Fixed bug because of which extent of previous axs was not respected

src/spatialdata_plot/pl/basic.py

@@ -7,6 +7,7 @@
 from typing import Any
 
 import matplotlib.pyplot as plt
+import numpy as np
 import scanpy as sc
 import spatialdata as sd
 from anndata import AnnData
@@ -39,6 +40,7 @@
  _get_cs_contents,
  _get_extent,
  _maybe_set_colors,
+ _mpl_ax_contains_elements,
  _multiscale_to_image,
  _prepare_cmap_norm,
  _prepare_params_plot,
@@ -454,6 +456,7 @@ def show(
  fig: Figure | None = None,
  title: None | str | Sequence[str] = None,
  share_extent: bool = True,
+ pad_extent: int = 0,
  ax: Axes | Sequence[Axes] | None = None,
  return_ax: bool = False,
  save: None | str | Path = None,
@@ -523,6 +526,14 @@ def show(
  # Simplicstic solution: If the images are multiscale, just use the first
  sdata = _multiscale_to_image(sdata)
 
+ # get original axis extent for later comparison
+ x_min_orig, x_max_orig = (np.inf, -np.inf)
+ y_min_orig, y_max_orig = (np.inf, -np.inf)
+
+ if isinstance(ax, Axes) and _mpl_ax_contains_elements(ax):
+ x_min_orig, x_max_orig = ax.get_xlim()
+ y_max_orig, y_min_orig = ax.get_ylim() # (0, 0) is top-left
+
  # handle coordinate system
  coordinate_systems = sdata.coordinate_systems if coordinate_systems is None else coordinate_systems
  if isinstance(coordinate_systems, str):
@@ -532,12 +543,38 @@ def show(
  if cs not in sdata.coordinate_systems:
  raise ValueError(f"Unknown coordinate system '{cs}', valid choices are: {sdata.coordinate_systems}")
 
+ # Check if user specified only certain elements to be plotted
+ cs_contents = _get_cs_contents(sdata)
+ elements_to_be_rendered = []
+ for cmd, params in render_cmds.items():
+ if cmd == "render_images" and cs_contents.query(f"cs == '{cs}'")["has_images"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_shapes" and cs_contents.query(f"cs == '{cs}'")["has_shapes"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_points" and cs_contents.query(f"cs == '{cs}'")["has_points"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_labels" and cs_contents.query(f"cs == '{cs}'")["has_labels"][0]: # noqa: SIM102
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+
  extent = _get_extent(
  sdata=sdata,
  has_images="render_images" in render_cmds,
  has_labels="render_labels" in render_cmds,
  has_points="render_points" in render_cmds,
  has_shapes="render_shapes" in render_cmds,
+ elements=elements_to_be_rendered,
  coordinate_systems=coordinate_systems,
  )
 
@@ -585,7 +622,6 @@ def show(
  )
 
  # go through tree
- cs_contents = _get_cs_contents(sdata)
  for i, cs in enumerate(coordinate_systems):
  sdata = self._copy()
  # properly transform all elements to the current coordinate system
@@ -693,12 +729,10 @@ def show(
  ]
  ):
  # If the axis already has limits, only expand them but not overwrite
- x_min, x_max = ax.get_xlim()
- y_min, y_max = ax.get_ylim()
- x_min = min(x_min, extent[cs][0])
- x_max = max(x_max, extent[cs][1])
- y_min = min(y_min, extent[cs][2])
- y_max = max(y_max, extent[cs][3])
+ x_min = min(x_min_orig, extent[cs][0]) - pad_extent
+ x_max = max(x_max_orig, extent[cs][1]) + pad_extent
+ y_min = min(y_min_orig, extent[cs][2]) - pad_extent
+ y_max = max(y_max_orig, extent[cs][3]) + pad_extent
  ax.set_xlim(x_min, x_max)
  ax.set_ylim(y_max, y_min) # (0, 0) is top-left
 

src/spatialdata_plot/pl/utils.py

@@ -178,11 +178,12 @@ def _get_cs_contents(sdata: sd.SpatialData) -> pd.DataFrame:
 
 def _get_extent(
  sdata: sd.SpatialData,
- coordinate_systems: None | str | Sequence[str] = None,
+ coordinate_systems: Sequence[str] | str | None = None,
  has_images: bool = True,
  has_labels: bool = True,
  has_points: bool = True,
  has_shapes: bool = True,
+ elements: Iterable[Any] | None = None,
  share_extent: bool = False,
 ) -> dict[str, tuple[int, int, int, int]]:
  """Return the extent of all elements in their respective coordinate systems.
@@ -191,16 +192,18 @@ def _get_extent(
  ----------
  sdata
  The sd.SpatialData object to retrieve the extent from
-images
+has_images
  Flag indicating whether to consider images when calculating the extent
-labels
+has_labels
  Flag indicating whether to consider labels when calculating the extent
-points
+has_points
  Flag indicating whether to consider points when calculating the extent
- shapes
- Flag indicating whether to consider shaoes when calculating the extent
- img_transformations
- List of transformations already applied to the images
+ has_shapes
+ Flag indicating whether to consider shapes when calculating the extent
+ elements
+ Optional list of element names to be considered. When None, all are used.
+ share_extent
+ Flag indicating whether to use the same extent for all coordinate systems
 
  Returns
  -------
@@ -212,6 +215,12 @@ def _get_extent(
  cs_mapping = _get_coordinate_system_mapping(sdata)
  cs_contents = _get_cs_contents(sdata)
 
+ if elements is None: # to shut up ruff
+ elements = []
+
+ if not isinstance(elements, list):
+ raise ValueError(f"Invalid type of `elements`: {type(elements)}, expected `list`.")
+
  if coordinate_systems is not None:
  if isinstance(coordinate_systems, str):
  coordinate_systems = [coordinate_systems]
@@ -220,6 +229,8 @@ def _get_extent(
 
  for cs_name, element_ids in cs_mapping.items():
  extent[cs_name] = {}
+ if len(elements) > 0:
+ element_ids = [e for e in element_ids if e in elements]
 
  def _get_extent_after_transformations(element: Any, cs_name: str) -> Sequence[int]:
  tmp = element.copy()
@@ -1127,3 +1138,17 @@ def _robust_transform(element: Any, cs: str) -> Any:
  raise ValueError("Unable to transform element.") from e
 
  return element
+
+
+def _mpl_ax_contains_elements(ax: Axes) -> bool:
+ """Check if any objects have been plotted on the axes object.
+
+ While extracting the extent, we need to know if the axes object has just been
+ initialised and therefore has extent (0, 1), (0,1) or if it has been plotted on
+ and therefore has a different extent.
+
+ Based on: https://stackoverflow.com/a/71966295
+ """
+ return (
+ len(ax.lines) > 0 or len(ax.collections) > 0 or len(ax.images) > 0 or len(ax.patches) > 0 or len(ax.tables) > 0
+ )

tests/pl/test_get_extent.py

@@ -0,0 +1,56 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestExtent(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_extent_of_img_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show()
+
+ def test_plot_extent_of_points_partial_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_points().pl.show()
+
+ def test_plot_extent_of_partial_canvas_on_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.render_points().pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles_and_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements=["blobs_circles", "blobs_polygons"]).pl.show()
+
+ def test_plot_extent_of_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.show()
+
+ def test_plot_extent_of_polygons_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_shapes().pl.show()
+
+ def test_plot_extent_of_polygons_on_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image", "blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.render_shapes().pl.show()

tests/pl/test_render_labels.py

@@ -19,5 +19,5 @@
 
 
 class TestLabels(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_labels(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_labels(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_labels(elements="blobs_labels").pl.show()

tests/pl/test_render_points.py

@@ -19,5 +19,5 @@
 
 
 class TestPoints(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_points(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_points(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_points(elements="blobs_points").pl.show()

tests/pl/test_render_shapes.py

@@ -20,7 +20,7 @@
 
 class TestShapes(PlotTester, metaclass=PlotTesterMeta):
  def test_plot_can_render_circles(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_circles").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
 
  def test_plot_can_render_polygons(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_polygons").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()

tests/pl/test_show.py

@@ -0,0 +1,23 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestShow(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_pad_extent_adds_padding(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show(pad_extent=100)

src/spatialdata_plot/pl/basic.py

@@ -7,6 +7,7 @@
 from typing import Any
 
 import matplotlib.pyplot as plt
+import numpy as np
 import scanpy as sc
 import spatialdata as sd
 from anndata import AnnData
@@ -39,6 +40,7 @@
  _get_cs_contents,
  _get_extent,
  _maybe_set_colors,
+ _mpl_ax_contains_elements,
  _multiscale_to_image,
  _prepare_cmap_norm,
  _prepare_params_plot,
@@ -454,6 +456,7 @@ def show(
  fig: Figure | None = None,
  title: None | str | Sequence[str] = None,
  share_extent: bool = True,
+ pad_extent: int = 0,
  ax: Axes | Sequence[Axes] | None = None,
  return_ax: bool = False,
  save: None | str | Path = None,
@@ -523,6 +526,14 @@ def show(
  # Simplicstic solution: If the images are multiscale, just use the first
  sdata = _multiscale_to_image(sdata)
 
+ # get original axis extent for later comparison
+ x_min_orig, x_max_orig = (np.inf, -np.inf)
+ y_min_orig, y_max_orig = (np.inf, -np.inf)
+
+ if isinstance(ax, Axes) and _mpl_ax_contains_elements(ax):
+ x_min_orig, x_max_orig = ax.get_xlim()
+ y_max_orig, y_min_orig = ax.get_ylim() # (0, 0) is top-left
+
  # handle coordinate system
  coordinate_systems = sdata.coordinate_systems if coordinate_systems is None else coordinate_systems
  if isinstance(coordinate_systems, str):
@@ -532,12 +543,38 @@ def show(
  if cs not in sdata.coordinate_systems:
  raise ValueError(f"Unknown coordinate system '{cs}', valid choices are: {sdata.coordinate_systems}")
 
+ # Check if user specified only certain elements to be plotted
+ cs_contents = _get_cs_contents(sdata)
+ elements_to_be_rendered = []
+ for cmd, params in render_cmds.items():
+ if cmd == "render_images" and cs_contents.query(f"cs == '{cs}'")["has_images"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_shapes" and cs_contents.query(f"cs == '{cs}'")["has_shapes"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_points" and cs_contents.query(f"cs == '{cs}'")["has_points"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_labels" and cs_contents.query(f"cs == '{cs}'")["has_labels"][0]: # noqa: SIM102
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+
  extent = _get_extent(
  sdata=sdata,
  has_images="render_images" in render_cmds,
  has_labels="render_labels" in render_cmds,
  has_points="render_points" in render_cmds,
  has_shapes="render_shapes" in render_cmds,
+ elements=elements_to_be_rendered,
  coordinate_systems=coordinate_systems,
  )
 
@@ -585,7 +622,6 @@ def show(
  )
 
  # go through tree
- cs_contents = _get_cs_contents(sdata)
  for i, cs in enumerate(coordinate_systems):
  sdata = self._copy()
  # properly transform all elements to the current coordinate system
@@ -693,12 +729,10 @@ def show(
  ]
  ):
  # If the axis already has limits, only expand them but not overwrite
- x_min, x_max = ax.get_xlim()
- y_min, y_max = ax.get_ylim()
- x_min = min(x_min, extent[cs][0])
- x_max = max(x_max, extent[cs][1])
- y_min = min(y_min, extent[cs][2])
- y_max = max(y_max, extent[cs][3])
+ x_min = min(x_min_orig, extent[cs][0]) - pad_extent
+ x_max = max(x_max_orig, extent[cs][1]) + pad_extent
+ y_min = min(y_min_orig, extent[cs][2]) - pad_extent
+ y_max = max(y_max_orig, extent[cs][3]) + pad_extent
  ax.set_xlim(x_min, x_max)
  ax.set_ylim(y_max, y_min) # (0, 0) is top-left
 

src/spatialdata_plot/pl/utils.py

@@ -178,11 +178,12 @@ def _get_cs_contents(sdata: sd.SpatialData) -> pd.DataFrame:
 
 def _get_extent(
  sdata: sd.SpatialData,
- coordinate_systems: None | str | Sequence[str] = None,
+ coordinate_systems: Sequence[str] | str | None = None,
  has_images: bool = True,
  has_labels: bool = True,
  has_points: bool = True,
  has_shapes: bool = True,
+ elements: Iterable[Any] | None = None,
  share_extent: bool = False,
 ) -> dict[str, tuple[int, int, int, int]]:
  """Return the extent of all elements in their respective coordinate systems.
@@ -191,16 +192,18 @@ def _get_extent(
  ----------
  sdata
  The sd.SpatialData object to retrieve the extent from
-images
+has_images
  Flag indicating whether to consider images when calculating the extent
-labels
+has_labels
  Flag indicating whether to consider labels when calculating the extent
-points
+has_points
  Flag indicating whether to consider points when calculating the extent
- shapes
- Flag indicating whether to consider shaoes when calculating the extent
- img_transformations
- List of transformations already applied to the images
+ has_shapes
+ Flag indicating whether to consider shapes when calculating the extent
+ elements
+ Optional list of element names to be considered. When None, all are used.
+ share_extent
+ Flag indicating whether to use the same extent for all coordinate systems
 
  Returns
  -------
@@ -212,6 +215,12 @@ def _get_extent(
  cs_mapping = _get_coordinate_system_mapping(sdata)
  cs_contents = _get_cs_contents(sdata)
 
+ if elements is None: # to shut up ruff
+ elements = []
+
+ if not isinstance(elements, list):
+ raise ValueError(f"Invalid type of `elements`: {type(elements)}, expected `list`.")
+
  if coordinate_systems is not None:
  if isinstance(coordinate_systems, str):
  coordinate_systems = [coordinate_systems]
@@ -220,6 +229,8 @@ def _get_extent(
 
  for cs_name, element_ids in cs_mapping.items():
  extent[cs_name] = {}
+ if len(elements) > 0:
+ element_ids = [e for e in element_ids if e in elements]
 
  def _get_extent_after_transformations(element: Any, cs_name: str) -> Sequence[int]:
  tmp = element.copy()
@@ -1127,3 +1138,17 @@ def _robust_transform(element: Any, cs: str) -> Any:
  raise ValueError("Unable to transform element.") from e
 
  return element
+
+
+def _mpl_ax_contains_elements(ax: Axes) -> bool:
+ """Check if any objects have been plotted on the axes object.
+
+ While extracting the extent, we need to know if the axes object has just been
+ initialised and therefore has extent (0, 1), (0,1) or if it has been plotted on
+ and therefore has a different extent.
+
+ Based on: https://stackoverflow.com/a/71966295
+ """
+ return (
+ len(ax.lines) > 0 or len(ax.collections) > 0 or len(ax.images) > 0 or len(ax.patches) > 0 or len(ax.tables) > 0
+ )

tests/pl/test_get_extent.py

@@ -0,0 +1,56 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestExtent(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_extent_of_img_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show()
+
+ def test_plot_extent_of_points_partial_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_points().pl.show()
+
+ def test_plot_extent_of_partial_canvas_on_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.render_points().pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles_and_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements=["blobs_circles", "blobs_polygons"]).pl.show()
+
+ def test_plot_extent_of_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.show()
+
+ def test_plot_extent_of_polygons_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_shapes().pl.show()
+
+ def test_plot_extent_of_polygons_on_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image", "blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.render_shapes().pl.show()

tests/pl/test_render_labels.py

@@ -19,5 +19,5 @@
 
 
 class TestLabels(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_labels(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_labels(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_labels(elements="blobs_labels").pl.show()

tests/pl/test_render_points.py

@@ -19,5 +19,5 @@
 
 
 class TestPoints(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_points(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_points(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_points(elements="blobs_points").pl.show()

tests/pl/test_render_shapes.py

@@ -20,7 +20,7 @@
 
 class TestShapes(PlotTester, metaclass=PlotTesterMeta):
  def test_plot_can_render_circles(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_circles").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
 
  def test_plot_can_render_polygons(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_polygons").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()

tests/pl/test_show.py

@@ -0,0 +1,23 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestShow(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_pad_extent_adds_padding(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show(pad_extent=100)

src/spatialdata_plot/pl/basic.py

@@ -7,6 +7,7 @@
 from typing import Any
 
 import matplotlib.pyplot as plt
+import numpy as np
 import scanpy as sc
 import spatialdata as sd
 from anndata import AnnData
@@ -39,6 +40,7 @@
  _get_cs_contents,
  _get_extent,
  _maybe_set_colors,
+ _mpl_ax_contains_elements,
  _multiscale_to_image,
  _prepare_cmap_norm,
  _prepare_params_plot,
@@ -454,6 +456,7 @@ def show(
  fig: Figure | None = None,
  title: None | str | Sequence[str] = None,
  share_extent: bool = True,
+ pad_extent: int = 0,
  ax: Axes | Sequence[Axes] | None = None,
  return_ax: bool = False,
  save: None | str | Path = None,
@@ -523,6 +526,14 @@ def show(
  # Simplicstic solution: If the images are multiscale, just use the first
  sdata = _multiscale_to_image(sdata)
 
+ # get original axis extent for later comparison
+ x_min_orig, x_max_orig = (np.inf, -np.inf)
+ y_min_orig, y_max_orig = (np.inf, -np.inf)
+
+ if isinstance(ax, Axes) and _mpl_ax_contains_elements(ax):
+ x_min_orig, x_max_orig = ax.get_xlim()
+ y_max_orig, y_min_orig = ax.get_ylim() # (0, 0) is top-left
+
  # handle coordinate system
  coordinate_systems = sdata.coordinate_systems if coordinate_systems is None else coordinate_systems
  if isinstance(coordinate_systems, str):
@@ -532,12 +543,38 @@ def show(
  if cs not in sdata.coordinate_systems:
  raise ValueError(f"Unknown coordinate system '{cs}', valid choices are: {sdata.coordinate_systems}")
 
+ # Check if user specified only certain elements to be plotted
+ cs_contents = _get_cs_contents(sdata)
+ elements_to_be_rendered = []
+ for cmd, params in render_cmds.items():
+ if cmd == "render_images" and cs_contents.query(f"cs == '{cs}'")["has_images"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_shapes" and cs_contents.query(f"cs == '{cs}'")["has_shapes"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_points" and cs_contents.query(f"cs == '{cs}'")["has_points"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_labels" and cs_contents.query(f"cs == '{cs}'")["has_labels"][0]: # noqa: SIM102
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+
  extent = _get_extent(
  sdata=sdata,
  has_images="render_images" in render_cmds,
  has_labels="render_labels" in render_cmds,
  has_points="render_points" in render_cmds,
  has_shapes="render_shapes" in render_cmds,
+ elements=elements_to_be_rendered,
  coordinate_systems=coordinate_systems,
  )
 
@@ -585,7 +622,6 @@ def show(
  )
 
  # go through tree
- cs_contents = _get_cs_contents(sdata)
  for i, cs in enumerate(coordinate_systems):
  sdata = self._copy()
  # properly transform all elements to the current coordinate system
@@ -693,12 +729,10 @@ def show(
  ]
  ):
  # If the axis already has limits, only expand them but not overwrite
- x_min, x_max = ax.get_xlim()
- y_min, y_max = ax.get_ylim()
- x_min = min(x_min, extent[cs][0])
- x_max = max(x_max, extent[cs][1])
- y_min = min(y_min, extent[cs][2])
- y_max = max(y_max, extent[cs][3])
+ x_min = min(x_min_orig, extent[cs][0]) - pad_extent
+ x_max = max(x_max_orig, extent[cs][1]) + pad_extent
+ y_min = min(y_min_orig, extent[cs][2]) - pad_extent
+ y_max = max(y_max_orig, extent[cs][3]) + pad_extent
  ax.set_xlim(x_min, x_max)
  ax.set_ylim(y_max, y_min) # (0, 0) is top-left
 

src/spatialdata_plot/pl/utils.py

@@ -178,11 +178,12 @@ def _get_cs_contents(sdata: sd.SpatialData) -> pd.DataFrame:
 
 def _get_extent(
  sdata: sd.SpatialData,
- coordinate_systems: None | str | Sequence[str] = None,
+ coordinate_systems: Sequence[str] | str | None = None,
  has_images: bool = True,
  has_labels: bool = True,
  has_points: bool = True,
  has_shapes: bool = True,
+ elements: Iterable[Any] | None = None,
  share_extent: bool = False,
 ) -> dict[str, tuple[int, int, int, int]]:
  """Return the extent of all elements in their respective coordinate systems.
@@ -191,16 +192,18 @@ def _get_extent(
  ----------
  sdata
  The sd.SpatialData object to retrieve the extent from
-images
+has_images
  Flag indicating whether to consider images when calculating the extent
-labels
+has_labels
  Flag indicating whether to consider labels when calculating the extent
-points
+has_points
  Flag indicating whether to consider points when calculating the extent
- shapes
- Flag indicating whether to consider shaoes when calculating the extent
- img_transformations
- List of transformations already applied to the images
+ has_shapes
+ Flag indicating whether to consider shapes when calculating the extent
+ elements
+ Optional list of element names to be considered. When None, all are used.
+ share_extent
+ Flag indicating whether to use the same extent for all coordinate systems
 
  Returns
  -------
@@ -212,6 +215,12 @@ def _get_extent(
  cs_mapping = _get_coordinate_system_mapping(sdata)
  cs_contents = _get_cs_contents(sdata)
 
+ if elements is None: # to shut up ruff
+ elements = []
+
+ if not isinstance(elements, list):
+ raise ValueError(f"Invalid type of `elements`: {type(elements)}, expected `list`.")
+
  if coordinate_systems is not None:
  if isinstance(coordinate_systems, str):
  coordinate_systems = [coordinate_systems]
@@ -220,6 +229,8 @@ def _get_extent(
 
  for cs_name, element_ids in cs_mapping.items():
  extent[cs_name] = {}
+ if len(elements) > 0:
+ element_ids = [e for e in element_ids if e in elements]
 
  def _get_extent_after_transformations(element: Any, cs_name: str) -> Sequence[int]:
  tmp = element.copy()
@@ -1127,3 +1138,17 @@ def _robust_transform(element: Any, cs: str) -> Any:
  raise ValueError("Unable to transform element.") from e
 
  return element
+
+
+def _mpl_ax_contains_elements(ax: Axes) -> bool:
+ """Check if any objects have been plotted on the axes object.
+
+ While extracting the extent, we need to know if the axes object has just been
+ initialised and therefore has extent (0, 1), (0,1) or if it has been plotted on
+ and therefore has a different extent.
+
+ Based on: https://stackoverflow.com/a/71966295
+ """
+ return (
+ len(ax.lines) > 0 or len(ax.collections) > 0 or len(ax.images) > 0 or len(ax.patches) > 0 or len(ax.tables) > 0
+ )

tests/pl/test_get_extent.py

@@ -0,0 +1,56 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestExtent(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_extent_of_img_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show()
+
+ def test_plot_extent_of_points_partial_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_points().pl.show()
+
+ def test_plot_extent_of_partial_canvas_on_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.render_points().pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles_and_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements=["blobs_circles", "blobs_polygons"]).pl.show()
+
+ def test_plot_extent_of_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.show()
+
+ def test_plot_extent_of_polygons_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_shapes().pl.show()
+
+ def test_plot_extent_of_polygons_on_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image", "blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.render_shapes().pl.show()

tests/pl/test_render_labels.py

@@ -19,5 +19,5 @@
 
 
 class TestLabels(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_labels(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_labels(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_labels(elements="blobs_labels").pl.show()

tests/pl/test_render_points.py

@@ -19,5 +19,5 @@
 
 
 class TestPoints(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_points(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_points(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_points(elements="blobs_points").pl.show()

tests/pl/test_render_shapes.py

@@ -20,7 +20,7 @@
 
 class TestShapes(PlotTester, metaclass=PlotTesterMeta):
  def test_plot_can_render_circles(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_circles").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
 
  def test_plot_can_render_polygons(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_polygons").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()

tests/pl/test_show.py

@@ -0,0 +1,23 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestShow(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_pad_extent_adds_padding(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show(pad_extent=100)

src/spatialdata_plot/pl/basic.py

@@ -7,6 +7,7 @@
 from typing import Any
 
 import matplotlib.pyplot as plt
+import numpy as np
 import scanpy as sc
 import spatialdata as sd
 from anndata import AnnData
@@ -39,6 +40,7 @@
  _get_cs_contents,
  _get_extent,
  _maybe_set_colors,
+ _mpl_ax_contains_elements,
  _multiscale_to_image,
  _prepare_cmap_norm,
  _prepare_params_plot,
@@ -454,6 +456,7 @@ def show(
  fig: Figure | None = None,
  title: None | str | Sequence[str] = None,
  share_extent: bool = True,
+ pad_extent: int = 0,
  ax: Axes | Sequence[Axes] | None = None,
  return_ax: bool = False,
  save: None | str | Path = None,
@@ -523,6 +526,14 @@ def show(
  # Simplicstic solution: If the images are multiscale, just use the first
  sdata = _multiscale_to_image(sdata)
 
+ # get original axis extent for later comparison
+ x_min_orig, x_max_orig = (np.inf, -np.inf)
+ y_min_orig, y_max_orig = (np.inf, -np.inf)
+
+ if isinstance(ax, Axes) and _mpl_ax_contains_elements(ax):
+ x_min_orig, x_max_orig = ax.get_xlim()
+ y_max_orig, y_min_orig = ax.get_ylim() # (0, 0) is top-left
+
  # handle coordinate system
  coordinate_systems = sdata.coordinate_systems if coordinate_systems is None else coordinate_systems
  if isinstance(coordinate_systems, str):
@@ -532,12 +543,38 @@ def show(
  if cs not in sdata.coordinate_systems:
  raise ValueError(f"Unknown coordinate system '{cs}', valid choices are: {sdata.coordinate_systems}")
 
+ # Check if user specified only certain elements to be plotted
+ cs_contents = _get_cs_contents(sdata)
+ elements_to_be_rendered = []
+ for cmd, params in render_cmds.items():
+ if cmd == "render_images" and cs_contents.query(f"cs == '{cs}'")["has_images"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_shapes" and cs_contents.query(f"cs == '{cs}'")["has_shapes"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_points" and cs_contents.query(f"cs == '{cs}'")["has_points"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_labels" and cs_contents.query(f"cs == '{cs}'")["has_labels"][0]: # noqa: SIM102
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+
  extent = _get_extent(
  sdata=sdata,
  has_images="render_images" in render_cmds,
  has_labels="render_labels" in render_cmds,
  has_points="render_points" in render_cmds,
  has_shapes="render_shapes" in render_cmds,
+ elements=elements_to_be_rendered,
  coordinate_systems=coordinate_systems,
  )
 
@@ -585,7 +622,6 @@ def show(
  )
 
  # go through tree
- cs_contents = _get_cs_contents(sdata)
  for i, cs in enumerate(coordinate_systems):
  sdata = self._copy()
  # properly transform all elements to the current coordinate system
@@ -693,12 +729,10 @@ def show(
  ]
  ):
  # If the axis already has limits, only expand them but not overwrite
- x_min, x_max = ax.get_xlim()
- y_min, y_max = ax.get_ylim()
- x_min = min(x_min, extent[cs][0])
- x_max = max(x_max, extent[cs][1])
- y_min = min(y_min, extent[cs][2])
- y_max = max(y_max, extent[cs][3])
+ x_min = min(x_min_orig, extent[cs][0]) - pad_extent
+ x_max = max(x_max_orig, extent[cs][1]) + pad_extent
+ y_min = min(y_min_orig, extent[cs][2]) - pad_extent
+ y_max = max(y_max_orig, extent[cs][3]) + pad_extent
  ax.set_xlim(x_min, x_max)
  ax.set_ylim(y_max, y_min) # (0, 0) is top-left
 

src/spatialdata_plot/pl/utils.py

@@ -178,11 +178,12 @@ def _get_cs_contents(sdata: sd.SpatialData) -> pd.DataFrame:
 
 def _get_extent(
  sdata: sd.SpatialData,
- coordinate_systems: None | str | Sequence[str] = None,
+ coordinate_systems: Sequence[str] | str | None = None,
  has_images: bool = True,
  has_labels: bool = True,
  has_points: bool = True,
  has_shapes: bool = True,
+ elements: Iterable[Any] | None = None,
  share_extent: bool = False,
 ) -> dict[str, tuple[int, int, int, int]]:
  """Return the extent of all elements in their respective coordinate systems.
@@ -191,16 +192,18 @@ def _get_extent(
  ----------
  sdata
  The sd.SpatialData object to retrieve the extent from
-images
+has_images
  Flag indicating whether to consider images when calculating the extent
-labels
+has_labels
  Flag indicating whether to consider labels when calculating the extent
-points
+has_points
  Flag indicating whether to consider points when calculating the extent
- shapes
- Flag indicating whether to consider shaoes when calculating the extent
- img_transformations
- List of transformations already applied to the images
+ has_shapes
+ Flag indicating whether to consider shapes when calculating the extent
+ elements
+ Optional list of element names to be considered. When None, all are used.
+ share_extent
+ Flag indicating whether to use the same extent for all coordinate systems
 
  Returns
  -------
@@ -212,6 +215,12 @@ def _get_extent(
  cs_mapping = _get_coordinate_system_mapping(sdata)
  cs_contents = _get_cs_contents(sdata)
 
+ if elements is None: # to shut up ruff
+ elements = []
+
+ if not isinstance(elements, list):
+ raise ValueError(f"Invalid type of `elements`: {type(elements)}, expected `list`.")
+
  if coordinate_systems is not None:
  if isinstance(coordinate_systems, str):
  coordinate_systems = [coordinate_systems]
@@ -220,6 +229,8 @@ def _get_extent(
 
  for cs_name, element_ids in cs_mapping.items():
  extent[cs_name] = {}
+ if len(elements) > 0:
+ element_ids = [e for e in element_ids if e in elements]
 
  def _get_extent_after_transformations(element: Any, cs_name: str) -> Sequence[int]:
  tmp = element.copy()
@@ -1127,3 +1138,17 @@ def _robust_transform(element: Any, cs: str) -> Any:
  raise ValueError("Unable to transform element.") from e
 
  return element
+
+
+def _mpl_ax_contains_elements(ax: Axes) -> bool:
+ """Check if any objects have been plotted on the axes object.
+
+ While extracting the extent, we need to know if the axes object has just been
+ initialised and therefore has extent (0, 1), (0,1) or if it has been plotted on
+ and therefore has a different extent.
+
+ Based on: https://stackoverflow.com/a/71966295
+ """
+ return (
+ len(ax.lines) > 0 or len(ax.collections) > 0 or len(ax.images) > 0 or len(ax.patches) > 0 or len(ax.tables) > 0
+ )

tests/pl/test_get_extent.py

@@ -0,0 +1,56 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestExtent(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_extent_of_img_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show()
+
+ def test_plot_extent_of_points_partial_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_points().pl.show()
+
+ def test_plot_extent_of_partial_canvas_on_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.render_points().pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles_and_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements=["blobs_circles", "blobs_polygons"]).pl.show()
+
+ def test_plot_extent_of_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.show()
+
+ def test_plot_extent_of_polygons_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_shapes().pl.show()
+
+ def test_plot_extent_of_polygons_on_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image", "blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.render_shapes().pl.show()

tests/pl/test_render_labels.py

@@ -19,5 +19,5 @@
 
 
 class TestLabels(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_labels(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_labels(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_labels(elements="blobs_labels").pl.show()

tests/pl/test_render_points.py

@@ -19,5 +19,5 @@
 
 
 class TestPoints(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_points(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_points(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_points(elements="blobs_points").pl.show()

tests/pl/test_render_shapes.py

@@ -20,7 +20,7 @@
 
 class TestShapes(PlotTester, metaclass=PlotTesterMeta):
  def test_plot_can_render_circles(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_circles").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
 
  def test_plot_can_render_polygons(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_polygons").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()

tests/pl/test_show.py

@@ -0,0 +1,23 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestShow(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_pad_extent_adds_padding(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show(pad_extent=100)

src/spatialdata_plot/pl/basic.py

@@ -7,6 +7,7 @@
 from typing import Any
 
 import matplotlib.pyplot as plt
+import numpy as np
 import scanpy as sc
 import spatialdata as sd
 from anndata import AnnData
@@ -39,6 +40,7 @@
  _get_cs_contents,
  _get_extent,
  _maybe_set_colors,
+ _mpl_ax_contains_elements,
  _multiscale_to_image,
  _prepare_cmap_norm,
  _prepare_params_plot,
@@ -454,6 +456,7 @@ def show(
  fig: Figure | None = None,
  title: None | str | Sequence[str] = None,
  share_extent: bool = True,
+ pad_extent: int = 0,
  ax: Axes | Sequence[Axes] | None = None,
  return_ax: bool = False,
  save: None | str | Path = None,
@@ -523,6 +526,14 @@ def show(
  # Simplicstic solution: If the images are multiscale, just use the first
  sdata = _multiscale_to_image(sdata)
 
+ # get original axis extent for later comparison
+ x_min_orig, x_max_orig = (np.inf, -np.inf)
+ y_min_orig, y_max_orig = (np.inf, -np.inf)
+
+ if isinstance(ax, Axes) and _mpl_ax_contains_elements(ax):
+ x_min_orig, x_max_orig = ax.get_xlim()
+ y_max_orig, y_min_orig = ax.get_ylim() # (0, 0) is top-left
+
  # handle coordinate system
  coordinate_systems = sdata.coordinate_systems if coordinate_systems is None else coordinate_systems
  if isinstance(coordinate_systems, str):
@@ -532,12 +543,38 @@ def show(
  if cs not in sdata.coordinate_systems:
  raise ValueError(f"Unknown coordinate system '{cs}', valid choices are: {sdata.coordinate_systems}")
 
+ # Check if user specified only certain elements to be plotted
+ cs_contents = _get_cs_contents(sdata)
+ elements_to_be_rendered = []
+ for cmd, params in render_cmds.items():
+ if cmd == "render_images" and cs_contents.query(f"cs == '{cs}'")["has_images"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_shapes" and cs_contents.query(f"cs == '{cs}'")["has_shapes"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_points" and cs_contents.query(f"cs == '{cs}'")["has_points"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_labels" and cs_contents.query(f"cs == '{cs}'")["has_labels"][0]: # noqa: SIM102
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+
  extent = _get_extent(
  sdata=sdata,
  has_images="render_images" in render_cmds,
  has_labels="render_labels" in render_cmds,
  has_points="render_points" in render_cmds,
  has_shapes="render_shapes" in render_cmds,
+ elements=elements_to_be_rendered,
  coordinate_systems=coordinate_systems,
  )
 
@@ -585,7 +622,6 @@ def show(
  )
 
  # go through tree
- cs_contents = _get_cs_contents(sdata)
  for i, cs in enumerate(coordinate_systems):
  sdata = self._copy()
  # properly transform all elements to the current coordinate system
@@ -693,12 +729,10 @@ def show(
  ]
  ):
  # If the axis already has limits, only expand them but not overwrite
- x_min, x_max = ax.get_xlim()
- y_min, y_max = ax.get_ylim()
- x_min = min(x_min, extent[cs][0])
- x_max = max(x_max, extent[cs][1])
- y_min = min(y_min, extent[cs][2])
- y_max = max(y_max, extent[cs][3])
+ x_min = min(x_min_orig, extent[cs][0]) - pad_extent
+ x_max = max(x_max_orig, extent[cs][1]) + pad_extent
+ y_min = min(y_min_orig, extent[cs][2]) - pad_extent
+ y_max = max(y_max_orig, extent[cs][3]) + pad_extent
  ax.set_xlim(x_min, x_max)
  ax.set_ylim(y_max, y_min) # (0, 0) is top-left
 

src/spatialdata_plot/pl/utils.py

@@ -178,11 +178,12 @@ def _get_cs_contents(sdata: sd.SpatialData) -> pd.DataFrame:
 
 def _get_extent(
  sdata: sd.SpatialData,
- coordinate_systems: None | str | Sequence[str] = None,
+ coordinate_systems: Sequence[str] | str | None = None,
  has_images: bool = True,
  has_labels: bool = True,
  has_points: bool = True,
  has_shapes: bool = True,
+ elements: Iterable[Any] | None = None,
  share_extent: bool = False,
 ) -> dict[str, tuple[int, int, int, int]]:
  """Return the extent of all elements in their respective coordinate systems.
@@ -191,16 +192,18 @@ def _get_extent(
  ----------
  sdata
  The sd.SpatialData object to retrieve the extent from
-images
+has_images
  Flag indicating whether to consider images when calculating the extent
-labels
+has_labels
  Flag indicating whether to consider labels when calculating the extent
-points
+has_points
  Flag indicating whether to consider points when calculating the extent
- shapes
- Flag indicating whether to consider shaoes when calculating the extent
- img_transformations
- List of transformations already applied to the images
+ has_shapes
+ Flag indicating whether to consider shapes when calculating the extent
+ elements
+ Optional list of element names to be considered. When None, all are used.
+ share_extent
+ Flag indicating whether to use the same extent for all coordinate systems
 
  Returns
  -------
@@ -212,6 +215,12 @@ def _get_extent(
  cs_mapping = _get_coordinate_system_mapping(sdata)
  cs_contents = _get_cs_contents(sdata)
 
+ if elements is None: # to shut up ruff
+ elements = []
+
+ if not isinstance(elements, list):
+ raise ValueError(f"Invalid type of `elements`: {type(elements)}, expected `list`.")
+
  if coordinate_systems is not None:
  if isinstance(coordinate_systems, str):
  coordinate_systems = [coordinate_systems]
@@ -220,6 +229,8 @@ def _get_extent(
 
  for cs_name, element_ids in cs_mapping.items():
  extent[cs_name] = {}
+ if len(elements) > 0:
+ element_ids = [e for e in element_ids if e in elements]
 
  def _get_extent_after_transformations(element: Any, cs_name: str) -> Sequence[int]:
  tmp = element.copy()
@@ -1127,3 +1138,17 @@ def _robust_transform(element: Any, cs: str) -> Any:
  raise ValueError("Unable to transform element.") from e
 
  return element
+
+
+def _mpl_ax_contains_elements(ax: Axes) -> bool:
+ """Check if any objects have been plotted on the axes object.
+
+ While extracting the extent, we need to know if the axes object has just been
+ initialised and therefore has extent (0, 1), (0,1) or if it has been plotted on
+ and therefore has a different extent.
+
+ Based on: https://stackoverflow.com/a/71966295
+ """
+ return (
+ len(ax.lines) > 0 or len(ax.collections) > 0 or len(ax.images) > 0 or len(ax.patches) > 0 or len(ax.tables) > 0
+ )

tests/pl/test_get_extent.py

@@ -0,0 +1,56 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestExtent(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_extent_of_img_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show()
+
+ def test_plot_extent_of_points_partial_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_points().pl.show()
+
+ def test_plot_extent_of_partial_canvas_on_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.render_points().pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles_and_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements=["blobs_circles", "blobs_polygons"]).pl.show()
+
+ def test_plot_extent_of_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.show()
+
+ def test_plot_extent_of_polygons_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_shapes().pl.show()
+
+ def test_plot_extent_of_polygons_on_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image", "blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.render_shapes().pl.show()

tests/pl/test_render_labels.py

@@ -19,5 +19,5 @@
 
 
 class TestLabels(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_labels(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_labels(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_labels(elements="blobs_labels").pl.show()

tests/pl/test_render_points.py

@@ -19,5 +19,5 @@
 
 
 class TestPoints(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_points(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_points(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_points(elements="blobs_points").pl.show()

tests/pl/test_render_shapes.py

@@ -20,7 +20,7 @@
 
 class TestShapes(PlotTester, metaclass=PlotTesterMeta):
  def test_plot_can_render_circles(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_circles").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
 
  def test_plot_can_render_polygons(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_polygons").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()

tests/pl/test_show.py

@@ -0,0 +1,23 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestShow(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_pad_extent_adds_padding(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show(pad_extent=100)

src/spatialdata_plot/pl/basic.py

@@ -7,6 +7,7 @@
 from typing import Any
 
 import matplotlib.pyplot as plt
+import numpy as np
 import scanpy as sc
 import spatialdata as sd
 from anndata import AnnData
@@ -39,6 +40,7 @@
  _get_cs_contents,
  _get_extent,
  _maybe_set_colors,
+ _mpl_ax_contains_elements,
  _multiscale_to_image,
  _prepare_cmap_norm,
  _prepare_params_plot,
@@ -454,6 +456,7 @@ def show(
  fig: Figure | None = None,
  title: None | str | Sequence[str] = None,
  share_extent: bool = True,
+ pad_extent: int = 0,
  ax: Axes | Sequence[Axes] | None = None,
  return_ax: bool = False,
  save: None | str | Path = None,
@@ -523,6 +526,14 @@ def show(
  # Simplicstic solution: If the images are multiscale, just use the first
  sdata = _multiscale_to_image(sdata)
 
+ # get original axis extent for later comparison
+ x_min_orig, x_max_orig = (np.inf, -np.inf)
+ y_min_orig, y_max_orig = (np.inf, -np.inf)
+
+ if isinstance(ax, Axes) and _mpl_ax_contains_elements(ax):
+ x_min_orig, x_max_orig = ax.get_xlim()
+ y_max_orig, y_min_orig = ax.get_ylim() # (0, 0) is top-left
+
  # handle coordinate system
  coordinate_systems = sdata.coordinate_systems if coordinate_systems is None else coordinate_systems
  if isinstance(coordinate_systems, str):
@@ -532,12 +543,38 @@ def show(
  if cs not in sdata.coordinate_systems:
  raise ValueError(f"Unknown coordinate system '{cs}', valid choices are: {sdata.coordinate_systems}")
 
+ # Check if user specified only certain elements to be plotted
+ cs_contents = _get_cs_contents(sdata)
+ elements_to_be_rendered = []
+ for cmd, params in render_cmds.items():
+ if cmd == "render_images" and cs_contents.query(f"cs == '{cs}'")["has_images"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_shapes" and cs_contents.query(f"cs == '{cs}'")["has_shapes"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_points" and cs_contents.query(f"cs == '{cs}'")["has_points"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_labels" and cs_contents.query(f"cs == '{cs}'")["has_labels"][0]: # noqa: SIM102
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+
  extent = _get_extent(
  sdata=sdata,
  has_images="render_images" in render_cmds,
  has_labels="render_labels" in render_cmds,
  has_points="render_points" in render_cmds,
  has_shapes="render_shapes" in render_cmds,
+ elements=elements_to_be_rendered,
  coordinate_systems=coordinate_systems,
  )
 
@@ -585,7 +622,6 @@ def show(
  )
 
  # go through tree
- cs_contents = _get_cs_contents(sdata)
  for i, cs in enumerate(coordinate_systems):
  sdata = self._copy()
  # properly transform all elements to the current coordinate system
@@ -693,12 +729,10 @@ def show(
  ]
  ):
  # If the axis already has limits, only expand them but not overwrite
- x_min, x_max = ax.get_xlim()
- y_min, y_max = ax.get_ylim()
- x_min = min(x_min, extent[cs][0])
- x_max = max(x_max, extent[cs][1])
- y_min = min(y_min, extent[cs][2])
- y_max = max(y_max, extent[cs][3])
+ x_min = min(x_min_orig, extent[cs][0]) - pad_extent
+ x_max = max(x_max_orig, extent[cs][1]) + pad_extent
+ y_min = min(y_min_orig, extent[cs][2]) - pad_extent
+ y_max = max(y_max_orig, extent[cs][3]) + pad_extent
  ax.set_xlim(x_min, x_max)
  ax.set_ylim(y_max, y_min) # (0, 0) is top-left
 

src/spatialdata_plot/pl/utils.py

@@ -178,11 +178,12 @@ def _get_cs_contents(sdata: sd.SpatialData) -> pd.DataFrame:
 
 def _get_extent(
  sdata: sd.SpatialData,
- coordinate_systems: None | str | Sequence[str] = None,
+ coordinate_systems: Sequence[str] | str | None = None,
  has_images: bool = True,
  has_labels: bool = True,
  has_points: bool = True,
  has_shapes: bool = True,
+ elements: Iterable[Any] | None = None,
  share_extent: bool = False,
 ) -> dict[str, tuple[int, int, int, int]]:
  """Return the extent of all elements in their respective coordinate systems.
@@ -191,16 +192,18 @@ def _get_extent(
  ----------
  sdata
  The sd.SpatialData object to retrieve the extent from
-images
+has_images
  Flag indicating whether to consider images when calculating the extent
-labels
+has_labels
  Flag indicating whether to consider labels when calculating the extent
-points
+has_points
  Flag indicating whether to consider points when calculating the extent
- shapes
- Flag indicating whether to consider shaoes when calculating the extent
- img_transformations
- List of transformations already applied to the images
+ has_shapes
+ Flag indicating whether to consider shapes when calculating the extent
+ elements
+ Optional list of element names to be considered. When None, all are used.
+ share_extent
+ Flag indicating whether to use the same extent for all coordinate systems
 
  Returns
  -------
@@ -212,6 +215,12 @@ def _get_extent(
  cs_mapping = _get_coordinate_system_mapping(sdata)
  cs_contents = _get_cs_contents(sdata)
 
+ if elements is None: # to shut up ruff
+ elements = []
+
+ if not isinstance(elements, list):
+ raise ValueError(f"Invalid type of `elements`: {type(elements)}, expected `list`.")
+
  if coordinate_systems is not None:
  if isinstance(coordinate_systems, str):
  coordinate_systems = [coordinate_systems]
@@ -220,6 +229,8 @@ def _get_extent(
 
  for cs_name, element_ids in cs_mapping.items():
  extent[cs_name] = {}
+ if len(elements) > 0:
+ element_ids = [e for e in element_ids if e in elements]
 
  def _get_extent_after_transformations(element: Any, cs_name: str) -> Sequence[int]:
  tmp = element.copy()
@@ -1127,3 +1138,17 @@ def _robust_transform(element: Any, cs: str) -> Any:
  raise ValueError("Unable to transform element.") from e
 
  return element
+
+
+def _mpl_ax_contains_elements(ax: Axes) -> bool:
+ """Check if any objects have been plotted on the axes object.
+
+ While extracting the extent, we need to know if the axes object has just been
+ initialised and therefore has extent (0, 1), (0,1) or if it has been plotted on
+ and therefore has a different extent.
+
+ Based on: https://stackoverflow.com/a/71966295
+ """
+ return (
+ len(ax.lines) > 0 or len(ax.collections) > 0 or len(ax.images) > 0 or len(ax.patches) > 0 or len(ax.tables) > 0
+ )

tests/pl/test_get_extent.py

@@ -0,0 +1,56 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestExtent(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_extent_of_img_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show()
+
+ def test_plot_extent_of_points_partial_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_points().pl.show()
+
+ def test_plot_extent_of_partial_canvas_on_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.render_points().pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles_and_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements=["blobs_circles", "blobs_polygons"]).pl.show()
+
+ def test_plot_extent_of_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.show()
+
+ def test_plot_extent_of_polygons_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_shapes().pl.show()
+
+ def test_plot_extent_of_polygons_on_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image", "blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.render_shapes().pl.show()

tests/pl/test_render_labels.py

@@ -19,5 +19,5 @@
 
 
 class TestLabels(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_labels(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_labels(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_labels(elements="blobs_labels").pl.show()

tests/pl/test_render_points.py

@@ -19,5 +19,5 @@
 
 
 class TestPoints(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_points(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_points(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_points(elements="blobs_points").pl.show()

tests/pl/test_render_shapes.py

@@ -20,7 +20,7 @@
 
 class TestShapes(PlotTester, metaclass=PlotTesterMeta):
  def test_plot_can_render_circles(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_circles").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
 
  def test_plot_can_render_polygons(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_polygons").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()

tests/pl/test_show.py

@@ -0,0 +1,23 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestShow(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_pad_extent_adds_padding(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show(pad_extent=100)

src/spatialdata_plot/pl/basic.py

@@ -7,6 +7,7 @@
 from typing import Any
 
 import matplotlib.pyplot as plt
+import numpy as np
 import scanpy as sc
 import spatialdata as sd
 from anndata import AnnData
@@ -39,6 +40,7 @@
  _get_cs_contents,
  _get_extent,
  _maybe_set_colors,
+ _mpl_ax_contains_elements,
  _multiscale_to_image,
  _prepare_cmap_norm,
  _prepare_params_plot,
@@ -454,6 +456,7 @@ def show(
  fig: Figure | None = None,
  title: None | str | Sequence[str] = None,
  share_extent: bool = True,
+ pad_extent: int = 0,
  ax: Axes | Sequence[Axes] | None = None,
  return_ax: bool = False,
  save: None | str | Path = None,
@@ -523,6 +526,14 @@ def show(
  # Simplicstic solution: If the images are multiscale, just use the first
  sdata = _multiscale_to_image(sdata)
 
+ # get original axis extent for later comparison
+ x_min_orig, x_max_orig = (np.inf, -np.inf)
+ y_min_orig, y_max_orig = (np.inf, -np.inf)
+
+ if isinstance(ax, Axes) and _mpl_ax_contains_elements(ax):
+ x_min_orig, x_max_orig = ax.get_xlim()
+ y_max_orig, y_min_orig = ax.get_ylim() # (0, 0) is top-left
+
  # handle coordinate system
  coordinate_systems = sdata.coordinate_systems if coordinate_systems is None else coordinate_systems
  if isinstance(coordinate_systems, str):
@@ -532,12 +543,38 @@ def show(
  if cs not in sdata.coordinate_systems:
  raise ValueError(f"Unknown coordinate system '{cs}', valid choices are: {sdata.coordinate_systems}")
 
+ # Check if user specified only certain elements to be plotted
+ cs_contents = _get_cs_contents(sdata)
+ elements_to_be_rendered = []
+ for cmd, params in render_cmds.items():
+ if cmd == "render_images" and cs_contents.query(f"cs == '{cs}'")["has_images"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_shapes" and cs_contents.query(f"cs == '{cs}'")["has_shapes"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_points" and cs_contents.query(f"cs == '{cs}'")["has_points"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_labels" and cs_contents.query(f"cs == '{cs}'")["has_labels"][0]: # noqa: SIM102
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+
  extent = _get_extent(
  sdata=sdata,
  has_images="render_images" in render_cmds,
  has_labels="render_labels" in render_cmds,
  has_points="render_points" in render_cmds,
  has_shapes="render_shapes" in render_cmds,
+ elements=elements_to_be_rendered,
  coordinate_systems=coordinate_systems,
  )
 
@@ -585,7 +622,6 @@ def show(
  )
 
  # go through tree
- cs_contents = _get_cs_contents(sdata)
  for i, cs in enumerate(coordinate_systems):
  sdata = self._copy()
  # properly transform all elements to the current coordinate system
@@ -693,12 +729,10 @@ def show(
  ]
  ):
  # If the axis already has limits, only expand them but not overwrite
- x_min, x_max = ax.get_xlim()
- y_min, y_max = ax.get_ylim()
- x_min = min(x_min, extent[cs][0])
- x_max = max(x_max, extent[cs][1])
- y_min = min(y_min, extent[cs][2])
- y_max = max(y_max, extent[cs][3])
+ x_min = min(x_min_orig, extent[cs][0]) - pad_extent
+ x_max = max(x_max_orig, extent[cs][1]) + pad_extent
+ y_min = min(y_min_orig, extent[cs][2]) - pad_extent
+ y_max = max(y_max_orig, extent[cs][3]) + pad_extent
  ax.set_xlim(x_min, x_max)
  ax.set_ylim(y_max, y_min) # (0, 0) is top-left
 

src/spatialdata_plot/pl/utils.py

@@ -178,11 +178,12 @@ def _get_cs_contents(sdata: sd.SpatialData) -> pd.DataFrame:
 
 def _get_extent(
  sdata: sd.SpatialData,
- coordinate_systems: None | str | Sequence[str] = None,
+ coordinate_systems: Sequence[str] | str | None = None,
  has_images: bool = True,
  has_labels: bool = True,
  has_points: bool = True,
  has_shapes: bool = True,
+ elements: Iterable[Any] | None = None,
  share_extent: bool = False,
 ) -> dict[str, tuple[int, int, int, int]]:
  """Return the extent of all elements in their respective coordinate systems.
@@ -191,16 +192,18 @@ def _get_extent(
  ----------
  sdata
  The sd.SpatialData object to retrieve the extent from
-images
+has_images
  Flag indicating whether to consider images when calculating the extent
-labels
+has_labels
  Flag indicating whether to consider labels when calculating the extent
-points
+has_points
  Flag indicating whether to consider points when calculating the extent
- shapes
- Flag indicating whether to consider shaoes when calculating the extent
- img_transformations
- List of transformations already applied to the images
+ has_shapes
+ Flag indicating whether to consider shapes when calculating the extent
+ elements
+ Optional list of element names to be considered. When None, all are used.
+ share_extent
+ Flag indicating whether to use the same extent for all coordinate systems
 
  Returns
  -------
@@ -212,6 +215,12 @@ def _get_extent(
  cs_mapping = _get_coordinate_system_mapping(sdata)
  cs_contents = _get_cs_contents(sdata)
 
+ if elements is None: # to shut up ruff
+ elements = []
+
+ if not isinstance(elements, list):
+ raise ValueError(f"Invalid type of `elements`: {type(elements)}, expected `list`.")
+
  if coordinate_systems is not None:
  if isinstance(coordinate_systems, str):
  coordinate_systems = [coordinate_systems]
@@ -220,6 +229,8 @@ def _get_extent(
 
  for cs_name, element_ids in cs_mapping.items():
  extent[cs_name] = {}
+ if len(elements) > 0:
+ element_ids = [e for e in element_ids if e in elements]
 
  def _get_extent_after_transformations(element: Any, cs_name: str) -> Sequence[int]:
  tmp = element.copy()
@@ -1127,3 +1138,17 @@ def _robust_transform(element: Any, cs: str) -> Any:
  raise ValueError("Unable to transform element.") from e
 
  return element
+
+
+def _mpl_ax_contains_elements(ax: Axes) -> bool:
+ """Check if any objects have been plotted on the axes object.
+
+ While extracting the extent, we need to know if the axes object has just been
+ initialised and therefore has extent (0, 1), (0,1) or if it has been plotted on
+ and therefore has a different extent.
+
+ Based on: https://stackoverflow.com/a/71966295
+ """
+ return (
+ len(ax.lines) > 0 or len(ax.collections) > 0 or len(ax.images) > 0 or len(ax.patches) > 0 or len(ax.tables) > 0
+ )

tests/pl/test_get_extent.py

@@ -0,0 +1,56 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestExtent(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_extent_of_img_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show()
+
+ def test_plot_extent_of_points_partial_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_points().pl.show()
+
+ def test_plot_extent_of_partial_canvas_on_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.render_points().pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles_and_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements=["blobs_circles", "blobs_polygons"]).pl.show()
+
+ def test_plot_extent_of_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.show()
+
+ def test_plot_extent_of_polygons_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_shapes().pl.show()
+
+ def test_plot_extent_of_polygons_on_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image", "blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.render_shapes().pl.show()

tests/pl/test_render_labels.py

@@ -19,5 +19,5 @@
 
 
 class TestLabels(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_labels(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_labels(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_labels(elements="blobs_labels").pl.show()

tests/pl/test_render_points.py

@@ -19,5 +19,5 @@
 
 
 class TestPoints(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_points(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_points(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_points(elements="blobs_points").pl.show()

tests/pl/test_render_shapes.py

@@ -20,7 +20,7 @@
 
 class TestShapes(PlotTester, metaclass=PlotTesterMeta):
  def test_plot_can_render_circles(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_circles").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
 
  def test_plot_can_render_polygons(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_polygons").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()

tests/pl/test_show.py

@@ -0,0 +1,23 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestShow(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_pad_extent_adds_padding(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show(pad_extent=100)

src/spatialdata_plot/pl/basic.py

@@ -7,6 +7,7 @@
 from typing import Any
 
 import matplotlib.pyplot as plt
+import numpy as np
 import scanpy as sc
 import spatialdata as sd
 from anndata import AnnData
@@ -39,6 +40,7 @@
  _get_cs_contents,
  _get_extent,
  _maybe_set_colors,
+ _mpl_ax_contains_elements,
  _multiscale_to_image,
  _prepare_cmap_norm,
  _prepare_params_plot,
@@ -454,6 +456,7 @@ def show(
  fig: Figure | None = None,
  title: None | str | Sequence[str] = None,
  share_extent: bool = True,
+ pad_extent: int = 0,
  ax: Axes | Sequence[Axes] | None = None,
  return_ax: bool = False,
  save: None | str | Path = None,
@@ -523,6 +526,14 @@ def show(
  # Simplicstic solution: If the images are multiscale, just use the first
  sdata = _multiscale_to_image(sdata)
 
+ # get original axis extent for later comparison
+ x_min_orig, x_max_orig = (np.inf, -np.inf)
+ y_min_orig, y_max_orig = (np.inf, -np.inf)
+
+ if isinstance(ax, Axes) and _mpl_ax_contains_elements(ax):
+ x_min_orig, x_max_orig = ax.get_xlim()
+ y_max_orig, y_min_orig = ax.get_ylim() # (0, 0) is top-left
+
  # handle coordinate system
  coordinate_systems = sdata.coordinate_systems if coordinate_systems is None else coordinate_systems
  if isinstance(coordinate_systems, str):
@@ -532,12 +543,38 @@ def show(
  if cs not in sdata.coordinate_systems:
  raise ValueError(f"Unknown coordinate system '{cs}', valid choices are: {sdata.coordinate_systems}")
 
+ # Check if user specified only certain elements to be plotted
+ cs_contents = _get_cs_contents(sdata)
+ elements_to_be_rendered = []
+ for cmd, params in render_cmds.items():
+ if cmd == "render_images" and cs_contents.query(f"cs == '{cs}'")["has_images"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_shapes" and cs_contents.query(f"cs == '{cs}'")["has_shapes"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_points" and cs_contents.query(f"cs == '{cs}'")["has_points"][0]: # noqa: SIM114
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+ elif cmd == "render_labels" and cs_contents.query(f"cs == '{cs}'")["has_labels"][0]: # noqa: SIM102
+ if params.elements is not None:
+ elements_to_be_rendered += (
+ [params.elements] if isinstance(params.elements, str) else params.elements
+ )
+
  extent = _get_extent(
  sdata=sdata,
  has_images="render_images" in render_cmds,
  has_labels="render_labels" in render_cmds,
  has_points="render_points" in render_cmds,
  has_shapes="render_shapes" in render_cmds,
+ elements=elements_to_be_rendered,
  coordinate_systems=coordinate_systems,
  )
 
@@ -585,7 +622,6 @@ def show(
  )
 
  # go through tree
- cs_contents = _get_cs_contents(sdata)
  for i, cs in enumerate(coordinate_systems):
  sdata = self._copy()
  # properly transform all elements to the current coordinate system
@@ -693,12 +729,10 @@ def show(
  ]
  ):
  # If the axis already has limits, only expand them but not overwrite
- x_min, x_max = ax.get_xlim()
- y_min, y_max = ax.get_ylim()
- x_min = min(x_min, extent[cs][0])
- x_max = max(x_max, extent[cs][1])
- y_min = min(y_min, extent[cs][2])
- y_max = max(y_max, extent[cs][3])
+ x_min = min(x_min_orig, extent[cs][0]) - pad_extent
+ x_max = max(x_max_orig, extent[cs][1]) + pad_extent
+ y_min = min(y_min_orig, extent[cs][2]) - pad_extent
+ y_max = max(y_max_orig, extent[cs][3]) + pad_extent
  ax.set_xlim(x_min, x_max)
  ax.set_ylim(y_max, y_min) # (0, 0) is top-left
 

src/spatialdata_plot/pl/utils.py

@@ -178,11 +178,12 @@ def _get_cs_contents(sdata: sd.SpatialData) -> pd.DataFrame:
 
 def _get_extent(
  sdata: sd.SpatialData,
- coordinate_systems: None | str | Sequence[str] = None,
+ coordinate_systems: Sequence[str] | str | None = None,
  has_images: bool = True,
  has_labels: bool = True,
  has_points: bool = True,
  has_shapes: bool = True,
+ elements: Iterable[Any] | None = None,
  share_extent: bool = False,
 ) -> dict[str, tuple[int, int, int, int]]:
  """Return the extent of all elements in their respective coordinate systems.
@@ -191,16 +192,18 @@ def _get_extent(
  ----------
  sdata
  The sd.SpatialData object to retrieve the extent from
-images
+has_images
  Flag indicating whether to consider images when calculating the extent
-labels
+has_labels
  Flag indicating whether to consider labels when calculating the extent
-points
+has_points
  Flag indicating whether to consider points when calculating the extent
- shapes
- Flag indicating whether to consider shaoes when calculating the extent
- img_transformations
- List of transformations already applied to the images
+ has_shapes
+ Flag indicating whether to consider shapes when calculating the extent
+ elements
+ Optional list of element names to be considered. When None, all are used.
+ share_extent
+ Flag indicating whether to use the same extent for all coordinate systems
 
  Returns
  -------
@@ -212,6 +215,12 @@ def _get_extent(
  cs_mapping = _get_coordinate_system_mapping(sdata)
  cs_contents = _get_cs_contents(sdata)
 
+ if elements is None: # to shut up ruff
+ elements = []
+
+ if not isinstance(elements, list):
+ raise ValueError(f"Invalid type of `elements`: {type(elements)}, expected `list`.")
+
  if coordinate_systems is not None:
  if isinstance(coordinate_systems, str):
  coordinate_systems = [coordinate_systems]
@@ -220,6 +229,8 @@ def _get_extent(
 
  for cs_name, element_ids in cs_mapping.items():
  extent[cs_name] = {}
+ if len(elements) > 0:
+ element_ids = [e for e in element_ids if e in elements]
 
  def _get_extent_after_transformations(element: Any, cs_name: str) -> Sequence[int]:
  tmp = element.copy()
@@ -1127,3 +1138,17 @@ def _robust_transform(element: Any, cs: str) -> Any:
  raise ValueError("Unable to transform element.") from e
 
  return element
+
+
+def _mpl_ax_contains_elements(ax: Axes) -> bool:
+ """Check if any objects have been plotted on the axes object.
+
+ While extracting the extent, we need to know if the axes object has just been
+ initialised and therefore has extent (0, 1), (0,1) or if it has been plotted on
+ and therefore has a different extent.
+
+ Based on: https://stackoverflow.com/a/71966295
+ """
+ return (
+ len(ax.lines) > 0 or len(ax.collections) > 0 or len(ax.images) > 0 or len(ax.patches) > 0 or len(ax.tables) > 0
+ )

tests/pl/test_get_extent.py

@@ -0,0 +1,56 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestExtent(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_extent_of_img_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show()
+
+ def test_plot_extent_of_points_partial_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_points().pl.show()
+
+ def test_plot_extent_of_partial_canvas_on_full_canvas(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.render_points().pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()
+
+ def test_plot_extent_calculation_respects_element_selection_circles_and_polygons(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_shapes(elements=["blobs_circles", "blobs_polygons"]).pl.show()
+
+ def test_plot_extent_of_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.show()
+
+ def test_plot_extent_of_polygons_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_shapes().pl.show()
+
+ def test_plot_extent_of_polygons_on_img_is_correct_after_spatial_query(self, sdata_blobs: SpatialData):
+ cropped_blobs = sdata_blobs.pp.get_elements(["blobs_image", "blobs_polygons"]).query.bounding_box(
+ axes=["x", "y"], min_coordinate=[100, 100], max_coordinate=[400, 400], target_coordinate_system="global"
+ )
+ cropped_blobs.pl.render_images().pl.render_shapes().pl.show()

tests/pl/test_render_labels.py

@@ -19,5 +19,5 @@
 
 
 class TestLabels(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_labels(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_labels(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_labels(elements="blobs_labels").pl.show()

tests/pl/test_render_points.py

@@ -19,5 +19,5 @@
 
 
 class TestPoints(PlotTester, metaclass=PlotTesterMeta):
- def test_plot_points(self, sdata_blobs: SpatialData):
+ def test_plot_can_render_points(self, sdata_blobs: SpatialData):
  sdata_blobs.pl.render_points(elements="blobs_points").pl.show()

tests/pl/test_render_shapes.py

@@ -20,7 +20,7 @@
 
 class TestShapes(PlotTester, metaclass=PlotTesterMeta):
  def test_plot_can_render_circles(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_circles").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_circles").pl.show()
 
  def test_plot_can_render_polygons(self, sdata_blobs: SpatialData):
- sdata_blobs.pl.render_shapes(element="blobs_polygons").pl.show()
+ sdata_blobs.pl.render_shapes(elements="blobs_polygons").pl.show()

tests/pl/test_show.py

@@ -0,0 +1,23 @@
+import matplotlib
+import scanpy as sc
+import spatialdata_plot # noqa: F401
+from spatialdata import SpatialData
+
+from tests.conftest import PlotTester, PlotTesterMeta
+
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=40, color_map="viridis")
+matplotlib.use("agg") # same as GitHub action runner
+_ = spatialdata_plot
+
+# WARNING:
+# 1. all classes must both subclass PlotTester and use metaclass=PlotTesterMeta
+# 2. tests which produce a plot must be prefixed with `test_plot_`
+# 3. if the tolerance needs to be changed, don't prefix the function with `test_plot_`, but with something else
+# the comp. function can be accessed as `self.compare(<your_filename>, tolerance=<your_tolerance>)`
+# ".png" is appended to <your_filename>, no need to set it
+
+
+class TestShow(PlotTester, metaclass=PlotTesterMeta):
+ def test_plot_pad_extent_adds_padding(self, sdata_blobs: SpatialData):
+ sdata_blobs.pl.render_images(elements="blobs_image").pl.show(pad_extent=100)