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add docstrings
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‎docs/conf.py

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@@ -90,6 +90,8 @@
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"python": ("https://docs.python.org/3", None),
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"anndata": ("https://anndata.readthedocs.io/en/stable/", None),
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"numpy": ("https://numpy.org/doc/stable/", None),
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"matplotlib": ("https://matplotlib.org/stable/", None),
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"spatialdata": ("https://scverse-spatialdata.readthedocs.io/en/latest/", None),
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}
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# List of patterns, relative to source directory, that match files and

‎src/spatialdata_plot/pl/basic.py

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@@ -154,24 +154,46 @@ def render_shapes(
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**kwargs: Any,
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) -> sd.SpatialData:
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"""
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Render the shapes contained in the given sd.SpatialData object
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Render shapes elements in SpatialData.
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Parameters
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----------
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self :
162-
The sd.SpatialData object.
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palette :
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A list of colors to use for rendering the images. If `None`, the
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default colors will be used.
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instance_key :
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The name of the column in the table that identifies individual shapes
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color_key :
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The name of the column in the table to use for coloring shapes.
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element
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The name of the shapes element to render. If `None`, the first
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shapes element in the `SpatialData` object will be used.
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color
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Key for annotations in :attr:`anndata.AnnData.obs` or variables/genes.
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groups
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For discrete annotation in ``color``, select which values
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to plot (other values are set to NAs).
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size
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Value to scale circles, if present.
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outline
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If `True`, a thin border around points/shapes is plotted.
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outline_width
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Width of the border.
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outline_color
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Color of the border.
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alt_var
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Which column to use in :attr:`anndata.AnnData.var` to select alternative ``var_name``.
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layer
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Key in :attr:`anndata.AnnData.layers` or `None` for :attr:`anndata.AnnData.X`.
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palette
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Palette for discrete annotations, see :class:`matplotlib.colors.Colormap`.
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cmap
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Colormap for continuous annotations, see :class:`matplotlib.colors.Colormap`.
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norm
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Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
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na_color
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Color to be used for NAs values, if present.
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alpha
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Alpha value for the shapes.
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kwargs
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Additional arguments to be passed to cmap and norm.
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Returns
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-------
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sd.SpatialData
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The input sd.SpatialData with a command added to the plotting tree
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None
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"""
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sdata = self._copy()
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sdata = _verify_plotting_tree(sdata)
@@ -210,25 +232,37 @@ def render_points(
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alpha: float = 1.0,
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**kwargs: Any,
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) -> sd.SpatialData:
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"""Render the points contained in the given sd.SpatialData object
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"""
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Render points elements in SpatialData.
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Parameters
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----------
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self :
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The sd.SpatialData object.
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palette :
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A list of colors to use for rendering the images. If `None`, the
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default colors will be used.
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instance_key :
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The name of the column in the table that identifies individual shapes
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color : str or None, optional (default: None)
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The name of the column in the table to use for coloring shapes.
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element
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The name of the points element to render. If `None`, the first
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shapes element in the `SpatialData` object will be used.
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color
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Key for annotations in :attr:`anndata.AnnData.obs` or variables/genes.
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groups
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For discrete annotation in ``color``, select which values
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to plot (other values are set to NAs).
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size
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Value to scale points.
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palette
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Palette for discrete annotations, see :class:`matplotlib.colors.Colormap`.
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cmap
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Colormap for continuous annotations, see :class:`matplotlib.colors.Colormap`.
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norm
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Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
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na_color
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Color to be used for NAs values, if present.
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alpha
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Alpha value for the shapes.
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kwargs
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Additional arguments to be passed to cmap and norm.
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Returns
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-------
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sd.SpatialData
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The input sd.SpatialData with a command added to the plotting tree
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None
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"""
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sdata = self._copy()
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sdata = _verify_plotting_tree(sdata)
@@ -261,24 +295,30 @@ def render_images(
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alpha: float = 1.0,
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**kwargs: Any,
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) -> sd.SpatialData:
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"""Render the images contained in the given sd.SpatialData object
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"""
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Render image elements in SpatialData.
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Parameters
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----------
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self :
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The sd.SpatialData object.
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palette :
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A list of colors to use for rendering the images. If `None`, the
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default colors will be used.
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trans_fun :
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A function to apply to the images before rendering. If `None`, no
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function will be applied.
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element
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The name of the image element to render. If `None`, the first
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shapes element in the `SpatialData` object will be used.
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channel
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To select which channel to plot (all by default).
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cmap
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Colormap for continuous annotations, see :class:`matplotlib.colors.Colormap`.
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norm
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Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
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na_color
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Color to be used for NAs values, if present.
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alpha
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Alpha value for the shapes.
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kwargs
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Additional arguments to be passed to cmap and norm.
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Returns
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-------
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sd.SpatialData
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The input sd.SpatialData with a command added to the plotting tree
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None
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"""
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sdata = self._copy()
284324
sdata = _verify_plotting_tree(sdata)
@@ -315,37 +355,44 @@ def render_labels(
315355
alpha: float = 1.0,
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**kwargs: Any,
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) -> sd.SpatialData:
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"""Render the labels contained in the given sd.SpatialData object
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"""
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Render labels elements in SpatialData.
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Parameters
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----------
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self :
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sd.SpatialData
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instance_key :
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The name of the column in the table that identifies individual labels
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element
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The name of the labels element to render. If `None`, the first
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labels element in the `SpatialData` object will be used.
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color
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Key for annotations in :attr:`anndata.AnnData.obs` or variables/genes.
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groups
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For discrete annotation in ``color``, select which values
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to plot (other values are set to NAs).
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contour_px
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Draw contour of specified width for each segment. If `None`, fills
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entire segment, see :func:`skimage.morphology.erosion`.
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outline
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Whether to plot boundaries around segmentation masks.
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alt_var
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Which column to use in :attr:`anndata.AnnData.var` to select alternative ``var_name``.
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layer
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Key in :attr:`anndata.AnnData.layers` or `None` for :attr:`anndata.AnnData.X`.
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palette
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Palette for discrete annotations, see :class:`matplotlib.colors.Colormap`.
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cmap
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Colormap for continuous annotations, see :class:`matplotlib.colors.Colormap`.
384+
norm
385+
Colormap normalization for continuous annotations, see :class:`matplotlib.colors.Normalize`.
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na_color
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Color to be used for NAs values, if present.
388+
alpha
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Alpha value for the labels.
390+
kwargs
391+
Additional arguments to be passed to cmap and norm.
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327393
Returns
328394
-------
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sd.SpatialData
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The input sd.SpatialData with a command added to the plotting tree
331-
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Raises
333-
------
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TypeError
335-
If any of the parameters have an invalid type.
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ValueError
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If any of the parameters have an invalid value.
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If the provided instance_key or color_key is not a valid table column.
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If the provided mode is not one of 'thick', 'inner', 'outer', or
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'subpixel'.
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Notes
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-----
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This function plots cell labels for a spatialdata object. The cell labels are
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based on a column in the table, and can optionally be colored based on another
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column in the table. The resulting plot can be customized by specifying the
347-
alpha, color, and rendering mode of the labels, as well as whether to add a
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legend to the plot.
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None
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"""
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if (
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color is not None

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