or continuous annotations using 'color', see :class:`matplotlib.colors.Colormap`.
  norm : bool | Normalize, default False
@@ -249,7 +249,6 @@ def render_shapes(
  palette=palette,
  color=color,
  na_color=na_color,
- outline=outline,
  outline_alpha=outline_alpha,
  outline_color=outline_color,
  outline_width=outline_width,
@@ -263,16 +262,15 @@ def render_shapes(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- outline_params = _set_outline(outline, outline_width, outline_color)
+ outline_params = _set_outline(outline_alpha > 0, outline_width, outline_color)
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_shapes"] = ShapesRenderParams(
  element=element,
  color=param_values["color"],
@@ -301,7 +299,7 @@ def render_points(
  alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
+ na_color: ColorLike | None = "default",
  cmap: Colormap | str | None = None,
  norm: None | Normalize = None,
  size: float | int = 1.0,
@@ -339,7 +337,7 @@ def render_points(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If `element` is `None`, broadcasting behaviour is attempted (use the same values
  for all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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.
@@ -389,14 +387,13 @@ def render_points(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_points"] = PointsRenderParams(
  element=element,
  color=param_values["color"],
@@ -422,7 +419,7 @@ def render_images(
  channel: list[str] | list[int] | str | int | None = None,
  cmap: list[Colormap | str] | Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
+ na_color: ColorLike | None = "default",
  palette: list[str] | str | None = None,
  alpha: float | int = 1.0,
  percentiles_for_norm: tuple[float, float] | None = None,
@@ -452,8 +449,10 @@ def render_images(
  norm : Normalize | None, optional
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
  Applies to all channels if set.
- na_color : ColorLike | None, default (0.0, 0.0, 0.0, 0.0)
- Color to be used for NA values. Accepts color-like values (string, hex, RGB(A)).
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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.
  palette : list[str] | str | None
  Palette to color images. The number of palettes should be equal to the number of channels.
  alpha : float | int, default 1.0
@@ -494,27 +493,32 @@ def render_images(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params: list[CmapParams] | CmapParams
- if isinstance(cmap, list):
- cmap_params = [
- _prepare_cmap_norm(
- cmap=c,
+ for element, param_values in params_dict.items():
+ # cmap_params = _prepare_cmap_norm(
+ # cmap=params_dict[element]["cmap"],
+ # norm=norm,
+ # na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ # **kwargs,
+ # )
+ cmap_params: list[CmapParams] | CmapParams
+ if isinstance(cmap, list):
+ cmap_params = [
+ _prepare_cmap_norm(
+ cmap=c,
+ norm=norm,
+ na_color=param_values["na_color"],
+ **kwargs,
+ )
+ for c in cmap
+ ]
+
+ else:
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
  norm=norm,
- na_color=na_color, # type: ignore[arg-type]
+ na_color=param_values["na_color"],
  **kwargs,
  )
- for c in cmap
- ]
-
- else:
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- for element, param_values in params_dict.items():
  sdata.plotting_tree[f"{n_steps+1}_render_images"] = ImageRenderParams(
  element=element,
  channel=param_values["channel"],
@@ -536,12 +540,11 @@ def render_labels(
  color: str | None = None,
  groups: list[str] | str | None = None,
  contour_px: int | None = 3,
- outline: bool = False,
  palette: list[str] | str | None = None,
  cmap: Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
- outline_alpha: float | int = 1.0,
+ na_color: ColorLike | None = "default",
+ outline_alpha: float | int = 0.0,
  fill_alpha: float | int = 0.4,
  scale: str | None = None,
  table_name: str | None = None,
@@ -576,16 +579,16 @@ def render_labels(
  contour_px : int, default 3
  Draw contour of specified width for each segment. If `None`, fills entire segment, see:
  func:`skimage.morphology.erosion`.
- outline : bool, default False
- Whether to plot boundaries around segmentation masks.
  cmap : Colormap | str | None
  Colormap for continuous annotations, see :class:`matplotlib.colors.Colormap`.
  norm : Normalize | None
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
- na_color : ColorLike | None
- Color to be used for NAs values, if present.
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of the labels.
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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 0.0
+ Alpha value for the outline of the labels. Invisible by default.
  fill_alpha : float | int, default 0.3
  Alpha value for the fill of the labels.
  scale : str | None
@@ -615,7 +618,6 @@ def render_labels(
  groups=groups,
  na_color=na_color,
  norm=norm,
- outline=outline,
  outline_alpha=outline_alpha,
  palette=palette,
  scale=scale,
@@ -625,20 +627,19 @@ def render_labels(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_labels"] = LabelsRenderParams(
  element=element,
  color=param_values["color"],
  groups=param_values["groups"],
  contour_px=param_values["contour_px"],
- outline=param_values["outline"],
  cmap_params=cmap_params,
  palette=param_values["palette"],
  outline_alpha=param_values["outline_alpha"],

CHANGELOG.md

@@ -10,18 +10,28 @@ and this project adheres to [Semantic Versioning][].
 
 ## [0.2.x] - tbd
 
-## [0.2.4] - 2024-08-07
-
 ### Added
 
-- Added utils function for 0-transparent cmaps (#302)
+- Replaced `outline` parameter in `render_labels` with alpha-based logic (#323)
+- Lowered RMSE-threshold for plot-based tests from 60 to 45 (#323)
+- Minor fixes for several tests as a result of the threshold change (#323)
 
 ### Changed
 
 -
 
 ### Fixed
 
+-
+
+## [0.2.4] - 2024-08-07
+
+### Added
+
+- Added utils function for 0-transparent cmaps (#302)
+
+### Fixed
+
 - Took RNG out of categorical label test (#306)
 - Performance bug when plotting shapes (#298)
 - scale parameter was ignored for single-scale images (#301)

src/spatialdata_plot/pl/basic.py

@@ -59,6 +59,9 @@
 )
 from spatialdata_plot.pp.utils import _verify_plotting_tree
 
+# replace with
+# from spatialdata._types import ColorLike
+# once https://github.com/scverse/spatialdata/pull/689/ is in a release
 ColorLike = Union[tuple[float, ...], str]
 
 
@@ -158,11 +161,10 @@ def render_shapes(
  fill_alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
- outline: bool = False,
+ na_color: ColorLike | None = "default",
  outline_width: float | int = 1.5,
  outline_color: str | list[float] = "#000000ff",
- outline_alpha: float | int = 1.0,
+ outline_alpha: float | int = 0.0,
  cmap: Colormap | str | None = None,
  norm: bool | Normalize = False,
  scale: float | int = 1.0,
@@ -201,19 +203,17 @@ def render_shapes(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If element is None, broadcasting behaviour is attempted (use the same values for
  all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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 : bool, default False
- If `True`, a border around the shape elements is plotted.
  outline_width : float | int, default 1.5
  Width of the border.
  outline_color : str | list[float], default "#000000ff"
  Color of the border. 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).
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of shapes.
+ outline_alpha : float | int, default 0.0
+ Alpha value for the outline of shapes. Invisible by default.
  cmap : Colormap | str | None, optional
  Colormap for discrete or continuous annotations using 'color', see :class:`matplotlib.colors.Colormap`.
  norm : bool | Normalize, default False
@@ -249,7 +249,6 @@ def render_shapes(
  palette=palette,
  color=color,
  na_color=na_color,
- outline=outline,
  outline_alpha=outline_alpha,
  outline_color=outline_color,
  outline_width=outline_width,
@@ -263,16 +262,15 @@ def render_shapes(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- outline_params = _set_outline(outline, outline_width, outline_color)
+ outline_params = _set_outline(outline_alpha > 0, outline_width, outline_color)
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_shapes"] = ShapesRenderParams(
  element=element,
  color=param_values["color"],
@@ -301,7 +299,7 @@ def render_points(
  alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
+ na_color: ColorLike | None = "default",
  cmap: Colormap | str | None = None,
  norm: None | Normalize = None,
  size: float | int = 1.0,
@@ -339,7 +337,7 @@ def render_points(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If `element` is `None`, broadcasting behaviour is attempted (use the same values
  for all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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.
@@ -389,14 +387,13 @@ def render_points(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_points"] = PointsRenderParams(
  element=element,
  color=param_values["color"],
@@ -422,7 +419,7 @@ def render_images(
  channel: list[str] | list[int] | str | int | None = None,
  cmap: list[Colormap | str] | Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
+ na_color: ColorLike | None = "default",
  palette: list[str] | str | None = None,
  alpha: float | int = 1.0,
  percentiles_for_norm: tuple[float, float] | None = None,
@@ -452,8 +449,10 @@ def render_images(
  norm : Normalize | None, optional
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
  Applies to all channels if set.
- na_color : ColorLike | None, default (0.0, 0.0, 0.0, 0.0)
- Color to be used for NA values. Accepts color-like values (string, hex, RGB(A)).
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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.
  palette : list[str] | str | None
  Palette to color images. The number of palettes should be equal to the number of channels.
  alpha : float | int, default 1.0
@@ -494,27 +493,32 @@ def render_images(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params: list[CmapParams] | CmapParams
- if isinstance(cmap, list):
- cmap_params = [
- _prepare_cmap_norm(
- cmap=c,
+ for element, param_values in params_dict.items():
+ # cmap_params = _prepare_cmap_norm(
+ # cmap=params_dict[element]["cmap"],
+ # norm=norm,
+ # na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ # **kwargs,
+ # )
+ cmap_params: list[CmapParams] | CmapParams
+ if isinstance(cmap, list):
+ cmap_params = [
+ _prepare_cmap_norm(
+ cmap=c,
+ norm=norm,
+ na_color=param_values["na_color"],
+ **kwargs,
+ )
+ for c in cmap
+ ]
+
+ else:
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
  norm=norm,
- na_color=na_color, # type: ignore[arg-type]
+ na_color=param_values["na_color"],
  **kwargs,
  )
- for c in cmap
- ]
-
- else:
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- for element, param_values in params_dict.items():
  sdata.plotting_tree[f"{n_steps+1}_render_images"] = ImageRenderParams(
  element=element,
  channel=param_values["channel"],
@@ -536,12 +540,11 @@ def render_labels(
  color: str | None = None,
  groups: list[str] | str | None = None,
  contour_px: int | None = 3,
- outline: bool = False,
  palette: list[str] | str | None = None,
  cmap: Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
- outline_alpha: float | int = 1.0,
+ na_color: ColorLike | None = "default",
+ outline_alpha: float | int = 0.0,
  fill_alpha: float | int = 0.4,
  scale: str | None = None,
  table_name: str | None = None,
@@ -576,16 +579,16 @@ def render_labels(
  contour_px : int, default 3
  Draw contour of specified width for each segment. If `None`, fills entire segment, see:
  func:`skimage.morphology.erosion`.
- outline : bool, default False
- Whether to plot boundaries around segmentation masks.
  cmap : Colormap | str | None
  Colormap for continuous annotations, see :class:`matplotlib.colors.Colormap`.
  norm : Normalize | None
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
- na_color : ColorLike | None
- Color to be used for NAs values, if present.
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of the labels.
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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 0.0
+ Alpha value for the outline of the labels. Invisible by default.
  fill_alpha : float | int, default 0.3
  Alpha value for the fill of the labels.
  scale : str | None
@@ -615,7 +618,6 @@ def render_labels(
  groups=groups,
  na_color=na_color,
  norm=norm,
- outline=outline,
  outline_alpha=outline_alpha,
  palette=palette,
  scale=scale,
@@ -625,20 +627,19 @@ def render_labels(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_labels"] = LabelsRenderParams(
  element=element,
  color=param_values["color"],
  groups=param_values["groups"],
  contour_px=param_values["contour_px"],
- outline=param_values["outline"],
  cmap_params=cmap_params,
  palette=param_values["palette"],
  outline_alpha=param_values["outline_alpha"],

CHANGELOG.md

@@ -10,18 +10,28 @@ and this project adheres to [Semantic Versioning][].
 
 ## [0.2.x] - tbd
 
-## [0.2.4] - 2024-08-07
-
 ### Added
 
-- Added utils function for 0-transparent cmaps (#302)
+- Replaced `outline` parameter in `render_labels` with alpha-based logic (#323)
+- Lowered RMSE-threshold for plot-based tests from 60 to 45 (#323)
+- Minor fixes for several tests as a result of the threshold change (#323)
 
 ### Changed
 
 -
 
 ### Fixed
 
+-
+
+## [0.2.4] - 2024-08-07
+
+### Added
+
+- Added utils function for 0-transparent cmaps (#302)
+
+### Fixed
+
 - Took RNG out of categorical label test (#306)
 - Performance bug when plotting shapes (#298)
 - scale parameter was ignored for single-scale images (#301)

src/spatialdata_plot/pl/basic.py

@@ -59,6 +59,9 @@
 )
 from spatialdata_plot.pp.utils import _verify_plotting_tree
 
+# replace with
+# from spatialdata._types import ColorLike
+# once https://github.com/scverse/spatialdata/pull/689/ is in a release
 ColorLike = Union[tuple[float, ...], str]
 
 
@@ -158,11 +161,10 @@ def render_shapes(
  fill_alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
- outline: bool = False,
+ na_color: ColorLike | None = "default",
  outline_width: float | int = 1.5,
  outline_color: str | list[float] = "#000000ff",
- outline_alpha: float | int = 1.0,
+ outline_alpha: float | int = 0.0,
  cmap: Colormap | str | None = None,
  norm: bool | Normalize = False,
  scale: float | int = 1.0,
@@ -201,19 +203,17 @@ def render_shapes(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If element is None, broadcasting behaviour is attempted (use the same values for
  all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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 : bool, default False
- If `True`, a border around the shape elements is plotted.
  outline_width : float | int, default 1.5
  Width of the border.
  outline_color : str | list[float], default "#000000ff"
  Color of the border. 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).
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of shapes.
+ outline_alpha : float | int, default 0.0
+ Alpha value for the outline of shapes. Invisible by default.
  cmap : Colormap | str | None, optional
  Colormap for discrete or continuous annotations using 'color', see :class:`matplotlib.colors.Colormap`.
  norm : bool | Normalize, default False
@@ -249,7 +249,6 @@ def render_shapes(
  palette=palette,
  color=color,
  na_color=na_color,
- outline=outline,
  outline_alpha=outline_alpha,
  outline_color=outline_color,
  outline_width=outline_width,
@@ -263,16 +262,15 @@ def render_shapes(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- outline_params = _set_outline(outline, outline_width, outline_color)
+ outline_params = _set_outline(outline_alpha > 0, outline_width, outline_color)
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_shapes"] = ShapesRenderParams(
  element=element,
  color=param_values["color"],
@@ -301,7 +299,7 @@ def render_points(
  alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
+ na_color: ColorLike | None = "default",
  cmap: Colormap | str | None = None,
  norm: None | Normalize = None,
  size: float | int = 1.0,
@@ -339,7 +337,7 @@ def render_points(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If `element` is `None`, broadcasting behaviour is attempted (use the same values
  for all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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.
@@ -389,14 +387,13 @@ def render_points(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_points"] = PointsRenderParams(
  element=element,
  color=param_values["color"],
@@ -422,7 +419,7 @@ def render_images(
  channel: list[str] | list[int] | str | int | None = None,
  cmap: list[Colormap | str] | Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
+ na_color: ColorLike | None = "default",
  palette: list[str] | str | None = None,
  alpha: float | int = 1.0,
  percentiles_for_norm: tuple[float, float] | None = None,
@@ -452,8 +449,10 @@ def render_images(
  norm : Normalize | None, optional
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
  Applies to all channels if set.
- na_color : ColorLike | None, default (0.0, 0.0, 0.0, 0.0)
- Color to be used for NA values. Accepts color-like values (string, hex, RGB(A)).
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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.
  palette : list[str] | str | None
  Palette to color images. The number of palettes should be equal to the number of channels.
  alpha : float | int, default 1.0
@@ -494,27 +493,32 @@ def render_images(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params: list[CmapParams] | CmapParams
- if isinstance(cmap, list):
- cmap_params = [
- _prepare_cmap_norm(
- cmap=c,
+ for element, param_values in params_dict.items():
+ # cmap_params = _prepare_cmap_norm(
+ # cmap=params_dict[element]["cmap"],
+ # norm=norm,
+ # na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ # **kwargs,
+ # )
+ cmap_params: list[CmapParams] | CmapParams
+ if isinstance(cmap, list):
+ cmap_params = [
+ _prepare_cmap_norm(
+ cmap=c,
+ norm=norm,
+ na_color=param_values["na_color"],
+ **kwargs,
+ )
+ for c in cmap
+ ]
+
+ else:
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
  norm=norm,
- na_color=na_color, # type: ignore[arg-type]
+ na_color=param_values["na_color"],
  **kwargs,
  )
- for c in cmap
- ]
-
- else:
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- for element, param_values in params_dict.items():
  sdata.plotting_tree[f"{n_steps+1}_render_images"] = ImageRenderParams(
  element=element,
  channel=param_values["channel"],
@@ -536,12 +540,11 @@ def render_labels(
  color: str | None = None,
  groups: list[str] | str | None = None,
  contour_px: int | None = 3,
- outline: bool = False,
  palette: list[str] | str | None = None,
  cmap: Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
- outline_alpha: float | int = 1.0,
+ na_color: ColorLike | None = "default",
+ outline_alpha: float | int = 0.0,
  fill_alpha: float | int = 0.4,
  scale: str | None = None,
  table_name: str | None = None,
@@ -576,16 +579,16 @@ def render_labels(
  contour_px : int, default 3
  Draw contour of specified width for each segment. If `None`, fills entire segment, see:
  func:`skimage.morphology.erosion`.
- outline : bool, default False
- Whether to plot boundaries around segmentation masks.
  cmap : Colormap | str | None
  Colormap for continuous annotations, see :class:`matplotlib.colors.Colormap`.
  norm : Normalize | None
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
- na_color : ColorLike | None
- Color to be used for NAs values, if present.
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of the labels.
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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 0.0
+ Alpha value for the outline of the labels. Invisible by default.
  fill_alpha : float | int, default 0.3
  Alpha value for the fill of the labels.
  scale : str | None
@@ -615,7 +618,6 @@ def render_labels(
  groups=groups,
  na_color=na_color,
  norm=norm,
- outline=outline,
  outline_alpha=outline_alpha,
  palette=palette,
  scale=scale,
@@ -625,20 +627,19 @@ def render_labels(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_labels"] = LabelsRenderParams(
  element=element,
  color=param_values["color"],
  groups=param_values["groups"],
  contour_px=param_values["contour_px"],
- outline=param_values["outline"],
  cmap_params=cmap_params,
  palette=param_values["palette"],
  outline_alpha=param_values["outline_alpha"],

CHANGELOG.md

@@ -10,18 +10,28 @@ and this project adheres to [Semantic Versioning][].
 
 ## [0.2.x] - tbd
 
-## [0.2.4] - 2024-08-07
-
 ### Added
 
-- Added utils function for 0-transparent cmaps (#302)
+- Replaced `outline` parameter in `render_labels` with alpha-based logic (#323)
+- Lowered RMSE-threshold for plot-based tests from 60 to 45 (#323)
+- Minor fixes for several tests as a result of the threshold change (#323)
 
 ### Changed
 
 -
 
 ### Fixed
 
+-
+
+## [0.2.4] - 2024-08-07
+
+### Added
+
+- Added utils function for 0-transparent cmaps (#302)
+
+### Fixed
+
 - Took RNG out of categorical label test (#306)
 - Performance bug when plotting shapes (#298)
 - scale parameter was ignored for single-scale images (#301)

src/spatialdata_plot/pl/basic.py

@@ -59,6 +59,9 @@
 )
 from spatialdata_plot.pp.utils import _verify_plotting_tree
 
+# replace with
+# from spatialdata._types import ColorLike
+# once https://github.com/scverse/spatialdata/pull/689/ is in a release
 ColorLike = Union[tuple[float, ...], str]
 
 
@@ -158,11 +161,10 @@ def render_shapes(
  fill_alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
- outline: bool = False,
+ na_color: ColorLike | None = "default",
  outline_width: float | int = 1.5,
  outline_color: str | list[float] = "#000000ff",
- outline_alpha: float | int = 1.0,
+ outline_alpha: float | int = 0.0,
  cmap: Colormap | str | None = None,
  norm: bool | Normalize = False,
  scale: float | int = 1.0,
@@ -201,19 +203,17 @@ def render_shapes(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If element is None, broadcasting behaviour is attempted (use the same values for
  all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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 : bool, default False
- If `True`, a border around the shape elements is plotted.
  outline_width : float | int, default 1.5
  Width of the border.
  outline_color : str | list[float], default "#000000ff"
  Color of the border. 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).
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of shapes.
+ outline_alpha : float | int, default 0.0
+ Alpha value for the outline of shapes. Invisible by default.
  cmap : Colormap | str | None, optional
  Colormap for discrete or continuous annotations using 'color', see :class:`matplotlib.colors.Colormap`.
  norm : bool | Normalize, default False
@@ -249,7 +249,6 @@ def render_shapes(
  palette=palette,
  color=color,
  na_color=na_color,
- outline=outline,
  outline_alpha=outline_alpha,
  outline_color=outline_color,
  outline_width=outline_width,
@@ -263,16 +262,15 @@ def render_shapes(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- outline_params = _set_outline(outline, outline_width, outline_color)
+ outline_params = _set_outline(outline_alpha > 0, outline_width, outline_color)
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_shapes"] = ShapesRenderParams(
  element=element,
  color=param_values["color"],
@@ -301,7 +299,7 @@ def render_points(
  alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
+ na_color: ColorLike | None = "default",
  cmap: Colormap | str | None = None,
  norm: None | Normalize = None,
  size: float | int = 1.0,
@@ -339,7 +337,7 @@ def render_points(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If `element` is `None`, broadcasting behaviour is attempted (use the same values
  for all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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.
@@ -389,14 +387,13 @@ def render_points(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_points"] = PointsRenderParams(
  element=element,
  color=param_values["color"],
@@ -422,7 +419,7 @@ def render_images(
  channel: list[str] | list[int] | str | int | None = None,
  cmap: list[Colormap | str] | Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
+ na_color: ColorLike | None = "default",
  palette: list[str] | str | None = None,
  alpha: float | int = 1.0,
  percentiles_for_norm: tuple[float, float] | None = None,
@@ -452,8 +449,10 @@ def render_images(
  norm : Normalize | None, optional
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
  Applies to all channels if set.
- na_color : ColorLike | None, default (0.0, 0.0, 0.0, 0.0)
- Color to be used for NA values. Accepts color-like values (string, hex, RGB(A)).
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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.
  palette : list[str] | str | None
  Palette to color images. The number of palettes should be equal to the number of channels.
  alpha : float | int, default 1.0
@@ -494,27 +493,32 @@ def render_images(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params: list[CmapParams] | CmapParams
- if isinstance(cmap, list):
- cmap_params = [
- _prepare_cmap_norm(
- cmap=c,
+ for element, param_values in params_dict.items():
+ # cmap_params = _prepare_cmap_norm(
+ # cmap=params_dict[element]["cmap"],
+ # norm=norm,
+ # na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ # **kwargs,
+ # )
+ cmap_params: list[CmapParams] | CmapParams
+ if isinstance(cmap, list):
+ cmap_params = [
+ _prepare_cmap_norm(
+ cmap=c,
+ norm=norm,
+ na_color=param_values["na_color"],
+ **kwargs,
+ )
+ for c in cmap
+ ]
+
+ else:
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
  norm=norm,
- na_color=na_color, # type: ignore[arg-type]
+ na_color=param_values["na_color"],
  **kwargs,
  )
- for c in cmap
- ]
-
- else:
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- for element, param_values in params_dict.items():
  sdata.plotting_tree[f"{n_steps+1}_render_images"] = ImageRenderParams(
  element=element,
  channel=param_values["channel"],
@@ -536,12 +540,11 @@ def render_labels(
  color: str | None = None,
  groups: list[str] | str | None = None,
  contour_px: int | None = 3,
- outline: bool = False,
  palette: list[str] | str | None = None,
  cmap: Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
- outline_alpha: float | int = 1.0,
+ na_color: ColorLike | None = "default",
+ outline_alpha: float | int = 0.0,
  fill_alpha: float | int = 0.4,
  scale: str | None = None,
  table_name: str | None = None,
@@ -576,16 +579,16 @@ def render_labels(
  contour_px : int, default 3
  Draw contour of specified width for each segment. If `None`, fills entire segment, see:
  func:`skimage.morphology.erosion`.
- outline : bool, default False
- Whether to plot boundaries around segmentation masks.
  cmap : Colormap | str | None
  Colormap for continuous annotations, see :class:`matplotlib.colors.Colormap`.
  norm : Normalize | None
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
- na_color : ColorLike | None
- Color to be used for NAs values, if present.
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of the labels.
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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 0.0
+ Alpha value for the outline of the labels. Invisible by default.
  fill_alpha : float | int, default 0.3
  Alpha value for the fill of the labels.
  scale : str | None
@@ -615,7 +618,6 @@ def render_labels(
  groups=groups,
  na_color=na_color,
  norm=norm,
- outline=outline,
  outline_alpha=outline_alpha,
  palette=palette,
  scale=scale,
@@ -625,20 +627,19 @@ def render_labels(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_labels"] = LabelsRenderParams(
  element=element,
  color=param_values["color"],
  groups=param_values["groups"],
  contour_px=param_values["contour_px"],
- outline=param_values["outline"],
  cmap_params=cmap_params,
  palette=param_values["palette"],
  outline_alpha=param_values["outline_alpha"],

CHANGELOG.md

@@ -10,18 +10,28 @@ and this project adheres to [Semantic Versioning][].
 
 ## [0.2.x] - tbd
 
-## [0.2.4] - 2024-08-07
-
 ### Added
 
-- Added utils function for 0-transparent cmaps (#302)
+- Replaced `outline` parameter in `render_labels` with alpha-based logic (#323)
+- Lowered RMSE-threshold for plot-based tests from 60 to 45 (#323)
+- Minor fixes for several tests as a result of the threshold change (#323)
 
 ### Changed
 
 -
 
 ### Fixed
 
+-
+
+## [0.2.4] - 2024-08-07
+
+### Added
+
+- Added utils function for 0-transparent cmaps (#302)
+
+### Fixed
+
 - Took RNG out of categorical label test (#306)
 - Performance bug when plotting shapes (#298)
 - scale parameter was ignored for single-scale images (#301)

src/spatialdata_plot/pl/basic.py

@@ -59,6 +59,9 @@
 )
 from spatialdata_plot.pp.utils import _verify_plotting_tree
 
+# replace with
+# from spatialdata._types import ColorLike
+# once https://github.com/scverse/spatialdata/pull/689/ is in a release
 ColorLike = Union[tuple[float, ...], str]
 
 
@@ -158,11 +161,10 @@ def render_shapes(
  fill_alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
- outline: bool = False,
+ na_color: ColorLike | None = "default",
  outline_width: float | int = 1.5,
  outline_color: str | list[float] = "#000000ff",
- outline_alpha: float | int = 1.0,
+ outline_alpha: float | int = 0.0,
  cmap: Colormap | str | None = None,
  norm: bool | Normalize = False,
  scale: float | int = 1.0,
@@ -201,19 +203,17 @@ def render_shapes(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If element is None, broadcasting behaviour is attempted (use the same values for
  all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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 : bool, default False
- If `True`, a border around the shape elements is plotted.
  outline_width : float | int, default 1.5
  Width of the border.
  outline_color : str | list[float], default "#000000ff"
  Color of the border. 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).
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of shapes.
+ outline_alpha : float | int, default 0.0
+ Alpha value for the outline of shapes. Invisible by default.
  cmap : Colormap | str | None, optional
  Colormap for discrete or continuous annotations using 'color', see :class:`matplotlib.colors.Colormap`.
  norm : bool | Normalize, default False
@@ -249,7 +249,6 @@ def render_shapes(
  palette=palette,
  color=color,
  na_color=na_color,
- outline=outline,
  outline_alpha=outline_alpha,
  outline_color=outline_color,
  outline_width=outline_width,
@@ -263,16 +262,15 @@ def render_shapes(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- outline_params = _set_outline(outline, outline_width, outline_color)
+ outline_params = _set_outline(outline_alpha > 0, outline_width, outline_color)
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_shapes"] = ShapesRenderParams(
  element=element,
  color=param_values["color"],
@@ -301,7 +299,7 @@ def render_points(
  alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
+ na_color: ColorLike | None = "default",
  cmap: Colormap | str | None = None,
  norm: None | Normalize = None,
  size: float | int = 1.0,
@@ -339,7 +337,7 @@ def render_points(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If `element` is `None`, broadcasting behaviour is attempted (use the same values
  for all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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.
@@ -389,14 +387,13 @@ def render_points(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_points"] = PointsRenderParams(
  element=element,
  color=param_values["color"],
@@ -422,7 +419,7 @@ def render_images(
  channel: list[str] | list[int] | str | int | None = None,
  cmap: list[Colormap | str] | Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
+ na_color: ColorLike | None = "default",
  palette: list[str] | str | None = None,
  alpha: float | int = 1.0,
  percentiles_for_norm: tuple[float, float] | None = None,
@@ -452,8 +449,10 @@ def render_images(
  norm : Normalize | None, optional
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
  Applies to all channels if set.
- na_color : ColorLike | None, default (0.0, 0.0, 0.0, 0.0)
- Color to be used for NA values. Accepts color-like values (string, hex, RGB(A)).
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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.
  palette : list[str] | str | None
  Palette to color images. The number of palettes should be equal to the number of channels.
  alpha : float | int, default 1.0
@@ -494,27 +493,32 @@ def render_images(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params: list[CmapParams] | CmapParams
- if isinstance(cmap, list):
- cmap_params = [
- _prepare_cmap_norm(
- cmap=c,
+ for element, param_values in params_dict.items():
+ # cmap_params = _prepare_cmap_norm(
+ # cmap=params_dict[element]["cmap"],
+ # norm=norm,
+ # na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ # **kwargs,
+ # )
+ cmap_params: list[CmapParams] | CmapParams
+ if isinstance(cmap, list):
+ cmap_params = [
+ _prepare_cmap_norm(
+ cmap=c,
+ norm=norm,
+ na_color=param_values["na_color"],
+ **kwargs,
+ )
+ for c in cmap
+ ]
+
+ else:
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
  norm=norm,
- na_color=na_color, # type: ignore[arg-type]
+ na_color=param_values["na_color"],
  **kwargs,
  )
- for c in cmap
- ]
-
- else:
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- for element, param_values in params_dict.items():
  sdata.plotting_tree[f"{n_steps+1}_render_images"] = ImageRenderParams(
  element=element,
  channel=param_values["channel"],
@@ -536,12 +540,11 @@ def render_labels(
  color: str | None = None,
  groups: list[str] | str | None = None,
  contour_px: int | None = 3,
- outline: bool = False,
  palette: list[str] | str | None = None,
  cmap: Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
- outline_alpha: float | int = 1.0,
+ na_color: ColorLike | None = "default",
+ outline_alpha: float | int = 0.0,
  fill_alpha: float | int = 0.4,
  scale: str | None = None,
  table_name: str | None = None,
@@ -576,16 +579,16 @@ def render_labels(
  contour_px : int, default 3
  Draw contour of specified width for each segment. If `None`, fills entire segment, see:
  func:`skimage.morphology.erosion`.
- outline : bool, default False
- Whether to plot boundaries around segmentation masks.
  cmap : Colormap | str | None
  Colormap for continuous annotations, see :class:`matplotlib.colors.Colormap`.
  norm : Normalize | None
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
- na_color : ColorLike | None
- Color to be used for NAs values, if present.
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of the labels.
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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 0.0
+ Alpha value for the outline of the labels. Invisible by default.
  fill_alpha : float | int, default 0.3
  Alpha value for the fill of the labels.
  scale : str | None
@@ -615,7 +618,6 @@ def render_labels(
  groups=groups,
  na_color=na_color,
  norm=norm,
- outline=outline,
  outline_alpha=outline_alpha,
  palette=palette,
  scale=scale,
@@ -625,20 +627,19 @@ def render_labels(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_labels"] = LabelsRenderParams(
  element=element,
  color=param_values["color"],
  groups=param_values["groups"],
  contour_px=param_values["contour_px"],
- outline=param_values["outline"],
  cmap_params=cmap_params,
  palette=param_values["palette"],
  outline_alpha=param_values["outline_alpha"],

CHANGELOG.md

@@ -10,18 +10,28 @@ and this project adheres to [Semantic Versioning][].
 
 ## [0.2.x] - tbd
 
-## [0.2.4] - 2024-08-07
-
 ### Added
 
-- Added utils function for 0-transparent cmaps (#302)
+- Replaced `outline` parameter in `render_labels` with alpha-based logic (#323)
+- Lowered RMSE-threshold for plot-based tests from 60 to 45 (#323)
+- Minor fixes for several tests as a result of the threshold change (#323)
 
 ### Changed
 
 -
 
 ### Fixed
 
+-
+
+## [0.2.4] - 2024-08-07
+
+### Added
+
+- Added utils function for 0-transparent cmaps (#302)
+
+### Fixed
+
 - Took RNG out of categorical label test (#306)
 - Performance bug when plotting shapes (#298)
 - scale parameter was ignored for single-scale images (#301)

src/spatialdata_plot/pl/basic.py

@@ -59,6 +59,9 @@
 )
 from spatialdata_plot.pp.utils import _verify_plotting_tree
 
+# replace with
+# from spatialdata._types import ColorLike
+# once https://github.com/scverse/spatialdata/pull/689/ is in a release
 ColorLike = Union[tuple[float, ...], str]
 
 
@@ -158,11 +161,10 @@ def render_shapes(
  fill_alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
- outline: bool = False,
+ na_color: ColorLike | None = "default",
  outline_width: float | int = 1.5,
  outline_color: str | list[float] = "#000000ff",
- outline_alpha: float | int = 1.0,
+ outline_alpha: float | int = 0.0,
  cmap: Colormap | str | None = None,
  norm: bool | Normalize = False,
  scale: float | int = 1.0,
@@ -201,19 +203,17 @@ def render_shapes(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If element is None, broadcasting behaviour is attempted (use the same values for
  all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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 : bool, default False
- If `True`, a border around the shape elements is plotted.
  outline_width : float | int, default 1.5
  Width of the border.
  outline_color : str | list[float], default "#000000ff"
  Color of the border. 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).
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of shapes.
+ outline_alpha : float | int, default 0.0
+ Alpha value for the outline of shapes. Invisible by default.
  cmap : Colormap | str | None, optional
  Colormap for discrete or continuous annotations using 'color', see :class:`matplotlib.colors.Colormap`.
  norm : bool | Normalize, default False
@@ -249,7 +249,6 @@ def render_shapes(
  palette=palette,
  color=color,
  na_color=na_color,
- outline=outline,
  outline_alpha=outline_alpha,
  outline_color=outline_color,
  outline_width=outline_width,
@@ -263,16 +262,15 @@ def render_shapes(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- outline_params = _set_outline(outline, outline_width, outline_color)
+ outline_params = _set_outline(outline_alpha > 0, outline_width, outline_color)
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_shapes"] = ShapesRenderParams(
  element=element,
  color=param_values["color"],
@@ -301,7 +299,7 @@ def render_points(
  alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
+ na_color: ColorLike | None = "default",
  cmap: Colormap | str | None = None,
  norm: None | Normalize = None,
  size: float | int = 1.0,
@@ -339,7 +337,7 @@ def render_points(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If `element` is `None`, broadcasting behaviour is attempted (use the same values
  for all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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.
@@ -389,14 +387,13 @@ def render_points(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_points"] = PointsRenderParams(
  element=element,
  color=param_values["color"],
@@ -422,7 +419,7 @@ def render_images(
  channel: list[str] | list[int] | str | int | None = None,
  cmap: list[Colormap | str] | Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
+ na_color: ColorLike | None = "default",
  palette: list[str] | str | None = None,
  alpha: float | int = 1.0,
  percentiles_for_norm: tuple[float, float] | None = None,
@@ -452,8 +449,10 @@ def render_images(
  norm : Normalize | None, optional
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
  Applies to all channels if set.
- na_color : ColorLike | None, default (0.0, 0.0, 0.0, 0.0)
- Color to be used for NA values. Accepts color-like values (string, hex, RGB(A)).
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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.
  palette : list[str] | str | None
  Palette to color images. The number of palettes should be equal to the number of channels.
  alpha : float | int, default 1.0
@@ -494,27 +493,32 @@ def render_images(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params: list[CmapParams] | CmapParams
- if isinstance(cmap, list):
- cmap_params = [
- _prepare_cmap_norm(
- cmap=c,
+ for element, param_values in params_dict.items():
+ # cmap_params = _prepare_cmap_norm(
+ # cmap=params_dict[element]["cmap"],
+ # norm=norm,
+ # na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ # **kwargs,
+ # )
+ cmap_params: list[CmapParams] | CmapParams
+ if isinstance(cmap, list):
+ cmap_params = [
+ _prepare_cmap_norm(
+ cmap=c,
+ norm=norm,
+ na_color=param_values["na_color"],
+ **kwargs,
+ )
+ for c in cmap
+ ]
+
+ else:
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
  norm=norm,
- na_color=na_color, # type: ignore[arg-type]
+ na_color=param_values["na_color"],
  **kwargs,
  )
- for c in cmap
- ]
-
- else:
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- for element, param_values in params_dict.items():
  sdata.plotting_tree[f"{n_steps+1}_render_images"] = ImageRenderParams(
  element=element,
  channel=param_values["channel"],
@@ -536,12 +540,11 @@ def render_labels(
  color: str | None = None,
  groups: list[str] | str | None = None,
  contour_px: int | None = 3,
- outline: bool = False,
  palette: list[str] | str | None = None,
  cmap: Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
- outline_alpha: float | int = 1.0,
+ na_color: ColorLike | None = "default",
+ outline_alpha: float | int = 0.0,
  fill_alpha: float | int = 0.4,
  scale: str | None = None,
  table_name: str | None = None,
@@ -576,16 +579,16 @@ def render_labels(
  contour_px : int, default 3
  Draw contour of specified width for each segment. If `None`, fills entire segment, see:
  func:`skimage.morphology.erosion`.
- outline : bool, default False
- Whether to plot boundaries around segmentation masks.
  cmap : Colormap | str | None
  Colormap for continuous annotations, see :class:`matplotlib.colors.Colormap`.
  norm : Normalize | None
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
- na_color : ColorLike | None
- Color to be used for NAs values, if present.
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of the labels.
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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 0.0
+ Alpha value for the outline of the labels. Invisible by default.
  fill_alpha : float | int, default 0.3
  Alpha value for the fill of the labels.
  scale : str | None
@@ -615,7 +618,6 @@ def render_labels(
  groups=groups,
  na_color=na_color,
  norm=norm,
- outline=outline,
  outline_alpha=outline_alpha,
  palette=palette,
  scale=scale,
@@ -625,20 +627,19 @@ def render_labels(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_labels"] = LabelsRenderParams(
  element=element,
  color=param_values["color"],
  groups=param_values["groups"],
  contour_px=param_values["contour_px"],
- outline=param_values["outline"],
  cmap_params=cmap_params,
  palette=param_values["palette"],
  outline_alpha=param_values["outline_alpha"],

CHANGELOG.md

@@ -10,18 +10,28 @@ and this project adheres to [Semantic Versioning][].
 
 ## [0.2.x] - tbd
 
-## [0.2.4] - 2024-08-07
-
 ### Added
 
-- Added utils function for 0-transparent cmaps (#302)
+- Replaced `outline` parameter in `render_labels` with alpha-based logic (#323)
+- Lowered RMSE-threshold for plot-based tests from 60 to 45 (#323)
+- Minor fixes for several tests as a result of the threshold change (#323)
 
 ### Changed
 
 -
 
 ### Fixed
 
+-
+
+## [0.2.4] - 2024-08-07
+
+### Added
+
+- Added utils function for 0-transparent cmaps (#302)
+
+### Fixed
+
 - Took RNG out of categorical label test (#306)
 - Performance bug when plotting shapes (#298)
 - scale parameter was ignored for single-scale images (#301)

src/spatialdata_plot/pl/basic.py

@@ -59,6 +59,9 @@
 )
 from spatialdata_plot.pp.utils import _verify_plotting_tree
 
+# replace with
+# from spatialdata._types import ColorLike
+# once https://github.com/scverse/spatialdata/pull/689/ is in a release
 ColorLike = Union[tuple[float, ...], str]
 
 
@@ -158,11 +161,10 @@ def render_shapes(
  fill_alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
- outline: bool = False,
+ na_color: ColorLike | None = "default",
  outline_width: float | int = 1.5,
  outline_color: str | list[float] = "#000000ff",
- outline_alpha: float | int = 1.0,
+ outline_alpha: float | int = 0.0,
  cmap: Colormap | str | None = None,
  norm: bool | Normalize = False,
  scale: float | int = 1.0,
@@ -201,19 +203,17 @@ def render_shapes(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If element is None, broadcasting behaviour is attempted (use the same values for
  all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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 : bool, default False
- If `True`, a border around the shape elements is plotted.
  outline_width : float | int, default 1.5
  Width of the border.
  outline_color : str | list[float], default "#000000ff"
  Color of the border. 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).
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of shapes.
+ outline_alpha : float | int, default 0.0
+ Alpha value for the outline of shapes. Invisible by default.
  cmap : Colormap | str | None, optional
  Colormap for discrete or continuous annotations using 'color', see :class:`matplotlib.colors.Colormap`.
  norm : bool | Normalize, default False
@@ -249,7 +249,6 @@ def render_shapes(
  palette=palette,
  color=color,
  na_color=na_color,
- outline=outline,
  outline_alpha=outline_alpha,
  outline_color=outline_color,
  outline_width=outline_width,
@@ -263,16 +262,15 @@ def render_shapes(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- outline_params = _set_outline(outline, outline_width, outline_color)
+ outline_params = _set_outline(outline_alpha > 0, outline_width, outline_color)
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_shapes"] = ShapesRenderParams(
  element=element,
  color=param_values["color"],
@@ -301,7 +299,7 @@ def render_points(
  alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
+ na_color: ColorLike | None = "default",
  cmap: Colormap | str | None = None,
  norm: None | Normalize = None,
  size: float | int = 1.0,
@@ -339,7 +337,7 @@ def render_points(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If `element` is `None`, broadcasting behaviour is attempted (use the same values
  for all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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.
@@ -389,14 +387,13 @@ def render_points(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_points"] = PointsRenderParams(
  element=element,
  color=param_values["color"],
@@ -422,7 +419,7 @@ def render_images(
  channel: list[str] | list[int] | str | int | None = None,
  cmap: list[Colormap | str] | Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
+ na_color: ColorLike | None = "default",
  palette: list[str] | str | None = None,
  alpha: float | int = 1.0,
  percentiles_for_norm: tuple[float, float] | None = None,
@@ -452,8 +449,10 @@ def render_images(
  norm : Normalize | None, optional
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
  Applies to all channels if set.
- na_color : ColorLike | None, default (0.0, 0.0, 0.0, 0.0)
- Color to be used for NA values. Accepts color-like values (string, hex, RGB(A)).
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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.
  palette : list[str] | str | None
  Palette to color images. The number of palettes should be equal to the number of channels.
  alpha : float | int, default 1.0
@@ -494,27 +493,32 @@ def render_images(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params: list[CmapParams] | CmapParams
- if isinstance(cmap, list):
- cmap_params = [
- _prepare_cmap_norm(
- cmap=c,
+ for element, param_values in params_dict.items():
+ # cmap_params = _prepare_cmap_norm(
+ # cmap=params_dict[element]["cmap"],
+ # norm=norm,
+ # na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ # **kwargs,
+ # )
+ cmap_params: list[CmapParams] | CmapParams
+ if isinstance(cmap, list):
+ cmap_params = [
+ _prepare_cmap_norm(
+ cmap=c,
+ norm=norm,
+ na_color=param_values["na_color"],
+ **kwargs,
+ )
+ for c in cmap
+ ]
+
+ else:
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
  norm=norm,
- na_color=na_color, # type: ignore[arg-type]
+ na_color=param_values["na_color"],
  **kwargs,
  )
- for c in cmap
- ]
-
- else:
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- for element, param_values in params_dict.items():
  sdata.plotting_tree[f"{n_steps+1}_render_images"] = ImageRenderParams(
  element=element,
  channel=param_values["channel"],
@@ -536,12 +540,11 @@ def render_labels(
  color: str | None = None,
  groups: list[str] | str | None = None,
  contour_px: int | None = 3,
- outline: bool = False,
  palette: list[str] | str | None = None,
  cmap: Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
- outline_alpha: float | int = 1.0,
+ na_color: ColorLike | None = "default",
+ outline_alpha: float | int = 0.0,
  fill_alpha: float | int = 0.4,
  scale: str | None = None,
  table_name: str | None = None,
@@ -576,16 +579,16 @@ def render_labels(
  contour_px : int, default 3
  Draw contour of specified width for each segment. If `None`, fills entire segment, see:
  func:`skimage.morphology.erosion`.
- outline : bool, default False
- Whether to plot boundaries around segmentation masks.
  cmap : Colormap | str | None
  Colormap for continuous annotations, see :class:`matplotlib.colors.Colormap`.
  norm : Normalize | None
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
- na_color : ColorLike | None
- Color to be used for NAs values, if present.
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of the labels.
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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 0.0
+ Alpha value for the outline of the labels. Invisible by default.
  fill_alpha : float | int, default 0.3
  Alpha value for the fill of the labels.
  scale : str | None
@@ -615,7 +618,6 @@ def render_labels(
  groups=groups,
  na_color=na_color,
  norm=norm,
- outline=outline,
  outline_alpha=outline_alpha,
  palette=palette,
  scale=scale,
@@ -625,20 +627,19 @@ def render_labels(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_labels"] = LabelsRenderParams(
  element=element,
  color=param_values["color"],
  groups=param_values["groups"],
  contour_px=param_values["contour_px"],
- outline=param_values["outline"],
  cmap_params=cmap_params,
  palette=param_values["palette"],
  outline_alpha=param_values["outline_alpha"],

CHANGELOG.md

@@ -10,18 +10,28 @@ and this project adheres to [Semantic Versioning][].
 
 ## [0.2.x] - tbd
 
-## [0.2.4] - 2024-08-07
-
 ### Added
 
-- Added utils function for 0-transparent cmaps (#302)
+- Replaced `outline` parameter in `render_labels` with alpha-based logic (#323)
+- Lowered RMSE-threshold for plot-based tests from 60 to 45 (#323)
+- Minor fixes for several tests as a result of the threshold change (#323)
 
 ### Changed
 
 -
 
 ### Fixed
 
+-
+
+## [0.2.4] - 2024-08-07
+
+### Added
+
+- Added utils function for 0-transparent cmaps (#302)
+
+### Fixed
+
 - Took RNG out of categorical label test (#306)
 - Performance bug when plotting shapes (#298)
 - scale parameter was ignored for single-scale images (#301)

src/spatialdata_plot/pl/basic.py

@@ -59,6 +59,9 @@
 )
 from spatialdata_plot.pp.utils import _verify_plotting_tree
 
+# replace with
+# from spatialdata._types import ColorLike
+# once https://github.com/scverse/spatialdata/pull/689/ is in a release
 ColorLike = Union[tuple[float, ...], str]
 
 
@@ -158,11 +161,10 @@ def render_shapes(
  fill_alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
- outline: bool = False,
+ na_color: ColorLike | None = "default",
  outline_width: float | int = 1.5,
  outline_color: str | list[float] = "#000000ff",
- outline_alpha: float | int = 1.0,
+ outline_alpha: float | int = 0.0,
  cmap: Colormap | str | None = None,
  norm: bool | Normalize = False,
  scale: float | int = 1.0,
@@ -201,19 +203,17 @@ def render_shapes(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If element is None, broadcasting behaviour is attempted (use the same values for
  all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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 : bool, default False
- If `True`, a border around the shape elements is plotted.
  outline_width : float | int, default 1.5
  Width of the border.
  outline_color : str | list[float], default "#000000ff"
  Color of the border. 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).
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of shapes.
+ outline_alpha : float | int, default 0.0
+ Alpha value for the outline of shapes. Invisible by default.
  cmap : Colormap | str | None, optional
  Colormap for discrete or continuous annotations using 'color', see :class:`matplotlib.colors.Colormap`.
  norm : bool | Normalize, default False
@@ -249,7 +249,6 @@ def render_shapes(
  palette=palette,
  color=color,
  na_color=na_color,
- outline=outline,
  outline_alpha=outline_alpha,
  outline_color=outline_color,
  outline_width=outline_width,
@@ -263,16 +262,15 @@ def render_shapes(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- outline_params = _set_outline(outline, outline_width, outline_color)
+ outline_params = _set_outline(outline_alpha > 0, outline_width, outline_color)
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_shapes"] = ShapesRenderParams(
  element=element,
  color=param_values["color"],
@@ -301,7 +299,7 @@ def render_points(
  alpha: float | int = 1.0,
  groups: list[str] | str | None = None,
  palette: list[str] | str | None = None,
- na_color: ColorLike | None = "lightgrey",
+ na_color: ColorLike | None = "default",
  cmap: Colormap | str | None = None,
  norm: None | Normalize = None,
  size: float | int = 1.0,
@@ -339,7 +337,7 @@ def render_points(
  Palette for discrete annotations. List of valid color names that should be used for the categories. Must
  match the number of groups. If `element` is `None`, broadcasting behaviour is attempted (use the same values
  for all elements). If groups is provided but not palette, palette is set to default "lightgray".
- na_color : ColorLike | None, default "lightgrey"
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
  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.
@@ -389,14 +387,13 @@ def render_points(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_points"] = PointsRenderParams(
  element=element,
  color=param_values["color"],
@@ -422,7 +419,7 @@ def render_images(
  channel: list[str] | list[int] | str | int | None = None,
  cmap: list[Colormap | str] | Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
+ na_color: ColorLike | None = "default",
  palette: list[str] | str | None = None,
  alpha: float | int = 1.0,
  percentiles_for_norm: tuple[float, float] | None = None,
@@ -452,8 +449,10 @@ def render_images(
  norm : Normalize | None, optional
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
  Applies to all channels if set.
- na_color : ColorLike | None, default (0.0, 0.0, 0.0, 0.0)
- Color to be used for NA values. Accepts color-like values (string, hex, RGB(A)).
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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.
  palette : list[str] | str | None
  Palette to color images. The number of palettes should be equal to the number of channels.
  alpha : float | int, default 1.0
@@ -494,27 +493,32 @@ def render_images(
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
 
- cmap_params: list[CmapParams] | CmapParams
- if isinstance(cmap, list):
- cmap_params = [
- _prepare_cmap_norm(
- cmap=c,
+ for element, param_values in params_dict.items():
+ # cmap_params = _prepare_cmap_norm(
+ # cmap=params_dict[element]["cmap"],
+ # norm=norm,
+ # na_color=params_dict[element]["na_color"], # type: ignore[arg-type]
+ # **kwargs,
+ # )
+ cmap_params: list[CmapParams] | CmapParams
+ if isinstance(cmap, list):
+ cmap_params = [
+ _prepare_cmap_norm(
+ cmap=c,
+ norm=norm,
+ na_color=param_values["na_color"],
+ **kwargs,
+ )
+ for c in cmap
+ ]
+
+ else:
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
  norm=norm,
- na_color=na_color, # type: ignore[arg-type]
+ na_color=param_values["na_color"],
  **kwargs,
  )
- for c in cmap
- ]
-
- else:
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
-
- for element, param_values in params_dict.items():
  sdata.plotting_tree[f"{n_steps+1}_render_images"] = ImageRenderParams(
  element=element,
  channel=param_values["channel"],
@@ -536,12 +540,11 @@ def render_labels(
  color: str | None = None,
  groups: list[str] | str | None = None,
  contour_px: int | None = 3,
- outline: bool = False,
  palette: list[str] | str | None = None,
  cmap: Colormap | str | None = None,
  norm: Normalize | None = None,
- na_color: ColorLike | None = (0.0, 0.0, 0.0, 0.0),
- outline_alpha: float | int = 1.0,
+ na_color: ColorLike | None = "default",
+ outline_alpha: float | int = 0.0,
  fill_alpha: float | int = 0.4,
  scale: str | None = None,
  table_name: str | None = None,
@@ -576,16 +579,16 @@ def render_labels(
  contour_px : int, default 3
  Draw contour of specified width for each segment. If `None`, fills entire segment, see:
  func:`skimage.morphology.erosion`.
- outline : bool, default False
- Whether to plot boundaries around segmentation masks.
  cmap : Colormap | str | None
  Colormap for continuous annotations, see :class:`matplotlib.colors.Colormap`.
  norm : Normalize | None
  Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
- na_color : ColorLike | None
- Color to be used for NAs values, if present.
- outline_alpha : float | int, default 1.0
- Alpha value for the outline of the labels.
+ na_color : ColorLike | None, default "default" (gets set to "lightgray")
+ 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 0.0
+ Alpha value for the outline of the labels. Invisible by default.
  fill_alpha : float | int, default 0.3
  Alpha value for the fill of the labels.
  scale : str | None
@@ -615,7 +618,6 @@ def render_labels(
  groups=groups,
  na_color=na_color,
  norm=norm,
- outline=outline,
  outline_alpha=outline_alpha,
  palette=palette,
  scale=scale,
@@ -625,20 +627,19 @@ def render_labels(
  sdata = self._copy()
  sdata = _verify_plotting_tree(sdata)
  n_steps = len(sdata.plotting_tree.keys())
- cmap_params = _prepare_cmap_norm(
- cmap=cmap,
- norm=norm,
- na_color=na_color, # type: ignore[arg-type]
- **kwargs,
- )
 
  for element, param_values in params_dict.items():
+ cmap_params = _prepare_cmap_norm(
+ cmap=cmap,
+ norm=norm,
+ na_color=param_values["na_color"], # type: ignore[arg-type]
+ **kwargs,
+ )
  sdata.plotting_tree[f"{n_steps+1}_render_labels"] = LabelsRenderParams(
  element=element,
  color=param_values["color"],
  groups=param_values["groups"],
  contour_px=param_values["contour_px"],
- outline=param_values["outline"],
  cmap_params=cmap_params,
  palette=param_values["palette"],
  outline_alpha=param_values["outline_alpha"],