allow for plotting using specific table (#217) (#220)

* allow for plotting using specific table (#217)

* allow for plotting using specific table

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Change into get with default return

* fix issues with pp

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* ensure instance key coercable to int dtype

* add table keys import

* allow feature branches tests

* remove table key getters

* extract into function

* add docstring

* don't create unnecessary anndata

* allow for label color without specified table

* refactor show param validations

* refactor show param validations

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* big refactor

* remove unused render_params.layer

* remove redundant code

* refactor to mapping

* allow later creation of mapping

* reimplement color label

* fix unused arguments

* change points shapes logic

* unfixed full implementation

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* fix tests

* fix tests

* remove duplicate checks

* implement nested list groups palette

* fix tests

* fix or mistake

* add dummy test

* Change to warning

* partial fix mypy

* add function type hints

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* silence table deprecation warning

* fix tests

* silence deprecations and other warnings

* Fix incorrect conditional

* refactor wanted_elements

* remove unwanted extend

* further refactor

* using getattr

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* change palette

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* Remove color if no table

* [pre-commit.ci] auto fixes from pre-commit.com hooks

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* fixed! (#222)

* fixed!

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* Partial fixes mypy (#224)

* fix mypy

* shut more mypy up

* some mypy

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Co-authored-by: LucaMarconato <[email protected]>

Author: 3 people

src/spatialdata_plot/pl/basic.py

@@ -75,12 +75,12 @@ class ShapesRenderParams:
     col_for_color: str | None = None
     groups: str | Sequence[str] | None = None
     contour_px: int | None = None
-    layer: str | None = None
     palette: ListedColormap | str | None = None
     outline_alpha: float = 1.0
     fill_alpha: float = 0.3
     scale: float = 1.0
     transfunc: Callable[[float], float] | None = None
+    element_table_mapping: dict[str, set[str] | str] | str | list[str] | None = None
 
 
 @dataclass
@@ -96,6 +96,7 @@ class PointsRenderParams:
     alpha: float = 1.0
     size: float = 1.0
     transfunc: Callable[[float], float] | None = None
+    element_table_mapping: dict[str, set[str] | str] | str | list[str] | None = None
 
 
 @dataclass
@@ -117,13 +118,13 @@ class LabelsRenderParams:
 
     cmap_params: CmapParams
     elements: str | Sequence[str] | None = None
-    color: str | None = None
+    color: list[str | None] | str | None = None
     groups: str | Sequence[str] | None = None
     contour_px: int | None = None
     outline: bool = False
-    layer: str | None = None
     palette: ListedColormap | str | None = None
     outline_alpha: float = 1.0
     fill_alpha: float = 0.4
     transfunc: Callable[[float], float] | None = None
     scale: str | list[str] | None = None
+    element_table_mapping: dict[str, set[str] | str] | str | list[str] | None = None