Drop vmin/vmax kwargs across all render functions#652

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timtreis merged 2 commits into from
May 8, 2026
Merged

Drop vmin/vmax kwargs across all render functions #652

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b8c5cde
Drop vmin/vmax kwargs and close render signatures (#612)
timtreis May 8, 2026
a4b67ab
Fix table= → table_name= typo in render_labels test calls
timtreis May 8, 2026
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53 changes: 21 additions & 32 deletions src/spatialdata_plot/pl/basic.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@
from xarray import DataArray, DataTree

from spatialdata_plot._accessor import register_spatial_data_accessor
from spatialdata_plot._logging import _log_context, logger
from spatialdata_plot._logging import _log_context
from spatialdata_plot.pl.render import (
_draw_channel_legend,
_render_images,
Expand DownExpand Up@@ -190,7 +190,8 @@ def render_shapes(
shape: Literal["circle", "hex", "visium_hex", "square"] | None = None,
colorbar: bool | str | None = "auto",
colorbar_params: dict[str, object] | None = None,
**kwargs: Any,
datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
transfunc: Callable[[float], float] | None = None,
) -> sd.SpatialData:
"""
Render shapes elements in SpatialData.
Expand DownExpand Up@@ -279,15 +280,10 @@ def render_shapes(
specified, the shapes are converted to a circle/hexagon/square before rendering. If "visium_hex" is
specified, the shapes are assumed to be Visium spots and the size of the hexagons is adjusted to be adjacent
to each other.

**kwargs : Any
Additional arguments for customization. This can include:

datashader_reduction : Literal[
"sum", "mean", "any", "count", "std", "var", "max", "min"
], default: "max"
Reduction method for datashader when coloring by continuous values. Defaults to 'max'.

datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"max"``.
transfunc : Callable[[float], float] | None, optional
Optional transformation applied to the continuous color vector before normalization and colormap mapping.

Notes
-----
Expand All@@ -300,8 +296,6 @@ def render_shapes(
sd.SpatialData
A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
"""
if "vmin" in kwargs or "vmax" in kwargs:
logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
params_dict = _validate_shape_render_params(
self._sdata,
element=element,
Expand All@@ -320,7 +314,7 @@ def render_shapes(
table_layer=table_layer,
shape=shape,
method=method,
ds_reduction=kwargs.get("datashader_reduction"),
ds_reduction=datashader_reduction,
colorbar=colorbar,
colorbar_params=colorbar_params,
gene_symbols=gene_symbols,
Expand DownExpand Up@@ -351,7 +345,7 @@ def render_shapes(
palette=param_values["palette"],
outline_alpha=final_outline_alpha,
fill_alpha=param_values["fill_alpha"],
transfunc=kwargs.get("transfunc"),
transfunc=transfunc,
table_name=param_values["table_name"],
table_layer=param_values["table_layer"],
shape=param_values["shape"],
Expand DownExpand Up@@ -384,7 +378,8 @@ def render_points(
gene_symbols: str | None = None,
colorbar: bool | str | None = "auto",
colorbar_params: dict[str, object] | None = None,
**kwargs: Any,
datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
transfunc: Callable[[float], float] | None = None,
) -> sd.SpatialData:
"""
Render points elements in SpatialData.
Expand DownExpand Up@@ -452,22 +447,16 @@ def render_points(
Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.

**kwargs : Any
Additional arguments for customization. This can include:

datashader_reduction : Literal[
"sum", "mean", "any", "count", "std", "var", "max", "min"
], default: "sum"
Reduction method for datashader when coloring by continuous values. Defaults to 'sum'.
datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"sum"``.
transfunc : Callable[[float], float] | None, optional
Optional transformation applied to the continuous color vector before normalization and colormap mapping.

Returns
-------
sd.SpatialData
A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
"""
if "vmin" in kwargs or "vmax" in kwargs:
logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
params_dict = _validate_points_render_params(
self._sdata,
element=element,
Expand All@@ -481,7 +470,7 @@ def render_points(
size=size,
table_name=table_name,
table_layer=table_layer,
ds_reduction=kwargs.get("datashader_reduction"),
ds_reduction=datashader_reduction,
colorbar=colorbar,
colorbar_params=colorbar_params,
gene_symbols=gene_symbols,
Expand DownExpand Up@@ -511,7 +500,7 @@ def render_points(
cmap_params=cmap_params,
palette=param_values["palette"],
alpha=param_values["alpha"],
transfunc=kwargs.get("transfunc"),
transfunc=transfunc,
size=param_values["size"],
table_name=param_values["table_name"],
table_layer=param_values["table_layer"],
Expand DownExpand Up@@ -730,7 +719,7 @@ def render_labels(
table_name: str | None = None,
table_layer: str | None = None,
gene_symbols: str | None = None,
**kwargs: Any,
transfunc: Callable[[float], float] | None = None,
) -> sd.SpatialData:
"""
Render labels elements in SpatialData.
Expand DownExpand Up@@ -806,14 +795,14 @@ def render_labels(
Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.
transfunc : Callable[[float], float] | None, optional
Optional transformation applied to the continuous color vector before normalization and colormap mapping.

Returns
-------
sd.SpatialData
A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
"""
if "vmin" in kwargs or "vmax" in kwargs:
logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
params_dict = _validate_label_render_params(
self._sdata,
element=element,
Expand DownExpand Up@@ -859,7 +848,7 @@ def render_labels(
scale=param_values["scale"],
table_name=param_values["table_name"],
table_layer=param_values["table_layer"],
transfunc=kwargs.get("transfunc"),
transfunc=transfunc,
zorder=n_steps,
colorbar=param_values["colorbar"],
colorbar_params=param_values["colorbar_params"],
Expand Down
15 changes: 15 additions & 0 deletions tests/pl/test_render_images.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -505,6 +505,21 @@ def test_cmap_matches_selected_channels_not_full_image(sdata_blobs: SpatialData)
plt.close(fig)


# Regression for #612: vmin/vmax kwargs are no longer accepted on any render
# function. The check covers all four to prevent the asymmetry from re-emerging.
@pytest.mark.parametrize("kwarg", ["vmin", "vmax"])
@pytest.mark.parametrize("func", ["render_images", "render_shapes", "render_points", "render_labels"])
def test_vmin_vmax_kwargs_rejected_uniformly(sdata_blobs: SpatialData, func: str, kwarg: str) -> None:
elements = {
"render_images": "blobs_image",
"render_labels": "blobs_labels",
"render_points": "blobs_points",
"render_shapes": "blobs_circles",
}
with pytest.raises(TypeError, match=kwarg):
getattr(sdata_blobs.pl, func)(elements[func], **{kwarg: 0})


# ---------------------------------------------------------------------------
# channels_as_legend visual tests (#459)
# ---------------------------------------------------------------------------
Expand Down
14 changes: 7 additions & 7 deletions tests/pl/test_render_labels.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -156,13 +156,13 @@ def _make_tablemodel_with_categorical_labels(sdata_blobs, label):

_, axs = plt.subplots(nrows=1, ncols=3, layout="tight")

sdata_blobs.pl.render_labels(label, color="channel_1_sum", table="other_table", scale="scale0").pl.show(
ax=axs[0], title="ch_1_sum", colorbar=False
)
sdata_blobs.pl.render_labels(label, color="channel_2_sum", table="other_table", scale="scale0").pl.show(
ax=axs[1], title="ch_2_sum", colorbar=False
)
sdata_blobs.pl.render_labels(label, color="which_max", table="other_table", scale="scale0").pl.show(
sdata_blobs.pl.render_labels(
label, color="channel_1_sum", table_name="other_table", scale="scale0"
).pl.show(ax=axs[0], title="ch_1_sum", colorbar=False)
sdata_blobs.pl.render_labels(
label, color="channel_2_sum", table_name="other_table", scale="scale0"
).pl.show(ax=axs[1], title="ch_2_sum", colorbar=False)
sdata_blobs.pl.render_labels(label, color="which_max", table_name="other_table", scale="scale0").pl.show(
ax=axs[2], legend_fontsize=6
)

Expand Down
4 changes: 2 additions & 2 deletions tests/pl/test_utils.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -68,14 +68,14 @@ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData
new_cmap = set_zero_in_cmap_to_transparent(cmap="viridis")

# baseline img
sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table="table").pl.show(
sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table_name="table").pl.show(
ax=axs[0], colorbar=False
)

sdata_blobs.tables["table"].obs.iloc[8:12, 2] = 0

# image with 0s as transparent, so some labels are "missing"
sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table="table").pl.show(
sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table_name="table").pl.show(
ax=axs[1], colorbar=False
)

Expand Down
Loading
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Drop vmin/vmax kwargs across all render functions#652

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 Merged

timtreis
merged 2 commits into

from

May 8, 2026
 Merged


Drop vmin/vmax kwargs across all render functions
#652
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b8c5cde

Drop vmin/vmax kwargs and close render signatures (#612)


timtreis May 8, 2026
a4b67ab

Fix table= → table_name= typo in render_labels test calls


timtreis May 8, 2026

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53 changes: 21 additions & 32 deletions
src/spatialdata_plot/pl/basic.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@
from xarray import DataArray, DataTree

from spatialdata_plot._accessor import register_spatial_data_accessor
from spatialdata_plot._logging import _log_context, logger
from spatialdata_plot._logging import _log_context
from spatialdata_plot.pl.render import (
 _draw_channel_legend,
 _render_images,
Expand DownExpand Up@@ -190,7 +190,8 @@ def render_shapes(
 shape: Literal["circle", "hex", "visium_hex", "square"] | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render shapes elements in SpatialData.
Expand DownExpand Up@@ -279,15 +280,10 @@ def render_shapes(
 specified, the shapes are converted to a circle/hexagon/square before rendering. If "visium_hex" is
 specified, the shapes are assumed to be Visium spots and the size of the hexagons is adjusted to be adjacent
 to each other.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "max"
 Reduction method for datashader when coloring by continuous values. Defaults to 'max'.

 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"max"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Notes
 -----
Expand All@@ -300,8 +296,6 @@ def render_shapes(
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_shape_render_params(
 self._sdata,
 element=element,
Expand All@@ -320,7 +314,7 @@ def render_shapes(
 table_layer=table_layer,
 shape=shape,
 method=method,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -351,7 +345,7 @@ def render_shapes(
 palette=param_values["palette"],
 outline_alpha=final_outline_alpha,
 fill_alpha=param_values["fill_alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 shape=param_values["shape"],
Expand DownExpand Up@@ -384,7 +378,8 @@ def render_points(
 gene_symbols: str | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render points elements in SpatialData.
Expand DownExpand Up@@ -452,22 +447,16 @@ def render_points(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "sum"
 Reduction method for datashader when coloring by continuous values. Defaults to 'sum'.
 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"sum"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_points_render_params(
 self._sdata,
 element=element,
Expand All@@ -481,7 +470,7 @@ def render_points(
 size=size,
 table_name=table_name,
 table_layer=table_layer,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -511,7 +500,7 @@ def render_points(
 cmap_params=cmap_params,
 palette=param_values["palette"],
 alpha=param_values["alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 size=param_values["size"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
Expand DownExpand Up@@ -730,7 +719,7 @@ def render_labels(
 table_name: str | None = None,
 table_layer: str | None = None,
 gene_symbols: str | None = None,
**kwargs: Any,
transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render labels elements in SpatialData.
Expand DownExpand Up@@ -806,14 +795,14 @@ def render_labels(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_label_render_params(
 self._sdata,
 element=element,
Expand DownExpand Up@@ -859,7 +848,7 @@ def render_labels(
 scale=param_values["scale"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 zorder=n_steps,
 colorbar=param_values["colorbar"],
 colorbar_params=param_values["colorbar_params"],
Expand Down

15 changes: 15 additions & 0 deletions
tests/pl/test_render_images.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -505,6 +505,21 @@ def test_cmap_matches_selected_channels_not_full_image(sdata_blobs: SpatialData)
 plt.close(fig)


# Regression for #612: vmin/vmax kwargs are no longer accepted on any render
# function. The check covers all four to prevent the asymmetry from re-emerging.
@pytest.mark.parametrize("kwarg", ["vmin", "vmax"])
@pytest.mark.parametrize("func", ["render_images", "render_shapes", "render_points", "render_labels"])
def test_vmin_vmax_kwargs_rejected_uniformly(sdata_blobs: SpatialData, func: str, kwarg: str) -> None:
 elements = {
 "render_images": "blobs_image",
 "render_labels": "blobs_labels",
 "render_points": "blobs_points",
 "render_shapes": "blobs_circles",
 }
 with pytest.raises(TypeError, match=kwarg):
 getattr(sdata_blobs.pl, func)(elements[func], **{kwarg: 0})


# ---------------------------------------------------------------------------
# channels_as_legend visual tests (#459)
# ---------------------------------------------------------------------------
Expand Down

14 changes: 7 additions & 7 deletions
tests/pl/test_render_labels.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -156,13 +156,13 @@ def _make_tablemodel_with_categorical_labels(sdata_blobs, label):

 _, axs = plt.subplots(nrows=1, ncols=3, layout="tight")

 sdata_blobs.pl.render_labels(label, color="channel_1_sum", table="other_table", scale="scale0").pl.show(
ax=axs[0], title="ch_1_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="channel_2_sum", table="other_table", scale="scale0").pl.show(
ax=axs[1], title="ch_2_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="which_max", table="other_table", scale="scale0").pl.show(
 sdata_blobs.pl.render_labels(
label, color="channel_1_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[0], title="ch_1_sum", colorbar=False)
 sdata_blobs.pl.render_labels(
label, color="channel_2_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[1], title="ch_2_sum", colorbar=False)
 sdata_blobs.pl.render_labels(label, color="which_max", table_name="other_table", scale="scale0").pl.show(
 ax=axs[2], legend_fontsize=6
 )

Expand Down

4 changes: 2 additions & 2 deletions
tests/pl/test_utils.py

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -68,14 +68,14 @@ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData
 new_cmap = set_zero_in_cmap_to_transparent(cmap="viridis")

 # baseline img
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table_name="table").pl.show(
 ax=axs[0], colorbar=False
 )

 sdata_blobs.tables["table"].obs.iloc[8:12, 2] = 0

 # image with 0s as transparent, so some labels are "missing"
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table_name="table").pl.show(
 ax=axs[1], colorbar=False
 )

Expand Down
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Drop vmin/vmax kwargs across all render functions#652

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Drop vmin/vmax kwargs across all render functions
#652
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b8c5cde

Drop vmin/vmax kwargs and close render signatures (#612)


timtreis May 8, 2026
a4b67ab

Fix table= → table_name= typo in render_labels test calls


timtreis May 8, 2026

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53 changes: 21 additions & 32 deletions
src/spatialdata_plot/pl/basic.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@
from xarray import DataArray, DataTree

from spatialdata_plot._accessor import register_spatial_data_accessor
from spatialdata_plot._logging import _log_context, logger
from spatialdata_plot._logging import _log_context
from spatialdata_plot.pl.render import (
 _draw_channel_legend,
 _render_images,
Expand DownExpand Up@@ -190,7 +190,8 @@ def render_shapes(
 shape: Literal["circle", "hex", "visium_hex", "square"] | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render shapes elements in SpatialData.
Expand DownExpand Up@@ -279,15 +280,10 @@ def render_shapes(
 specified, the shapes are converted to a circle/hexagon/square before rendering. If "visium_hex" is
 specified, the shapes are assumed to be Visium spots and the size of the hexagons is adjusted to be adjacent
 to each other.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "max"
 Reduction method for datashader when coloring by continuous values. Defaults to 'max'.

 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"max"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Notes
 -----
Expand All@@ -300,8 +296,6 @@ def render_shapes(
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_shape_render_params(
 self._sdata,
 element=element,
Expand All@@ -320,7 +314,7 @@ def render_shapes(
 table_layer=table_layer,
 shape=shape,
 method=method,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -351,7 +345,7 @@ def render_shapes(
 palette=param_values["palette"],
 outline_alpha=final_outline_alpha,
 fill_alpha=param_values["fill_alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 shape=param_values["shape"],
Expand DownExpand Up@@ -384,7 +378,8 @@ def render_points(
 gene_symbols: str | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render points elements in SpatialData.
Expand DownExpand Up@@ -452,22 +447,16 @@ def render_points(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "sum"
 Reduction method for datashader when coloring by continuous values. Defaults to 'sum'.
 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"sum"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_points_render_params(
 self._sdata,
 element=element,
Expand All@@ -481,7 +470,7 @@ def render_points(
 size=size,
 table_name=table_name,
 table_layer=table_layer,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -511,7 +500,7 @@ def render_points(
 cmap_params=cmap_params,
 palette=param_values["palette"],
 alpha=param_values["alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 size=param_values["size"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
Expand DownExpand Up@@ -730,7 +719,7 @@ def render_labels(
 table_name: str | None = None,
 table_layer: str | None = None,
 gene_symbols: str | None = None,
**kwargs: Any,
transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render labels elements in SpatialData.
Expand DownExpand Up@@ -806,14 +795,14 @@ def render_labels(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_label_render_params(
 self._sdata,
 element=element,
Expand DownExpand Up@@ -859,7 +848,7 @@ def render_labels(
 scale=param_values["scale"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 zorder=n_steps,
 colorbar=param_values["colorbar"],
 colorbar_params=param_values["colorbar_params"],
Expand Down

15 changes: 15 additions & 0 deletions
tests/pl/test_render_images.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -505,6 +505,21 @@ def test_cmap_matches_selected_channels_not_full_image(sdata_blobs: SpatialData)
 plt.close(fig)


# Regression for #612: vmin/vmax kwargs are no longer accepted on any render
# function. The check covers all four to prevent the asymmetry from re-emerging.
@pytest.mark.parametrize("kwarg", ["vmin", "vmax"])
@pytest.mark.parametrize("func", ["render_images", "render_shapes", "render_points", "render_labels"])
def test_vmin_vmax_kwargs_rejected_uniformly(sdata_blobs: SpatialData, func: str, kwarg: str) -> None:
 elements = {
 "render_images": "blobs_image",
 "render_labels": "blobs_labels",
 "render_points": "blobs_points",
 "render_shapes": "blobs_circles",
 }
 with pytest.raises(TypeError, match=kwarg):
 getattr(sdata_blobs.pl, func)(elements[func], **{kwarg: 0})


# ---------------------------------------------------------------------------
# channels_as_legend visual tests (#459)
# ---------------------------------------------------------------------------
Expand Down

14 changes: 7 additions & 7 deletions
tests/pl/test_render_labels.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -156,13 +156,13 @@ def _make_tablemodel_with_categorical_labels(sdata_blobs, label):

 _, axs = plt.subplots(nrows=1, ncols=3, layout="tight")

 sdata_blobs.pl.render_labels(label, color="channel_1_sum", table="other_table", scale="scale0").pl.show(
ax=axs[0], title="ch_1_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="channel_2_sum", table="other_table", scale="scale0").pl.show(
ax=axs[1], title="ch_2_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="which_max", table="other_table", scale="scale0").pl.show(
 sdata_blobs.pl.render_labels(
label, color="channel_1_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[0], title="ch_1_sum", colorbar=False)
 sdata_blobs.pl.render_labels(
label, color="channel_2_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[1], title="ch_2_sum", colorbar=False)
 sdata_blobs.pl.render_labels(label, color="which_max", table_name="other_table", scale="scale0").pl.show(
 ax=axs[2], legend_fontsize=6
 )

Expand Down

4 changes: 2 additions & 2 deletions
tests/pl/test_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -68,14 +68,14 @@ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData
 new_cmap = set_zero_in_cmap_to_transparent(cmap="viridis")

 # baseline img
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table_name="table").pl.show(
 ax=axs[0], colorbar=False
 )

 sdata_blobs.tables["table"].obs.iloc[8:12, 2] = 0

 # image with 0s as transparent, so some labels are "missing"
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table_name="table").pl.show(
 ax=axs[1], colorbar=False
 )

Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Drop vmin/vmax kwargs across all render functions#652

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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 Merged

timtreis
merged 2 commits into

from

May 8, 2026
 Merged


Drop vmin/vmax kwargs across all render functions
#652
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b8c5cde

Drop vmin/vmax kwargs and close render signatures (#612)


timtreis May 8, 2026
a4b67ab

Fix table= → table_name= typo in render_labels test calls


timtreis May 8, 2026

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53 changes: 21 additions & 32 deletions
src/spatialdata_plot/pl/basic.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@
from xarray import DataArray, DataTree

from spatialdata_plot._accessor import register_spatial_data_accessor
from spatialdata_plot._logging import _log_context, logger
from spatialdata_plot._logging import _log_context
from spatialdata_plot.pl.render import (
 _draw_channel_legend,
 _render_images,
Expand DownExpand Up@@ -190,7 +190,8 @@ def render_shapes(
 shape: Literal["circle", "hex", "visium_hex", "square"] | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render shapes elements in SpatialData.
Expand DownExpand Up@@ -279,15 +280,10 @@ def render_shapes(
 specified, the shapes are converted to a circle/hexagon/square before rendering. If "visium_hex" is
 specified, the shapes are assumed to be Visium spots and the size of the hexagons is adjusted to be adjacent
 to each other.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "max"
 Reduction method for datashader when coloring by continuous values. Defaults to 'max'.

 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"max"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Notes
 -----
Expand All@@ -300,8 +296,6 @@ def render_shapes(
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_shape_render_params(
 self._sdata,
 element=element,
Expand All@@ -320,7 +314,7 @@ def render_shapes(
 table_layer=table_layer,
 shape=shape,
 method=method,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -351,7 +345,7 @@ def render_shapes(
 palette=param_values["palette"],
 outline_alpha=final_outline_alpha,
 fill_alpha=param_values["fill_alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 shape=param_values["shape"],
Expand DownExpand Up@@ -384,7 +378,8 @@ def render_points(
 gene_symbols: str | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render points elements in SpatialData.
Expand DownExpand Up@@ -452,22 +447,16 @@ def render_points(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "sum"
 Reduction method for datashader when coloring by continuous values. Defaults to 'sum'.
 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"sum"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_points_render_params(
 self._sdata,
 element=element,
Expand All@@ -481,7 +470,7 @@ def render_points(
 size=size,
 table_name=table_name,
 table_layer=table_layer,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -511,7 +500,7 @@ def render_points(
 cmap_params=cmap_params,
 palette=param_values["palette"],
 alpha=param_values["alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 size=param_values["size"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
Expand DownExpand Up@@ -730,7 +719,7 @@ def render_labels(
 table_name: str | None = None,
 table_layer: str | None = None,
 gene_symbols: str | None = None,
**kwargs: Any,
transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render labels elements in SpatialData.
Expand DownExpand Up@@ -806,14 +795,14 @@ def render_labels(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_label_render_params(
 self._sdata,
 element=element,
Expand DownExpand Up@@ -859,7 +848,7 @@ def render_labels(
 scale=param_values["scale"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 zorder=n_steps,
 colorbar=param_values["colorbar"],
 colorbar_params=param_values["colorbar_params"],
Expand Down

15 changes: 15 additions & 0 deletions
tests/pl/test_render_images.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -505,6 +505,21 @@ def test_cmap_matches_selected_channels_not_full_image(sdata_blobs: SpatialData)
 plt.close(fig)


# Regression for #612: vmin/vmax kwargs are no longer accepted on any render
# function. The check covers all four to prevent the asymmetry from re-emerging.
@pytest.mark.parametrize("kwarg", ["vmin", "vmax"])
@pytest.mark.parametrize("func", ["render_images", "render_shapes", "render_points", "render_labels"])
def test_vmin_vmax_kwargs_rejected_uniformly(sdata_blobs: SpatialData, func: str, kwarg: str) -> None:
 elements = {
 "render_images": "blobs_image",
 "render_labels": "blobs_labels",
 "render_points": "blobs_points",
 "render_shapes": "blobs_circles",
 }
 with pytest.raises(TypeError, match=kwarg):
 getattr(sdata_blobs.pl, func)(elements[func], **{kwarg: 0})


# ---------------------------------------------------------------------------
# channels_as_legend visual tests (#459)
# ---------------------------------------------------------------------------
Expand Down

14 changes: 7 additions & 7 deletions
tests/pl/test_render_labels.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -156,13 +156,13 @@ def _make_tablemodel_with_categorical_labels(sdata_blobs, label):

 _, axs = plt.subplots(nrows=1, ncols=3, layout="tight")

 sdata_blobs.pl.render_labels(label, color="channel_1_sum", table="other_table", scale="scale0").pl.show(
ax=axs[0], title="ch_1_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="channel_2_sum", table="other_table", scale="scale0").pl.show(
ax=axs[1], title="ch_2_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="which_max", table="other_table", scale="scale0").pl.show(
 sdata_blobs.pl.render_labels(
label, color="channel_1_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[0], title="ch_1_sum", colorbar=False)
 sdata_blobs.pl.render_labels(
label, color="channel_2_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[1], title="ch_2_sum", colorbar=False)
 sdata_blobs.pl.render_labels(label, color="which_max", table_name="other_table", scale="scale0").pl.show(
 ax=axs[2], legend_fontsize=6
 )

Expand Down

4 changes: 2 additions & 2 deletions
tests/pl/test_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -68,14 +68,14 @@ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData
 new_cmap = set_zero_in_cmap_to_transparent(cmap="viridis")

 # baseline img
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table_name="table").pl.show(
 ax=axs[0], colorbar=False
 )

 sdata_blobs.tables["table"].obs.iloc[8:12, 2] = 0

 # image with 0s as transparent, so some labels are "missing"
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table_name="table").pl.show(
 ax=axs[1], colorbar=False
 )

Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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Drop vmin/vmax kwargs across all render functions#652

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timtreis
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May 8, 2026
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Drop vmin/vmax kwargs across all render functions
#652
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b8c5cde

Drop vmin/vmax kwargs and close render signatures (#612)


timtreis May 8, 2026
a4b67ab

Fix table= → table_name= typo in render_labels test calls


timtreis May 8, 2026

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53 changes: 21 additions & 32 deletions
src/spatialdata_plot/pl/basic.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@
from xarray import DataArray, DataTree

from spatialdata_plot._accessor import register_spatial_data_accessor
from spatialdata_plot._logging import _log_context, logger
from spatialdata_plot._logging import _log_context
from spatialdata_plot.pl.render import (
 _draw_channel_legend,
 _render_images,
Expand DownExpand Up@@ -190,7 +190,8 @@ def render_shapes(
 shape: Literal["circle", "hex", "visium_hex", "square"] | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render shapes elements in SpatialData.
Expand DownExpand Up@@ -279,15 +280,10 @@ def render_shapes(
 specified, the shapes are converted to a circle/hexagon/square before rendering. If "visium_hex" is
 specified, the shapes are assumed to be Visium spots and the size of the hexagons is adjusted to be adjacent
 to each other.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "max"
 Reduction method for datashader when coloring by continuous values. Defaults to 'max'.

 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"max"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Notes
 -----
Expand All@@ -300,8 +296,6 @@ def render_shapes(
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_shape_render_params(
 self._sdata,
 element=element,
Expand All@@ -320,7 +314,7 @@ def render_shapes(
 table_layer=table_layer,
 shape=shape,
 method=method,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -351,7 +345,7 @@ def render_shapes(
 palette=param_values["palette"],
 outline_alpha=final_outline_alpha,
 fill_alpha=param_values["fill_alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 shape=param_values["shape"],
Expand DownExpand Up@@ -384,7 +378,8 @@ def render_points(
 gene_symbols: str | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render points elements in SpatialData.
Expand DownExpand Up@@ -452,22 +447,16 @@ def render_points(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "sum"
 Reduction method for datashader when coloring by continuous values. Defaults to 'sum'.
 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"sum"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_points_render_params(
 self._sdata,
 element=element,
Expand All@@ -481,7 +470,7 @@ def render_points(
 size=size,
 table_name=table_name,
 table_layer=table_layer,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -511,7 +500,7 @@ def render_points(
 cmap_params=cmap_params,
 palette=param_values["palette"],
 alpha=param_values["alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 size=param_values["size"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
Expand DownExpand Up@@ -730,7 +719,7 @@ def render_labels(
 table_name: str | None = None,
 table_layer: str | None = None,
 gene_symbols: str | None = None,
**kwargs: Any,
transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render labels elements in SpatialData.
Expand DownExpand Up@@ -806,14 +795,14 @@ def render_labels(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_label_render_params(
 self._sdata,
 element=element,
Expand DownExpand Up@@ -859,7 +848,7 @@ def render_labels(
 scale=param_values["scale"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 zorder=n_steps,
 colorbar=param_values["colorbar"],
 colorbar_params=param_values["colorbar_params"],
Expand Down

15 changes: 15 additions & 0 deletions
tests/pl/test_render_images.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -505,6 +505,21 @@ def test_cmap_matches_selected_channels_not_full_image(sdata_blobs: SpatialData)
 plt.close(fig)


# Regression for #612: vmin/vmax kwargs are no longer accepted on any render
# function. The check covers all four to prevent the asymmetry from re-emerging.
@pytest.mark.parametrize("kwarg", ["vmin", "vmax"])
@pytest.mark.parametrize("func", ["render_images", "render_shapes", "render_points", "render_labels"])
def test_vmin_vmax_kwargs_rejected_uniformly(sdata_blobs: SpatialData, func: str, kwarg: str) -> None:
 elements = {
 "render_images": "blobs_image",
 "render_labels": "blobs_labels",
 "render_points": "blobs_points",
 "render_shapes": "blobs_circles",
 }
 with pytest.raises(TypeError, match=kwarg):
 getattr(sdata_blobs.pl, func)(elements[func], **{kwarg: 0})


# ---------------------------------------------------------------------------
# channels_as_legend visual tests (#459)
# ---------------------------------------------------------------------------
Expand Down

14 changes: 7 additions & 7 deletions
tests/pl/test_render_labels.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -156,13 +156,13 @@ def _make_tablemodel_with_categorical_labels(sdata_blobs, label):

 _, axs = plt.subplots(nrows=1, ncols=3, layout="tight")

 sdata_blobs.pl.render_labels(label, color="channel_1_sum", table="other_table", scale="scale0").pl.show(
ax=axs[0], title="ch_1_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="channel_2_sum", table="other_table", scale="scale0").pl.show(
ax=axs[1], title="ch_2_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="which_max", table="other_table", scale="scale0").pl.show(
 sdata_blobs.pl.render_labels(
label, color="channel_1_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[0], title="ch_1_sum", colorbar=False)
 sdata_blobs.pl.render_labels(
label, color="channel_2_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[1], title="ch_2_sum", colorbar=False)
 sdata_blobs.pl.render_labels(label, color="which_max", table_name="other_table", scale="scale0").pl.show(
 ax=axs[2], legend_fontsize=6
 )

Expand Down

4 changes: 2 additions & 2 deletions
tests/pl/test_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -68,14 +68,14 @@ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData
 new_cmap = set_zero_in_cmap_to_transparent(cmap="viridis")

 # baseline img
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table_name="table").pl.show(
 ax=axs[0], colorbar=False
 )

 sdata_blobs.tables["table"].obs.iloc[8:12, 2] = 0

 # image with 0s as transparent, so some labels are "missing"
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table_name="table").pl.show(
 ax=axs[1], colorbar=False
 )

Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
Drop vmin/vmax kwargs across all render functions#652

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

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to your account

 Merged

timtreis
merged 2 commits into

from

May 8, 2026
 Merged


Drop vmin/vmax kwargs across all render functions
#652
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b8c5cde

Drop vmin/vmax kwargs and close render signatures (#612)


timtreis May 8, 2026
a4b67ab

Fix table= → table_name= typo in render_labels test calls


timtreis May 8, 2026

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53 changes: 21 additions & 32 deletions
src/spatialdata_plot/pl/basic.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@
from xarray import DataArray, DataTree

from spatialdata_plot._accessor import register_spatial_data_accessor
from spatialdata_plot._logging import _log_context, logger
from spatialdata_plot._logging import _log_context
from spatialdata_plot.pl.render import (
 _draw_channel_legend,
 _render_images,
Expand DownExpand Up@@ -190,7 +190,8 @@ def render_shapes(
 shape: Literal["circle", "hex", "visium_hex", "square"] | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render shapes elements in SpatialData.
Expand DownExpand Up@@ -279,15 +280,10 @@ def render_shapes(
 specified, the shapes are converted to a circle/hexagon/square before rendering. If "visium_hex" is
 specified, the shapes are assumed to be Visium spots and the size of the hexagons is adjusted to be adjacent
 to each other.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "max"
 Reduction method for datashader when coloring by continuous values. Defaults to 'max'.

 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"max"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Notes
 -----
Expand All@@ -300,8 +296,6 @@ def render_shapes(
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_shape_render_params(
 self._sdata,
 element=element,
Expand All@@ -320,7 +314,7 @@ def render_shapes(
 table_layer=table_layer,
 shape=shape,
 method=method,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -351,7 +345,7 @@ def render_shapes(
 palette=param_values["palette"],
 outline_alpha=final_outline_alpha,
 fill_alpha=param_values["fill_alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 shape=param_values["shape"],
Expand DownExpand Up@@ -384,7 +378,8 @@ def render_points(
 gene_symbols: str | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render points elements in SpatialData.
Expand DownExpand Up@@ -452,22 +447,16 @@ def render_points(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "sum"
 Reduction method for datashader when coloring by continuous values. Defaults to 'sum'.
 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"sum"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_points_render_params(
 self._sdata,
 element=element,
Expand All@@ -481,7 +470,7 @@ def render_points(
 size=size,
 table_name=table_name,
 table_layer=table_layer,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -511,7 +500,7 @@ def render_points(
 cmap_params=cmap_params,
 palette=param_values["palette"],
 alpha=param_values["alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 size=param_values["size"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
Expand DownExpand Up@@ -730,7 +719,7 @@ def render_labels(
 table_name: str | None = None,
 table_layer: str | None = None,
 gene_symbols: str | None = None,
**kwargs: Any,
transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render labels elements in SpatialData.
Expand DownExpand Up@@ -806,14 +795,14 @@ def render_labels(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_label_render_params(
 self._sdata,
 element=element,
Expand DownExpand Up@@ -859,7 +848,7 @@ def render_labels(
 scale=param_values["scale"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 zorder=n_steps,
 colorbar=param_values["colorbar"],
 colorbar_params=param_values["colorbar_params"],
Expand Down

15 changes: 15 additions & 0 deletions
tests/pl/test_render_images.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -505,6 +505,21 @@ def test_cmap_matches_selected_channels_not_full_image(sdata_blobs: SpatialData)
 plt.close(fig)


# Regression for #612: vmin/vmax kwargs are no longer accepted on any render
# function. The check covers all four to prevent the asymmetry from re-emerging.
@pytest.mark.parametrize("kwarg", ["vmin", "vmax"])
@pytest.mark.parametrize("func", ["render_images", "render_shapes", "render_points", "render_labels"])
def test_vmin_vmax_kwargs_rejected_uniformly(sdata_blobs: SpatialData, func: str, kwarg: str) -> None:
 elements = {
 "render_images": "blobs_image",
 "render_labels": "blobs_labels",
 "render_points": "blobs_points",
 "render_shapes": "blobs_circles",
 }
 with pytest.raises(TypeError, match=kwarg):
 getattr(sdata_blobs.pl, func)(elements[func], **{kwarg: 0})


# ---------------------------------------------------------------------------
# channels_as_legend visual tests (#459)
# ---------------------------------------------------------------------------
Expand Down

14 changes: 7 additions & 7 deletions
tests/pl/test_render_labels.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -156,13 +156,13 @@ def _make_tablemodel_with_categorical_labels(sdata_blobs, label):

 _, axs = plt.subplots(nrows=1, ncols=3, layout="tight")

 sdata_blobs.pl.render_labels(label, color="channel_1_sum", table="other_table", scale="scale0").pl.show(
ax=axs[0], title="ch_1_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="channel_2_sum", table="other_table", scale="scale0").pl.show(
ax=axs[1], title="ch_2_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="which_max", table="other_table", scale="scale0").pl.show(
 sdata_blobs.pl.render_labels(
label, color="channel_1_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[0], title="ch_1_sum", colorbar=False)
 sdata_blobs.pl.render_labels(
label, color="channel_2_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[1], title="ch_2_sum", colorbar=False)
 sdata_blobs.pl.render_labels(label, color="which_max", table_name="other_table", scale="scale0").pl.show(
 ax=axs[2], legend_fontsize=6
 )

Expand Down

4 changes: 2 additions & 2 deletions
tests/pl/test_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -68,14 +68,14 @@ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData
 new_cmap = set_zero_in_cmap_to_transparent(cmap="viridis")

 # baseline img
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table_name="table").pl.show(
 ax=axs[0], colorbar=False
 )

 sdata_blobs.tables["table"].obs.iloc[8:12, 2] = 0

 # image with 0s as transparent, so some labels are "missing"
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table_name="table").pl.show(
 ax=axs[1], colorbar=False
 )

Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Drop vmin/vmax kwargs across all render functions#652

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timtreis
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May 8, 2026
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Drop vmin/vmax kwargs across all render functions
#652
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b8c5cde

Drop vmin/vmax kwargs and close render signatures (#612)


timtreis May 8, 2026
a4b67ab

Fix table= → table_name= typo in render_labels test calls


timtreis May 8, 2026

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53 changes: 21 additions & 32 deletions
src/spatialdata_plot/pl/basic.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@
from xarray import DataArray, DataTree

from spatialdata_plot._accessor import register_spatial_data_accessor
from spatialdata_plot._logging import _log_context, logger
from spatialdata_plot._logging import _log_context
from spatialdata_plot.pl.render import (
 _draw_channel_legend,
 _render_images,
Expand DownExpand Up@@ -190,7 +190,8 @@ def render_shapes(
 shape: Literal["circle", "hex", "visium_hex", "square"] | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render shapes elements in SpatialData.
Expand DownExpand Up@@ -279,15 +280,10 @@ def render_shapes(
 specified, the shapes are converted to a circle/hexagon/square before rendering. If "visium_hex" is
 specified, the shapes are assumed to be Visium spots and the size of the hexagons is adjusted to be adjacent
 to each other.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "max"
 Reduction method for datashader when coloring by continuous values. Defaults to 'max'.

 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"max"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Notes
 -----
Expand All@@ -300,8 +296,6 @@ def render_shapes(
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_shape_render_params(
 self._sdata,
 element=element,
Expand All@@ -320,7 +314,7 @@ def render_shapes(
 table_layer=table_layer,
 shape=shape,
 method=method,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -351,7 +345,7 @@ def render_shapes(
 palette=param_values["palette"],
 outline_alpha=final_outline_alpha,
 fill_alpha=param_values["fill_alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 shape=param_values["shape"],
Expand DownExpand Up@@ -384,7 +378,8 @@ def render_points(
 gene_symbols: str | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render points elements in SpatialData.
Expand DownExpand Up@@ -452,22 +447,16 @@ def render_points(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "sum"
 Reduction method for datashader when coloring by continuous values. Defaults to 'sum'.
 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"sum"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_points_render_params(
 self._sdata,
 element=element,
Expand All@@ -481,7 +470,7 @@ def render_points(
 size=size,
 table_name=table_name,
 table_layer=table_layer,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -511,7 +500,7 @@ def render_points(
 cmap_params=cmap_params,
 palette=param_values["palette"],
 alpha=param_values["alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 size=param_values["size"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
Expand DownExpand Up@@ -730,7 +719,7 @@ def render_labels(
 table_name: str | None = None,
 table_layer: str | None = None,
 gene_symbols: str | None = None,
**kwargs: Any,
transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render labels elements in SpatialData.
Expand DownExpand Up@@ -806,14 +795,14 @@ def render_labels(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_label_render_params(
 self._sdata,
 element=element,
Expand DownExpand Up@@ -859,7 +848,7 @@ def render_labels(
 scale=param_values["scale"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 zorder=n_steps,
 colorbar=param_values["colorbar"],
 colorbar_params=param_values["colorbar_params"],
Expand Down

15 changes: 15 additions & 0 deletions
tests/pl/test_render_images.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -505,6 +505,21 @@ def test_cmap_matches_selected_channels_not_full_image(sdata_blobs: SpatialData)
 plt.close(fig)


# Regression for #612: vmin/vmax kwargs are no longer accepted on any render
# function. The check covers all four to prevent the asymmetry from re-emerging.
@pytest.mark.parametrize("kwarg", ["vmin", "vmax"])
@pytest.mark.parametrize("func", ["render_images", "render_shapes", "render_points", "render_labels"])
def test_vmin_vmax_kwargs_rejected_uniformly(sdata_blobs: SpatialData, func: str, kwarg: str) -> None:
 elements = {
 "render_images": "blobs_image",
 "render_labels": "blobs_labels",
 "render_points": "blobs_points",
 "render_shapes": "blobs_circles",
 }
 with pytest.raises(TypeError, match=kwarg):
 getattr(sdata_blobs.pl, func)(elements[func], **{kwarg: 0})


# ---------------------------------------------------------------------------
# channels_as_legend visual tests (#459)
# ---------------------------------------------------------------------------
Expand Down

14 changes: 7 additions & 7 deletions
tests/pl/test_render_labels.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -156,13 +156,13 @@ def _make_tablemodel_with_categorical_labels(sdata_blobs, label):

 _, axs = plt.subplots(nrows=1, ncols=3, layout="tight")

 sdata_blobs.pl.render_labels(label, color="channel_1_sum", table="other_table", scale="scale0").pl.show(
ax=axs[0], title="ch_1_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="channel_2_sum", table="other_table", scale="scale0").pl.show(
ax=axs[1], title="ch_2_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="which_max", table="other_table", scale="scale0").pl.show(
 sdata_blobs.pl.render_labels(
label, color="channel_1_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[0], title="ch_1_sum", colorbar=False)
 sdata_blobs.pl.render_labels(
label, color="channel_2_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[1], title="ch_2_sum", colorbar=False)
 sdata_blobs.pl.render_labels(label, color="which_max", table_name="other_table", scale="scale0").pl.show(
 ax=axs[2], legend_fontsize=6
 )

Expand Down

4 changes: 2 additions & 2 deletions
tests/pl/test_utils.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -68,14 +68,14 @@ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData
 new_cmap = set_zero_in_cmap_to_transparent(cmap="viridis")

 # baseline img
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table_name="table").pl.show(
 ax=axs[0], colorbar=False
 )

 sdata_blobs.tables["table"].obs.iloc[8:12, 2] = 0

 # image with 0s as transparent, so some labels are "missing"
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table_name="table").pl.show(
 ax=axs[1], colorbar=False
 )

Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

Skip to content
Drop vmin/vmax kwargs across all render functions#652

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 Merged

timtreis
merged 2 commits into

from

May 8, 2026
 Merged


Drop vmin/vmax kwargs across all render functions
#652
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b8c5cde

Drop vmin/vmax kwargs and close render signatures (#612)


timtreis May 8, 2026
a4b67ab

Fix table= → table_name= typo in render_labels test calls


timtreis May 8, 2026

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53 changes: 21 additions & 32 deletions
src/spatialdata_plot/pl/basic.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -28,7 +28,7 @@
from xarray import DataArray, DataTree

from spatialdata_plot._accessor import register_spatial_data_accessor
from spatialdata_plot._logging import _log_context, logger
from spatialdata_plot._logging import _log_context
from spatialdata_plot.pl.render import (
 _draw_channel_legend,
 _render_images,
Expand DownExpand Up@@ -190,7 +190,8 @@ def render_shapes(
 shape: Literal["circle", "hex", "visium_hex", "square"] | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render shapes elements in SpatialData.
Expand DownExpand Up@@ -279,15 +280,10 @@ def render_shapes(
 specified, the shapes are converted to a circle/hexagon/square before rendering. If "visium_hex" is
 specified, the shapes are assumed to be Visium spots and the size of the hexagons is adjusted to be adjacent
 to each other.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "max"
 Reduction method for datashader when coloring by continuous values. Defaults to 'max'.

 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"max"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Notes
 -----
Expand All@@ -300,8 +296,6 @@ def render_shapes(
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_shape_render_params(
 self._sdata,
 element=element,
Expand All@@ -320,7 +314,7 @@ def render_shapes(
 table_layer=table_layer,
 shape=shape,
 method=method,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -351,7 +345,7 @@ def render_shapes(
 palette=param_values["palette"],
 outline_alpha=final_outline_alpha,
 fill_alpha=param_values["fill_alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 shape=param_values["shape"],
Expand DownExpand Up@@ -384,7 +378,8 @@ def render_points(
 gene_symbols: str | None = None,
 colorbar: bool | str | None = "auto",
 colorbar_params: dict[str, object] | None = None,
 **kwargs: Any,
 datashader_reduction: Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None = None,
 transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render points elements in SpatialData.
Expand DownExpand Up@@ -452,22 +447,16 @@ def render_points(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.

 **kwargs : Any
 Additional arguments for customization. This can include:

 datashader_reduction : Literal[
 "sum", "mean", "any", "count", "std", "var", "max", "min"
 ], default: "sum"
 Reduction method for datashader when coloring by continuous values. Defaults to 'sum'.
 datashader_reduction : Literal["sum", "mean", "any", "count", "std", "var", "max", "min"] | None, optional
 Reduction method for datashader when coloring by continuous values. When ``None``, defaults to ``"sum"``.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_points_render_params(
 self._sdata,
 element=element,
Expand All@@ -481,7 +470,7 @@ def render_points(
 size=size,
 table_name=table_name,
 table_layer=table_layer,
 ds_reduction=kwargs.get("datashader_reduction"),
 ds_reduction=datashader_reduction,
 colorbar=colorbar,
 colorbar_params=colorbar_params,
 gene_symbols=gene_symbols,
Expand DownExpand Up@@ -511,7 +500,7 @@ def render_points(
 cmap_params=cmap_params,
 palette=param_values["palette"],
 alpha=param_values["alpha"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 size=param_values["size"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
Expand DownExpand Up@@ -730,7 +719,7 @@ def render_labels(
 table_name: str | None = None,
 table_layer: str | None = None,
 gene_symbols: str | None = None,
**kwargs: Any,
transfunc: Callable[[float], float] | None = None,
 ) -> sd.SpatialData:
 """
 Render labels elements in SpatialData.
Expand DownExpand Up@@ -806,14 +795,14 @@ def render_labels(
 Column name in :attr:`sdata.table.var` to use for looking up ``color``. Use this when
 ``var_names`` are e.g. ENSEMBL IDs but you want to refer to genes by their symbols stored
 in another column of ``var``. Mimics scanpy's ``gene_symbols`` parameter.
 transfunc : Callable[[float], float] | None, optional
 Optional transformation applied to the continuous color vector before normalization and colormap mapping.

 Returns
 -------
 sd.SpatialData
 A copy of the SpatialData object with the rendering parameters stored in its plotting tree.
 """
 if "vmin" in kwargs or "vmax" in kwargs:
 logger.warning("`vmin` and `vmax` are deprecated. Pass matplotlib `Normalize` object to norm instead.")
 params_dict = _validate_label_render_params(
 self._sdata,
 element=element,
Expand DownExpand Up@@ -859,7 +848,7 @@ def render_labels(
 scale=param_values["scale"],
 table_name=param_values["table_name"],
 table_layer=param_values["table_layer"],
 transfunc=kwargs.get("transfunc"),
 transfunc=transfunc,
 zorder=n_steps,
 colorbar=param_values["colorbar"],
 colorbar_params=param_values["colorbar_params"],
Expand Down

15 changes: 15 additions & 0 deletions
tests/pl/test_render_images.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -505,6 +505,21 @@ def test_cmap_matches_selected_channels_not_full_image(sdata_blobs: SpatialData)
 plt.close(fig)


# Regression for #612: vmin/vmax kwargs are no longer accepted on any render
# function. The check covers all four to prevent the asymmetry from re-emerging.
@pytest.mark.parametrize("kwarg", ["vmin", "vmax"])
@pytest.mark.parametrize("func", ["render_images", "render_shapes", "render_points", "render_labels"])
def test_vmin_vmax_kwargs_rejected_uniformly(sdata_blobs: SpatialData, func: str, kwarg: str) -> None:
 elements = {
 "render_images": "blobs_image",
 "render_labels": "blobs_labels",
 "render_points": "blobs_points",
 "render_shapes": "blobs_circles",
 }
 with pytest.raises(TypeError, match=kwarg):
 getattr(sdata_blobs.pl, func)(elements[func], **{kwarg: 0})


# ---------------------------------------------------------------------------
# channels_as_legend visual tests (#459)
# ---------------------------------------------------------------------------
Expand Down

14 changes: 7 additions & 7 deletions
tests/pl/test_render_labels.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -156,13 +156,13 @@ def _make_tablemodel_with_categorical_labels(sdata_blobs, label):

 _, axs = plt.subplots(nrows=1, ncols=3, layout="tight")

 sdata_blobs.pl.render_labels(label, color="channel_1_sum", table="other_table", scale="scale0").pl.show(
ax=axs[0], title="ch_1_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="channel_2_sum", table="other_table", scale="scale0").pl.show(
ax=axs[1], title="ch_2_sum", colorbar=False
 )
 sdata_blobs.pl.render_labels(label, color="which_max", table="other_table", scale="scale0").pl.show(
 sdata_blobs.pl.render_labels(
label, color="channel_1_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[0], title="ch_1_sum", colorbar=False)
 sdata_blobs.pl.render_labels(
label, color="channel_2_sum", table_name="other_table", scale="scale0"
 ).pl.show(ax=axs[1], title="ch_2_sum", colorbar=False)
 sdata_blobs.pl.render_labels(label, color="which_max", table_name="other_table", scale="scale0").pl.show(
 ax=axs[2], legend_fontsize=6
 )

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4 changes: 2 additions & 2 deletions
tests/pl/test_utils.py

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Original file line numberDiff line numberDiff line change
Expand Up@@ -68,14 +68,14 @@ def test_plot_can_set_zero_in_cmap_to_transparent(self, sdata_blobs: SpatialData
 new_cmap = set_zero_in_cmap_to_transparent(cmap="viridis")

 # baseline img
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap="viridis", table_name="table").pl.show(
 ax=axs[0], colorbar=False
 )

 sdata_blobs.tables["table"].obs.iloc[8:12, 2] = 0

 # image with 0s as transparent, so some labels are "missing"
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table="table").pl.show(
 sdata_blobs.pl.render_labels("blobs_labels", color="my_var", cmap=new_cmap, table_name="table").pl.show(
 ax=axs[1], colorbar=False
 )

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