Added utils function for 0-transparent cmaps

CHANGELOG.md

@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- Added utils function for 0-transparent cmaps (#302)
+
 ### Changed
 
 -

src/spatialdata_plot/pl/utils.py

@@ -10,6 +10,7 @@
 from typing import Any, Literal, Union
 
 import matplotlib
+import matplotlib.cm as cm
 import matplotlib.patches as mpatches
 import matplotlib.patches as mplp
 import matplotlib.path as mpath
@@ -1961,3 +1962,25 @@ def _ax_show_and_transform(
  zorder=zorder,
  )
  im.set_transform(trans_data)
+
+
+def set_zero_in_cmap_to_transparent(cmap: Colormap | str, steps: int | None = None) -> ListedColormap:
+ """
+ Modify colormap so that 0s are transparent.
+
+ Parameters
+ ----------
+ cmap (Colormap | str): A matplotlib Colormap instance or a colormap name string.
+ steps (int): The number of steps in the colormap.
+
+ Returns
+ -------
+ ListedColormap: A new colormap instance with modified alpha values.
+ """
+ if isinstance(cmap, str):
+ cmap = cm.get_cmap(cmap)
+
+ colors = cmap(np.arange(steps or cmap.N))
+ colors[0, :] = [1.0, 1.0, 1.0, 0.0]
+
+ return ListedColormap(colors)

tests/pl/test_utils.py

@@ -1,14 +1,58 @@
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
 import pytest
-from spatialdata.datasets import blobs
-
-
-@pytest.mark.parametrize(
- "outline_color",
- [
- (0.0, 1.0, 0.0, 1.0),
- "#00ff00",
- ],
-)
-def test_set_outline_accepts_str_or_float_or_list_thereof(outline_color):
- sdata = blobs()
- sdata.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+import scanpy as sc
+import spatialdata_plot
+from spatialdata import SpatialData
+
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
+
+RNG = np.random.default_rng(seed=42)
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=DPI, 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 TestUtils(PlotTester, metaclass=PlotTesterMeta):
+ @pytest.mark.parametrize(
+ "outline_color",
+ [
+ (0.0, 1.0, 0.0, 1.0),
+ "#00ff00",
+ ],
+ )
+ def test_plot_set_outline_accepts_str_or_float_or_list_thereof(self, sdata_blobs: SpatialData, outline_color):
+ sdata_blobs.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+
+ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData):
+ from spatialdata_plot.pl.utils import set_zero_in_cmap_to_transparent
+
+ # set up figure and modify the data to add 0s
+ fig, axs = plt.subplots(ncols=2, figsize=(6, 3))
+ table = sdata_blobs.table.copy()
+ x = table.X.todense()
+ x[:10, 0] = 0
+ table.X = x
+ sdata_blobs.tables["modified_table"] = table
+
+ # create a new cmap with 0 as transparent
+ new_cmap = set_zero_in_cmap_to_transparent(cmap="plasma")
+
+ # baseline img
+ sdata_blobs.pl.render_labels("blobs_labels", color="channel_0_sum", cmap="viridis", table="table").pl.show(
+ ax=axs[0], colorbar=False
+ )
+
+ # image with 0s as transparent, so some labels are "missing"
+ sdata_blobs.pl.render_labels(
+ "blobs_labels", color="channel_0_sum", cmap=new_cmap, table="modified_table"
+ ).pl.show(ax=axs[1], colorbar=False)

CHANGELOG.md

@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- Added utils function for 0-transparent cmaps (#302)
+
 ### Changed
 
 -

src/spatialdata_plot/pl/utils.py

@@ -10,6 +10,7 @@
 from typing import Any, Literal, Union
 
 import matplotlib
+import matplotlib.cm as cm
 import matplotlib.patches as mpatches
 import matplotlib.patches as mplp
 import matplotlib.path as mpath
@@ -1961,3 +1962,25 @@ def _ax_show_and_transform(
  zorder=zorder,
  )
  im.set_transform(trans_data)
+
+
+def set_zero_in_cmap_to_transparent(cmap: Colormap | str, steps: int | None = None) -> ListedColormap:
+ """
+ Modify colormap so that 0s are transparent.
+
+ Parameters
+ ----------
+ cmap (Colormap | str): A matplotlib Colormap instance or a colormap name string.
+ steps (int): The number of steps in the colormap.
+
+ Returns
+ -------
+ ListedColormap: A new colormap instance with modified alpha values.
+ """
+ if isinstance(cmap, str):
+ cmap = cm.get_cmap(cmap)
+
+ colors = cmap(np.arange(steps or cmap.N))
+ colors[0, :] = [1.0, 1.0, 1.0, 0.0]
+
+ return ListedColormap(colors)

tests/pl/test_utils.py

@@ -1,14 +1,58 @@
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
 import pytest
-from spatialdata.datasets import blobs
-
-
-@pytest.mark.parametrize(
- "outline_color",
- [
- (0.0, 1.0, 0.0, 1.0),
- "#00ff00",
- ],
-)
-def test_set_outline_accepts_str_or_float_or_list_thereof(outline_color):
- sdata = blobs()
- sdata.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+import scanpy as sc
+import spatialdata_plot
+from spatialdata import SpatialData
+
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
+
+RNG = np.random.default_rng(seed=42)
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=DPI, 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 TestUtils(PlotTester, metaclass=PlotTesterMeta):
+ @pytest.mark.parametrize(
+ "outline_color",
+ [
+ (0.0, 1.0, 0.0, 1.0),
+ "#00ff00",
+ ],
+ )
+ def test_plot_set_outline_accepts_str_or_float_or_list_thereof(self, sdata_blobs: SpatialData, outline_color):
+ sdata_blobs.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+
+ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData):
+ from spatialdata_plot.pl.utils import set_zero_in_cmap_to_transparent
+
+ # set up figure and modify the data to add 0s
+ fig, axs = plt.subplots(ncols=2, figsize=(6, 3))
+ table = sdata_blobs.table.copy()
+ x = table.X.todense()
+ x[:10, 0] = 0
+ table.X = x
+ sdata_blobs.tables["modified_table"] = table
+
+ # create a new cmap with 0 as transparent
+ new_cmap = set_zero_in_cmap_to_transparent(cmap="plasma")
+
+ # baseline img
+ sdata_blobs.pl.render_labels("blobs_labels", color="channel_0_sum", cmap="viridis", table="table").pl.show(
+ ax=axs[0], colorbar=False
+ )
+
+ # image with 0s as transparent, so some labels are "missing"
+ sdata_blobs.pl.render_labels(
+ "blobs_labels", color="channel_0_sum", cmap=new_cmap, table="modified_table"
+ ).pl.show(ax=axs[1], colorbar=False)

CHANGELOG.md

@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- Added utils function for 0-transparent cmaps (#302)
+
 ### Changed
 
 -

src/spatialdata_plot/pl/utils.py

@@ -10,6 +10,7 @@
 from typing import Any, Literal, Union
 
 import matplotlib
+import matplotlib.cm as cm
 import matplotlib.patches as mpatches
 import matplotlib.patches as mplp
 import matplotlib.path as mpath
@@ -1961,3 +1962,25 @@ def _ax_show_and_transform(
  zorder=zorder,
  )
  im.set_transform(trans_data)
+
+
+def set_zero_in_cmap_to_transparent(cmap: Colormap | str, steps: int | None = None) -> ListedColormap:
+ """
+ Modify colormap so that 0s are transparent.
+
+ Parameters
+ ----------
+ cmap (Colormap | str): A matplotlib Colormap instance or a colormap name string.
+ steps (int): The number of steps in the colormap.
+
+ Returns
+ -------
+ ListedColormap: A new colormap instance with modified alpha values.
+ """
+ if isinstance(cmap, str):
+ cmap = cm.get_cmap(cmap)
+
+ colors = cmap(np.arange(steps or cmap.N))
+ colors[0, :] = [1.0, 1.0, 1.0, 0.0]
+
+ return ListedColormap(colors)

tests/pl/test_utils.py

@@ -1,14 +1,58 @@
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
 import pytest
-from spatialdata.datasets import blobs
-
-
-@pytest.mark.parametrize(
- "outline_color",
- [
- (0.0, 1.0, 0.0, 1.0),
- "#00ff00",
- ],
-)
-def test_set_outline_accepts_str_or_float_or_list_thereof(outline_color):
- sdata = blobs()
- sdata.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+import scanpy as sc
+import spatialdata_plot
+from spatialdata import SpatialData
+
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
+
+RNG = np.random.default_rng(seed=42)
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=DPI, 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 TestUtils(PlotTester, metaclass=PlotTesterMeta):
+ @pytest.mark.parametrize(
+ "outline_color",
+ [
+ (0.0, 1.0, 0.0, 1.0),
+ "#00ff00",
+ ],
+ )
+ def test_plot_set_outline_accepts_str_or_float_or_list_thereof(self, sdata_blobs: SpatialData, outline_color):
+ sdata_blobs.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+
+ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData):
+ from spatialdata_plot.pl.utils import set_zero_in_cmap_to_transparent
+
+ # set up figure and modify the data to add 0s
+ fig, axs = plt.subplots(ncols=2, figsize=(6, 3))
+ table = sdata_blobs.table.copy()
+ x = table.X.todense()
+ x[:10, 0] = 0
+ table.X = x
+ sdata_blobs.tables["modified_table"] = table
+
+ # create a new cmap with 0 as transparent
+ new_cmap = set_zero_in_cmap_to_transparent(cmap="plasma")
+
+ # baseline img
+ sdata_blobs.pl.render_labels("blobs_labels", color="channel_0_sum", cmap="viridis", table="table").pl.show(
+ ax=axs[0], colorbar=False
+ )
+
+ # image with 0s as transparent, so some labels are "missing"
+ sdata_blobs.pl.render_labels(
+ "blobs_labels", color="channel_0_sum", cmap=new_cmap, table="modified_table"
+ ).pl.show(ax=axs[1], colorbar=False)

CHANGELOG.md

@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- Added utils function for 0-transparent cmaps (#302)
+
 ### Changed
 
 -

src/spatialdata_plot/pl/utils.py

@@ -10,6 +10,7 @@
 from typing import Any, Literal, Union
 
 import matplotlib
+import matplotlib.cm as cm
 import matplotlib.patches as mpatches
 import matplotlib.patches as mplp
 import matplotlib.path as mpath
@@ -1961,3 +1962,25 @@ def _ax_show_and_transform(
  zorder=zorder,
  )
  im.set_transform(trans_data)
+
+
+def set_zero_in_cmap_to_transparent(cmap: Colormap | str, steps: int | None = None) -> ListedColormap:
+ """
+ Modify colormap so that 0s are transparent.
+
+ Parameters
+ ----------
+ cmap (Colormap | str): A matplotlib Colormap instance or a colormap name string.
+ steps (int): The number of steps in the colormap.
+
+ Returns
+ -------
+ ListedColormap: A new colormap instance with modified alpha values.
+ """
+ if isinstance(cmap, str):
+ cmap = cm.get_cmap(cmap)
+
+ colors = cmap(np.arange(steps or cmap.N))
+ colors[0, :] = [1.0, 1.0, 1.0, 0.0]
+
+ return ListedColormap(colors)

tests/pl/test_utils.py

@@ -1,14 +1,58 @@
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
 import pytest
-from spatialdata.datasets import blobs
-
-
-@pytest.mark.parametrize(
- "outline_color",
- [
- (0.0, 1.0, 0.0, 1.0),
- "#00ff00",
- ],
-)
-def test_set_outline_accepts_str_or_float_or_list_thereof(outline_color):
- sdata = blobs()
- sdata.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+import scanpy as sc
+import spatialdata_plot
+from spatialdata import SpatialData
+
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
+
+RNG = np.random.default_rng(seed=42)
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=DPI, 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 TestUtils(PlotTester, metaclass=PlotTesterMeta):
+ @pytest.mark.parametrize(
+ "outline_color",
+ [
+ (0.0, 1.0, 0.0, 1.0),
+ "#00ff00",
+ ],
+ )
+ def test_plot_set_outline_accepts_str_or_float_or_list_thereof(self, sdata_blobs: SpatialData, outline_color):
+ sdata_blobs.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+
+ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData):
+ from spatialdata_plot.pl.utils import set_zero_in_cmap_to_transparent
+
+ # set up figure and modify the data to add 0s
+ fig, axs = plt.subplots(ncols=2, figsize=(6, 3))
+ table = sdata_blobs.table.copy()
+ x = table.X.todense()
+ x[:10, 0] = 0
+ table.X = x
+ sdata_blobs.tables["modified_table"] = table
+
+ # create a new cmap with 0 as transparent
+ new_cmap = set_zero_in_cmap_to_transparent(cmap="plasma")
+
+ # baseline img
+ sdata_blobs.pl.render_labels("blobs_labels", color="channel_0_sum", cmap="viridis", table="table").pl.show(
+ ax=axs[0], colorbar=False
+ )
+
+ # image with 0s as transparent, so some labels are "missing"
+ sdata_blobs.pl.render_labels(
+ "blobs_labels", color="channel_0_sum", cmap=new_cmap, table="modified_table"
+ ).pl.show(ax=axs[1], colorbar=False)

CHANGELOG.md

@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- Added utils function for 0-transparent cmaps (#302)
+
 ### Changed
 
 -

src/spatialdata_plot/pl/utils.py

@@ -10,6 +10,7 @@
 from typing import Any, Literal, Union
 
 import matplotlib
+import matplotlib.cm as cm
 import matplotlib.patches as mpatches
 import matplotlib.patches as mplp
 import matplotlib.path as mpath
@@ -1961,3 +1962,25 @@ def _ax_show_and_transform(
  zorder=zorder,
  )
  im.set_transform(trans_data)
+
+
+def set_zero_in_cmap_to_transparent(cmap: Colormap | str, steps: int | None = None) -> ListedColormap:
+ """
+ Modify colormap so that 0s are transparent.
+
+ Parameters
+ ----------
+ cmap (Colormap | str): A matplotlib Colormap instance or a colormap name string.
+ steps (int): The number of steps in the colormap.
+
+ Returns
+ -------
+ ListedColormap: A new colormap instance with modified alpha values.
+ """
+ if isinstance(cmap, str):
+ cmap = cm.get_cmap(cmap)
+
+ colors = cmap(np.arange(steps or cmap.N))
+ colors[0, :] = [1.0, 1.0, 1.0, 0.0]
+
+ return ListedColormap(colors)

tests/pl/test_utils.py

@@ -1,14 +1,58 @@
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
 import pytest
-from spatialdata.datasets import blobs
-
-
-@pytest.mark.parametrize(
- "outline_color",
- [
- (0.0, 1.0, 0.0, 1.0),
- "#00ff00",
- ],
-)
-def test_set_outline_accepts_str_or_float_or_list_thereof(outline_color):
- sdata = blobs()
- sdata.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+import scanpy as sc
+import spatialdata_plot
+from spatialdata import SpatialData
+
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
+
+RNG = np.random.default_rng(seed=42)
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=DPI, 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 TestUtils(PlotTester, metaclass=PlotTesterMeta):
+ @pytest.mark.parametrize(
+ "outline_color",
+ [
+ (0.0, 1.0, 0.0, 1.0),
+ "#00ff00",
+ ],
+ )
+ def test_plot_set_outline_accepts_str_or_float_or_list_thereof(self, sdata_blobs: SpatialData, outline_color):
+ sdata_blobs.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+
+ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData):
+ from spatialdata_plot.pl.utils import set_zero_in_cmap_to_transparent
+
+ # set up figure and modify the data to add 0s
+ fig, axs = plt.subplots(ncols=2, figsize=(6, 3))
+ table = sdata_blobs.table.copy()
+ x = table.X.todense()
+ x[:10, 0] = 0
+ table.X = x
+ sdata_blobs.tables["modified_table"] = table
+
+ # create a new cmap with 0 as transparent
+ new_cmap = set_zero_in_cmap_to_transparent(cmap="plasma")
+
+ # baseline img
+ sdata_blobs.pl.render_labels("blobs_labels", color="channel_0_sum", cmap="viridis", table="table").pl.show(
+ ax=axs[0], colorbar=False
+ )
+
+ # image with 0s as transparent, so some labels are "missing"
+ sdata_blobs.pl.render_labels(
+ "blobs_labels", color="channel_0_sum", cmap=new_cmap, table="modified_table"
+ ).pl.show(ax=axs[1], colorbar=False)

CHANGELOG.md

@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- Added utils function for 0-transparent cmaps (#302)
+
 ### Changed
 
 -

src/spatialdata_plot/pl/utils.py

@@ -10,6 +10,7 @@
 from typing import Any, Literal, Union
 
 import matplotlib
+import matplotlib.cm as cm
 import matplotlib.patches as mpatches
 import matplotlib.patches as mplp
 import matplotlib.path as mpath
@@ -1961,3 +1962,25 @@ def _ax_show_and_transform(
  zorder=zorder,
  )
  im.set_transform(trans_data)
+
+
+def set_zero_in_cmap_to_transparent(cmap: Colormap | str, steps: int | None = None) -> ListedColormap:
+ """
+ Modify colormap so that 0s are transparent.
+
+ Parameters
+ ----------
+ cmap (Colormap | str): A matplotlib Colormap instance or a colormap name string.
+ steps (int): The number of steps in the colormap.
+
+ Returns
+ -------
+ ListedColormap: A new colormap instance with modified alpha values.
+ """
+ if isinstance(cmap, str):
+ cmap = cm.get_cmap(cmap)
+
+ colors = cmap(np.arange(steps or cmap.N))
+ colors[0, :] = [1.0, 1.0, 1.0, 0.0]
+
+ return ListedColormap(colors)

tests/pl/test_utils.py

@@ -1,14 +1,58 @@
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
 import pytest
-from spatialdata.datasets import blobs
-
-
-@pytest.mark.parametrize(
- "outline_color",
- [
- (0.0, 1.0, 0.0, 1.0),
- "#00ff00",
- ],
-)
-def test_set_outline_accepts_str_or_float_or_list_thereof(outline_color):
- sdata = blobs()
- sdata.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+import scanpy as sc
+import spatialdata_plot
+from spatialdata import SpatialData
+
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
+
+RNG = np.random.default_rng(seed=42)
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=DPI, 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 TestUtils(PlotTester, metaclass=PlotTesterMeta):
+ @pytest.mark.parametrize(
+ "outline_color",
+ [
+ (0.0, 1.0, 0.0, 1.0),
+ "#00ff00",
+ ],
+ )
+ def test_plot_set_outline_accepts_str_or_float_or_list_thereof(self, sdata_blobs: SpatialData, outline_color):
+ sdata_blobs.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+
+ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData):
+ from spatialdata_plot.pl.utils import set_zero_in_cmap_to_transparent
+
+ # set up figure and modify the data to add 0s
+ fig, axs = plt.subplots(ncols=2, figsize=(6, 3))
+ table = sdata_blobs.table.copy()
+ x = table.X.todense()
+ x[:10, 0] = 0
+ table.X = x
+ sdata_blobs.tables["modified_table"] = table
+
+ # create a new cmap with 0 as transparent
+ new_cmap = set_zero_in_cmap_to_transparent(cmap="plasma")
+
+ # baseline img
+ sdata_blobs.pl.render_labels("blobs_labels", color="channel_0_sum", cmap="viridis", table="table").pl.show(
+ ax=axs[0], colorbar=False
+ )
+
+ # image with 0s as transparent, so some labels are "missing"
+ sdata_blobs.pl.render_labels(
+ "blobs_labels", color="channel_0_sum", cmap=new_cmap, table="modified_table"
+ ).pl.show(ax=axs[1], colorbar=False)

CHANGELOG.md

@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- Added utils function for 0-transparent cmaps (#302)
+
 ### Changed
 
 -

src/spatialdata_plot/pl/utils.py

@@ -10,6 +10,7 @@
 from typing import Any, Literal, Union
 
 import matplotlib
+import matplotlib.cm as cm
 import matplotlib.patches as mpatches
 import matplotlib.patches as mplp
 import matplotlib.path as mpath
@@ -1961,3 +1962,25 @@ def _ax_show_and_transform(
  zorder=zorder,
  )
  im.set_transform(trans_data)
+
+
+def set_zero_in_cmap_to_transparent(cmap: Colormap | str, steps: int | None = None) -> ListedColormap:
+ """
+ Modify colormap so that 0s are transparent.
+
+ Parameters
+ ----------
+ cmap (Colormap | str): A matplotlib Colormap instance or a colormap name string.
+ steps (int): The number of steps in the colormap.
+
+ Returns
+ -------
+ ListedColormap: A new colormap instance with modified alpha values.
+ """
+ if isinstance(cmap, str):
+ cmap = cm.get_cmap(cmap)
+
+ colors = cmap(np.arange(steps or cmap.N))
+ colors[0, :] = [1.0, 1.0, 1.0, 0.0]
+
+ return ListedColormap(colors)

tests/pl/test_utils.py

@@ -1,14 +1,58 @@
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
 import pytest
-from spatialdata.datasets import blobs
-
-
-@pytest.mark.parametrize(
- "outline_color",
- [
- (0.0, 1.0, 0.0, 1.0),
- "#00ff00",
- ],
-)
-def test_set_outline_accepts_str_or_float_or_list_thereof(outline_color):
- sdata = blobs()
- sdata.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+import scanpy as sc
+import spatialdata_plot
+from spatialdata import SpatialData
+
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
+
+RNG = np.random.default_rng(seed=42)
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=DPI, 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 TestUtils(PlotTester, metaclass=PlotTesterMeta):
+ @pytest.mark.parametrize(
+ "outline_color",
+ [
+ (0.0, 1.0, 0.0, 1.0),
+ "#00ff00",
+ ],
+ )
+ def test_plot_set_outline_accepts_str_or_float_or_list_thereof(self, sdata_blobs: SpatialData, outline_color):
+ sdata_blobs.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+
+ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData):
+ from spatialdata_plot.pl.utils import set_zero_in_cmap_to_transparent
+
+ # set up figure and modify the data to add 0s
+ fig, axs = plt.subplots(ncols=2, figsize=(6, 3))
+ table = sdata_blobs.table.copy()
+ x = table.X.todense()
+ x[:10, 0] = 0
+ table.X = x
+ sdata_blobs.tables["modified_table"] = table
+
+ # create a new cmap with 0 as transparent
+ new_cmap = set_zero_in_cmap_to_transparent(cmap="plasma")
+
+ # baseline img
+ sdata_blobs.pl.render_labels("blobs_labels", color="channel_0_sum", cmap="viridis", table="table").pl.show(
+ ax=axs[0], colorbar=False
+ )
+
+ # image with 0s as transparent, so some labels are "missing"
+ sdata_blobs.pl.render_labels(
+ "blobs_labels", color="channel_0_sum", cmap=new_cmap, table="modified_table"
+ ).pl.show(ax=axs[1], colorbar=False)

CHANGELOG.md

@@ -12,6 +12,8 @@ and this project adheres to [Semantic Versioning][].
 
 ### Added
 
+- Added utils function for 0-transparent cmaps (#302)
+
 ### Changed
 
 -

src/spatialdata_plot/pl/utils.py

@@ -10,6 +10,7 @@
 from typing import Any, Literal, Union
 
 import matplotlib
+import matplotlib.cm as cm
 import matplotlib.patches as mpatches
 import matplotlib.patches as mplp
 import matplotlib.path as mpath
@@ -1961,3 +1962,25 @@ def _ax_show_and_transform(
  zorder=zorder,
  )
  im.set_transform(trans_data)
+
+
+def set_zero_in_cmap_to_transparent(cmap: Colormap | str, steps: int | None = None) -> ListedColormap:
+ """
+ Modify colormap so that 0s are transparent.
+
+ Parameters
+ ----------
+ cmap (Colormap | str): A matplotlib Colormap instance or a colormap name string.
+ steps (int): The number of steps in the colormap.
+
+ Returns
+ -------
+ ListedColormap: A new colormap instance with modified alpha values.
+ """
+ if isinstance(cmap, str):
+ cmap = cm.get_cmap(cmap)
+
+ colors = cmap(np.arange(steps or cmap.N))
+ colors[0, :] = [1.0, 1.0, 1.0, 0.0]
+
+ return ListedColormap(colors)

tests/pl/test_utils.py

@@ -1,14 +1,58 @@
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
 import pytest
-from spatialdata.datasets import blobs
-
-
-@pytest.mark.parametrize(
- "outline_color",
- [
- (0.0, 1.0, 0.0, 1.0),
- "#00ff00",
- ],
-)
-def test_set_outline_accepts_str_or_float_or_list_thereof(outline_color):
- sdata = blobs()
- sdata.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+import scanpy as sc
+import spatialdata_plot
+from spatialdata import SpatialData
+
+from tests.conftest import DPI, PlotTester, PlotTesterMeta
+
+RNG = np.random.default_rng(seed=42)
+sc.pl.set_rcParams_defaults()
+sc.set_figure_params(dpi=DPI, 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 TestUtils(PlotTester, metaclass=PlotTesterMeta):
+ @pytest.mark.parametrize(
+ "outline_color",
+ [
+ (0.0, 1.0, 0.0, 1.0),
+ "#00ff00",
+ ],
+ )
+ def test_plot_set_outline_accepts_str_or_float_or_list_thereof(self, sdata_blobs: SpatialData, outline_color):
+ sdata_blobs.pl.render_shapes(element="blobs_polygons", outline=True, outline_color=outline_color).pl.show()
+
+ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData):
+ from spatialdata_plot.pl.utils import set_zero_in_cmap_to_transparent
+
+ # set up figure and modify the data to add 0s
+ fig, axs = plt.subplots(ncols=2, figsize=(6, 3))
+ table = sdata_blobs.table.copy()
+ x = table.X.todense()
+ x[:10, 0] = 0
+ table.X = x
+ sdata_blobs.tables["modified_table"] = table
+
+ # create a new cmap with 0 as transparent
+ new_cmap = set_zero_in_cmap_to_transparent(cmap="plasma")
+
+ # baseline img
+ sdata_blobs.pl.render_labels("blobs_labels", color="channel_0_sum", cmap="viridis", table="table").pl.show(
+ ax=axs[0], colorbar=False
+ )
+
+ # image with 0s as transparent, so some labels are "missing"
+ sdata_blobs.pl.render_labels(
+ "blobs_labels", color="channel_0_sum", cmap=new_cmap, table="modified_table"
+ ).pl.show(ax=axs[1], colorbar=False)