allow for plotting using specific table by melonora · Pull Request #217 · scverse/spatialdata-plot

.github/workflows/test_and_deploy.yaml

-Original file line number
+Diff line change
@@ Expand Up / @@ -6,7 +6,7 @@ on: @@
  tags:
  - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10
  pull_request:
- branches: [main]
+ branches: "*"
 jobs:
  test:
@@ Expand Down @@

src/spatialdata_plot/pl/basic.py

Large diffs are not rendered by default.

src/spatialdata_plot/pl/render.py

Large diffs are not rendered by default.

src/spatialdata_plot/pl/render_params.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -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
@@ Expand All / @@ -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
@@ Expand All / @@ -121,9 +122,9 @@ class LabelsRenderParams: @@
  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

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Sign in to your account Merged melonora merged 39 commits into scverse:multi_table from melonora:multi_tableFeb 29, 2024 Conversation 0 Commits 39 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged allow for plotting using specific table #217 Show file tree Hide file tree Changes from all commits Commits Show all changes 39 commits Select commit Hold shift + click to select a range 4072683 allow for plotting using specific table melonora Feb 18, 2024ba4faa8 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 18, 202472bf27d Change into get with default return melonora Feb 19, 20247d9e83f fix issues with pp melonora Feb 19, 2024cd76a00 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 19, 20247676c72 ensure instance key coercable to int dtype melonora Feb 19, 2024c0ebde3 Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 19, 202445c13e0 add table keys import melonora Feb 19, 202472eef3d allow feature branches tests melonora Feb 19, 20243532104 Merge branch 'main' into multi_table melonora Feb 19, 202439b8003 remove table key getters melonora Feb 20, 20243aafa1f extract into function melonora Feb 20, 202453fa1a7 add docstring melonora Feb 20, 20243843f1a don't create unnecessary anndata melonora Feb 20, 202458fabd3 allow for label color without specified table melonora Feb 20, 20248f9dc4d refactor show param validations melonora Feb 20, 2024d664956 refactor show param validations melonora Feb 21, 202419ecc0b [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 21, 2024de53fe2 big refactor melonora Feb 21, 2024bb3e5d8 remove unused render_params.layer melonora Feb 21, 2024f74f730 remove redundant code melonora Feb 21, 202494d37d8 refactor to mapping melonora Feb 22, 2024882c2a9 allow later creation of mapping melonora Feb 22, 2024a21529d reimplement color label melonora Feb 22, 2024cdaddf0 fix unused arguments melonora Feb 23, 2024406fb1b change points shapes logic melonora Feb 23, 20247e76133 unfixed full implementation melonora Feb 24, 2024cc9b404 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 24, 202421c05f1 fix tests melonora Feb 24, 2024a13361a Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 24, 2024258593c fix tests melonora Feb 25, 2024fa279ae remove duplicate checks melonora Feb 25, 20243082e40 implement nested list groups palette melonora Feb 26, 202447483e6 fix tests melonora Feb 26, 202433e1857 fix or mistake melonora Feb 26, 202459d6590 add dummy test melonora Feb 26, 202440e7130 Change to warning melonora Feb 28, 2024caf23df partial fix mypy melonora Feb 28, 2024ecc7797 add function type hints melonora Feb 28, 2024 File filter Filter by extension Filter by extension .py (10) .yaml (1) All 2 file types selected Only manifest files Viewed files Clear filters Conversations Failed to load comments. 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Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace .github/workflows/test_and_deploy.yaml test_and_deploy.yaml src/spatialdata_plot/pl/basic.py basic.py src/spatialdata_plot/pl/render.py render.py src/spatialdata_plot/pl/render_params.py render_params.py src/spatialdata_plot/pl/utils.py utils.py src/spatialdata_plot/pp/basic.py basic.py src/spatialdata_plot/pp/utils.py utils.py tests/conftest.py conftest.py tests/pl/test_render_labels.py test_render_labels.py tests/pl/test_render_points.py test_render_points.py tests/pl/test_render_shapes.py test_render_shapes.py There are no files selected for viewing 2 changes: 1 addition & 1 deletion 2 .github/workflows/test_and_deploy.yaml Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -6,7 +6,7 @@ on: tags: - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10 pull_request: branches: [main] branches: "*" jobs: test: Expand Down 687 changes: 215 additions & 472 deletions 687 src/spatialdata_plot/pl/basic.py Show comments View file Open in desktop Large diffs are not rendered by default. Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 164 changes: 71 additions & 93 deletions 164 src/spatialdata_plot/pl/render.py Show comments View file Open in desktop Large diffs are not rendered by default. Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 5 changes: 3 additions & 2 deletions 5 src/spatialdata_plot/pl/render_params.py Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -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 Expand All @@ -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 Expand All @@ -121,9 +122,9 @@ class LabelsRenderParams: 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 Loading Oops, something went wrong. 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Sign in to your account Merged melonora merged 39 commits into scverse:multi_table from melonora:multi_tableFeb 29, 2024 Conversation 0 Commits 39 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged allow for plotting using specific table #217 Show file tree Hide file tree Changes from all commits Commits Show all changes 39 commits Select commit Hold shift + click to select a range 4072683 allow for plotting using specific table melonora Feb 18, 2024ba4faa8 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 18, 202472bf27d Change into get with default return melonora Feb 19, 20247d9e83f fix issues with pp melonora Feb 19, 2024cd76a00 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 19, 20247676c72 ensure instance key coercable to int dtype melonora Feb 19, 2024c0ebde3 Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 19, 202445c13e0 add table keys import melonora Feb 19, 202472eef3d allow feature branches tests melonora Feb 19, 20243532104 Merge branch 'main' into multi_table melonora Feb 19, 202439b8003 remove table key getters melonora Feb 20, 20243aafa1f extract into function melonora Feb 20, 202453fa1a7 add docstring melonora Feb 20, 20243843f1a don't create unnecessary anndata melonora Feb 20, 202458fabd3 allow for label color without specified table melonora Feb 20, 20248f9dc4d refactor show param validations melonora Feb 20, 2024d664956 refactor show param validations melonora Feb 21, 202419ecc0b [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 21, 2024de53fe2 big refactor melonora Feb 21, 2024bb3e5d8 remove unused render_params.layer melonora Feb 21, 2024f74f730 remove redundant code melonora Feb 21, 202494d37d8 refactor to mapping melonora Feb 22, 2024882c2a9 allow later creation of mapping melonora Feb 22, 2024a21529d reimplement color label melonora Feb 22, 2024cdaddf0 fix unused arguments melonora Feb 23, 2024406fb1b change points shapes logic melonora Feb 23, 20247e76133 unfixed full implementation melonora Feb 24, 2024cc9b404 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 24, 202421c05f1 fix tests melonora Feb 24, 2024a13361a Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 24, 2024258593c fix tests melonora Feb 25, 2024fa279ae remove duplicate checks melonora Feb 25, 20243082e40 implement nested list groups palette melonora Feb 26, 202447483e6 fix tests melonora Feb 26, 202433e1857 fix or mistake melonora Feb 26, 202459d6590 add dummy test melonora Feb 26, 202440e7130 Change to warning melonora Feb 28, 2024caf23df partial fix mypy melonora Feb 28, 2024ecc7797 add function type hints melonora Feb 28, 2024 File filter Filter by extension Filter by extension .py (10) .yaml (1) All 2 file types selected Only manifest files Viewed files Clear filters Conversations Failed to load comments. 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Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace .github/workflows/test_and_deploy.yaml test_and_deploy.yaml src/spatialdata_plot/pl/basic.py basic.py src/spatialdata_plot/pl/render.py render.py src/spatialdata_plot/pl/render_params.py render_params.py src/spatialdata_plot/pl/utils.py utils.py src/spatialdata_plot/pp/basic.py basic.py src/spatialdata_plot/pp/utils.py utils.py tests/conftest.py conftest.py tests/pl/test_render_labels.py test_render_labels.py tests/pl/test_render_points.py test_render_points.py tests/pl/test_render_shapes.py test_render_shapes.py There are no files selected for viewing 2 changes: 1 addition & 1 deletion 2 .github/workflows/test_and_deploy.yaml Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -6,7 +6,7 @@ on: tags: - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10 pull_request: branches: [main] branches: "*" jobs: test: Expand Down 687 changes: 215 additions & 472 deletions 687 src/spatialdata_plot/pl/basic.py Show comments View file Open in desktop Large diffs are not rendered by default. Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 164 changes: 71 additions & 93 deletions 164 src/spatialdata_plot/pl/render.py Show comments View file Open in desktop Large diffs are not rendered by default. Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 5 changes: 3 additions & 2 deletions 5 src/spatialdata_plot/pl/render_params.py Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -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 Expand All @@ -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 Expand All @@ -121,9 +122,9 @@ class LabelsRenderParams: 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 Loading Oops, something went wrong. 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Sign in to your account Merged melonora merged 39 commits into scverse:multi_table from melonora:multi_tableFeb 29, 2024 Conversation 0 Commits 39 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged allow for plotting using specific table #217 Show file tree Hide file tree Changes from all commits Commits Show all changes 39 commits Select commit Hold shift + click to select a range 4072683 allow for plotting using specific table melonora Feb 18, 2024ba4faa8 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 18, 202472bf27d Change into get with default return melonora Feb 19, 20247d9e83f fix issues with pp melonora Feb 19, 2024cd76a00 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 19, 20247676c72 ensure instance key coercable to int dtype melonora Feb 19, 2024c0ebde3 Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 19, 202445c13e0 add table keys import melonora Feb 19, 202472eef3d allow feature branches tests melonora Feb 19, 20243532104 Merge branch 'main' into multi_table melonora Feb 19, 202439b8003 remove table key getters melonora Feb 20, 20243aafa1f extract into function melonora Feb 20, 202453fa1a7 add docstring melonora Feb 20, 20243843f1a don't create unnecessary anndata melonora Feb 20, 202458fabd3 allow for label color without specified table melonora Feb 20, 20248f9dc4d refactor show param validations melonora Feb 20, 2024d664956 refactor show param validations melonora Feb 21, 202419ecc0b [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 21, 2024de53fe2 big refactor melonora Feb 21, 2024bb3e5d8 remove unused render_params.layer melonora Feb 21, 2024f74f730 remove redundant code melonora Feb 21, 202494d37d8 refactor to mapping melonora Feb 22, 2024882c2a9 allow later creation of mapping melonora Feb 22, 2024a21529d reimplement color label melonora Feb 22, 2024cdaddf0 fix unused arguments melonora Feb 23, 2024406fb1b change points shapes logic melonora Feb 23, 20247e76133 unfixed full implementation melonora Feb 24, 2024cc9b404 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 24, 202421c05f1 fix tests melonora Feb 24, 2024a13361a Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 24, 2024258593c fix tests melonora Feb 25, 2024fa279ae remove duplicate checks melonora Feb 25, 20243082e40 implement nested list groups palette melonora Feb 26, 202447483e6 fix tests melonora Feb 26, 202433e1857 fix or mistake melonora Feb 26, 202459d6590 add dummy test melonora Feb 26, 202440e7130 Change to warning melonora Feb 28, 2024caf23df partial fix mypy melonora Feb 28, 2024ecc7797 add function type hints melonora Feb 28, 2024 File filter Filter by extension Filter by extension .py (10) .yaml (1) All 2 file types selected Only manifest files Viewed files Clear filters Conversations Failed to load comments. 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Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace .github/workflows/test_and_deploy.yaml test_and_deploy.yaml src/spatialdata_plot/pl/basic.py basic.py src/spatialdata_plot/pl/render.py render.py src/spatialdata_plot/pl/render_params.py render_params.py src/spatialdata_plot/pl/utils.py utils.py src/spatialdata_plot/pp/basic.py basic.py src/spatialdata_plot/pp/utils.py utils.py tests/conftest.py conftest.py tests/pl/test_render_labels.py test_render_labels.py tests/pl/test_render_points.py test_render_points.py tests/pl/test_render_shapes.py test_render_shapes.py There are no files selected for viewing 2 changes: 1 addition & 1 deletion 2 .github/workflows/test_and_deploy.yaml Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -6,7 +6,7 @@ on: tags: - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10 pull_request: branches: [main] branches: "*" jobs: test: Expand Down 687 changes: 215 additions & 472 deletions 687 src/spatialdata_plot/pl/basic.py Show comments View file Open in desktop Large diffs are not rendered by default. 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Please reload this page. 5 changes: 3 additions & 2 deletions 5 src/spatialdata_plot/pl/render_params.py Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -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 Expand All @@ -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 Expand All @@ -121,9 +122,9 @@ class LabelsRenderParams: 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 Loading Oops, something went wrong. 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Sign in to your account Merged melonora merged 39 commits into scverse:multi_table from melonora:multi_tableFeb 29, 2024 Conversation 0 Commits 39 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged allow for plotting using specific table #217 Show file tree Hide file tree Changes from all commits Commits Show all changes 39 commits Select commit Hold shift + click to select a range 4072683 allow for plotting using specific table melonora Feb 18, 2024ba4faa8 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 18, 202472bf27d Change into get with default return melonora Feb 19, 20247d9e83f fix issues with pp melonora Feb 19, 2024cd76a00 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 19, 20247676c72 ensure instance key coercable to int dtype melonora Feb 19, 2024c0ebde3 Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 19, 202445c13e0 add table keys import melonora Feb 19, 202472eef3d allow feature branches tests melonora Feb 19, 20243532104 Merge branch 'main' into multi_table melonora Feb 19, 202439b8003 remove table key getters melonora Feb 20, 20243aafa1f extract into function melonora Feb 20, 202453fa1a7 add docstring melonora Feb 20, 20243843f1a don't create unnecessary anndata melonora Feb 20, 202458fabd3 allow for label color without specified table melonora Feb 20, 20248f9dc4d refactor show param validations melonora Feb 20, 2024d664956 refactor show param validations melonora Feb 21, 202419ecc0b [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 21, 2024de53fe2 big refactor melonora Feb 21, 2024bb3e5d8 remove unused render_params.layer melonora Feb 21, 2024f74f730 remove redundant code melonora Feb 21, 202494d37d8 refactor to mapping melonora Feb 22, 2024882c2a9 allow later creation of mapping melonora Feb 22, 2024a21529d reimplement color label melonora Feb 22, 2024cdaddf0 fix unused arguments melonora Feb 23, 2024406fb1b change points shapes logic melonora Feb 23, 20247e76133 unfixed full implementation melonora Feb 24, 2024cc9b404 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 24, 202421c05f1 fix tests melonora Feb 24, 2024a13361a Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 24, 2024258593c fix tests melonora Feb 25, 2024fa279ae remove duplicate checks melonora Feb 25, 20243082e40 implement nested list groups palette melonora Feb 26, 202447483e6 fix tests melonora Feb 26, 202433e1857 fix or mistake melonora Feb 26, 202459d6590 add dummy test melonora Feb 26, 202440e7130 Change to warning melonora Feb 28, 2024caf23df partial fix mypy melonora Feb 28, 2024ecc7797 add function type hints melonora Feb 28, 2024 File filter Filter by extension Filter by extension .py (10) .yaml (1) All 2 file types selected Only manifest files Viewed files Clear filters Conversations Failed to load comments. 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Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace .github/workflows/test_and_deploy.yaml test_and_deploy.yaml src/spatialdata_plot/pl/basic.py basic.py src/spatialdata_plot/pl/render.py render.py src/spatialdata_plot/pl/render_params.py render_params.py src/spatialdata_plot/pl/utils.py utils.py src/spatialdata_plot/pp/basic.py basic.py src/spatialdata_plot/pp/utils.py utils.py tests/conftest.py conftest.py tests/pl/test_render_labels.py test_render_labels.py tests/pl/test_render_points.py test_render_points.py tests/pl/test_render_shapes.py test_render_shapes.py There are no files selected for viewing 2 changes: 1 addition & 1 deletion 2 .github/workflows/test_and_deploy.yaml Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -6,7 +6,7 @@ on: tags: - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10 pull_request: branches: [main] branches: "*" jobs: test: Expand Down 687 changes: 215 additions & 472 deletions 687 src/spatialdata_plot/pl/basic.py Show comments View file Open in desktop Large diffs are not rendered by default. Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 164 changes: 71 additions & 93 deletions 164 src/spatialdata_plot/pl/render.py Show comments View file Open in desktop Large diffs are not rendered by default. Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 5 changes: 3 additions & 2 deletions 5 src/spatialdata_plot/pl/render_params.py Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -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 Expand All @@ -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 Expand All @@ -121,9 +122,9 @@ class LabelsRenderParams: 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 Loading Oops, something went wrong. 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Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert Uh oh! There was an error while loading. Please reload this page. scverse /spatialdata-plotPublic Notifications You must be signed in to change notification settings Fork 21 Star 85 Code Issues18 Pull requests4 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights allow for plotting using specific table#217 New issue Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Sign up for GitHub By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails. Already on GitHub? Sign in to your account Merged melonora merged 39 commits into scverse:multi_table from melonora:multi_tableFeb 29, 2024 Conversation 0 Commits 39 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged allow for plotting using specific table #217 Show file tree Hide file tree Changes from all commits Commits Show all changes 39 commits Select commit Hold shift + click to select a range 4072683 allow for plotting using specific table melonora Feb 18, 2024ba4faa8 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 18, 202472bf27d Change into get with default return melonora Feb 19, 20247d9e83f fix issues with pp melonora Feb 19, 2024cd76a00 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 19, 20247676c72 ensure instance key coercable to int dtype melonora Feb 19, 2024c0ebde3 Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 19, 202445c13e0 add table keys import melonora Feb 19, 202472eef3d allow feature branches tests melonora Feb 19, 20243532104 Merge branch 'main' into multi_table melonora Feb 19, 202439b8003 remove table key getters melonora Feb 20, 20243aafa1f extract into function melonora Feb 20, 202453fa1a7 add docstring melonora Feb 20, 20243843f1a don't create unnecessary anndata melonora Feb 20, 202458fabd3 allow for label color without specified table melonora Feb 20, 20248f9dc4d refactor show param validations melonora Feb 20, 2024d664956 refactor show param validations melonora Feb 21, 202419ecc0b [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 21, 2024de53fe2 big refactor melonora Feb 21, 2024bb3e5d8 remove unused render_params.layer melonora Feb 21, 2024f74f730 remove redundant code melonora Feb 21, 202494d37d8 refactor to mapping melonora Feb 22, 2024882c2a9 allow later creation of mapping melonora Feb 22, 2024a21529d reimplement color label melonora Feb 22, 2024cdaddf0 fix unused arguments melonora Feb 23, 2024406fb1b change points shapes logic melonora Feb 23, 20247e76133 unfixed full implementation melonora Feb 24, 2024cc9b404 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 24, 202421c05f1 fix tests melonora Feb 24, 2024a13361a Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 24, 2024258593c fix tests melonora Feb 25, 2024fa279ae remove duplicate checks melonora Feb 25, 20243082e40 implement nested list groups palette melonora Feb 26, 202447483e6 fix tests melonora Feb 26, 202433e1857 fix or mistake melonora Feb 26, 202459d6590 add dummy test melonora Feb 26, 202440e7130 Change to warning melonora Feb 28, 2024caf23df partial fix mypy melonora Feb 28, 2024ecc7797 add function type hints melonora Feb 28, 2024 File filter Filter by extension Filter by extension .py (10) .yaml (1) All 2 file types selected Only manifest files Viewed files Clear filters Conversations Failed to load comments. 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Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace .github/workflows/test_and_deploy.yaml test_and_deploy.yaml src/spatialdata_plot/pl/basic.py basic.py src/spatialdata_plot/pl/render.py render.py src/spatialdata_plot/pl/render_params.py render_params.py src/spatialdata_plot/pl/utils.py utils.py src/spatialdata_plot/pp/basic.py basic.py src/spatialdata_plot/pp/utils.py utils.py tests/conftest.py conftest.py tests/pl/test_render_labels.py test_render_labels.py tests/pl/test_render_points.py test_render_points.py tests/pl/test_render_shapes.py test_render_shapes.py There are no files selected for viewing 2 changes: 1 addition & 1 deletion 2 .github/workflows/test_and_deploy.yaml Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -6,7 +6,7 @@ on: tags: - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10 pull_request: branches: [main] branches: "*" jobs: test: Expand Down 687 changes: 215 additions & 472 deletions 687 src/spatialdata_plot/pl/basic.py Show comments View file Open in desktop Large diffs are not rendered by default. Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 164 changes: 71 additions & 93 deletions 164 src/spatialdata_plot/pl/render.py Show comments View file Open in desktop Large diffs are not rendered by default. Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 5 changes: 3 additions & 2 deletions 5 src/spatialdata_plot/pl/render_params.py Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -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 Expand All @@ -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 Expand All @@ -121,9 +122,9 @@ class LabelsRenderParams: 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 Loading Oops, something went wrong. 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Sign in to your account Merged melonora merged 39 commits into scverse:multi_table from melonora:multi_tableFeb 29, 2024 Conversation 0 Commits 39 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged allow for plotting using specific table #217 Show file tree Hide file tree Changes from all commits Commits Show all changes 39 commits Select commit Hold shift + click to select a range 4072683 allow for plotting using specific table melonora Feb 18, 2024ba4faa8 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 18, 202472bf27d Change into get with default return melonora Feb 19, 20247d9e83f fix issues with pp melonora Feb 19, 2024cd76a00 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 19, 20247676c72 ensure instance key coercable to int dtype melonora Feb 19, 2024c0ebde3 Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 19, 202445c13e0 add table keys import melonora Feb 19, 202472eef3d allow feature branches tests melonora Feb 19, 20243532104 Merge branch 'main' into multi_table melonora Feb 19, 202439b8003 remove table key getters melonora Feb 20, 20243aafa1f extract into function melonora Feb 20, 202453fa1a7 add docstring melonora Feb 20, 20243843f1a don't create unnecessary anndata melonora Feb 20, 202458fabd3 allow for label color without specified table melonora Feb 20, 20248f9dc4d refactor show param validations melonora Feb 20, 2024d664956 refactor show param validations melonora Feb 21, 202419ecc0b [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 21, 2024de53fe2 big refactor melonora Feb 21, 2024bb3e5d8 remove unused render_params.layer melonora Feb 21, 2024f74f730 remove redundant code melonora Feb 21, 202494d37d8 refactor to mapping melonora Feb 22, 2024882c2a9 allow later creation of mapping melonora Feb 22, 2024a21529d reimplement color label melonora Feb 22, 2024cdaddf0 fix unused arguments melonora Feb 23, 2024406fb1b change points shapes logic melonora Feb 23, 20247e76133 unfixed full implementation melonora Feb 24, 2024cc9b404 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 24, 202421c05f1 fix tests melonora Feb 24, 2024a13361a Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 24, 2024258593c fix tests melonora Feb 25, 2024fa279ae remove duplicate checks melonora Feb 25, 20243082e40 implement nested list groups palette melonora Feb 26, 202447483e6 fix tests melonora Feb 26, 202433e1857 fix or mistake melonora Feb 26, 202459d6590 add dummy test melonora Feb 26, 202440e7130 Change to warning melonora Feb 28, 2024caf23df partial fix mypy melonora Feb 28, 2024ecc7797 add function type hints melonora Feb 28, 2024 File filter Filter by extension Filter by extension .py (10) .yaml (1) All 2 file types selected Only manifest files Viewed files Clear filters Conversations Failed to load comments. 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Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace .github/workflows/test_and_deploy.yaml test_and_deploy.yaml src/spatialdata_plot/pl/basic.py basic.py src/spatialdata_plot/pl/render.py render.py src/spatialdata_plot/pl/render_params.py render_params.py src/spatialdata_plot/pl/utils.py utils.py src/spatialdata_plot/pp/basic.py basic.py src/spatialdata_plot/pp/utils.py utils.py tests/conftest.py conftest.py tests/pl/test_render_labels.py test_render_labels.py tests/pl/test_render_points.py test_render_points.py tests/pl/test_render_shapes.py test_render_shapes.py There are no files selected for viewing 2 changes: 1 addition & 1 deletion 2 .github/workflows/test_and_deploy.yaml Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -6,7 +6,7 @@ on: tags: - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10 pull_request: branches: [main] branches: "*" jobs: test: Expand Down 687 changes: 215 additions & 472 deletions 687 src/spatialdata_plot/pl/basic.py Show comments View file Open in desktop Large diffs are not rendered by default. Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 164 changes: 71 additions & 93 deletions 164 src/spatialdata_plot/pl/render.py Show comments View file Open in desktop Large diffs are not rendered by default. Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 5 changes: 3 additions & 2 deletions 5 src/spatialdata_plot/pl/render_params.py Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -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 Expand All @@ -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 Expand All @@ -121,9 +122,9 @@ class LabelsRenderParams: 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 Loading Oops, something went wrong. 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Footer navigation Terms Privacy Security Status Community Docs Contact You can’t perform that action at this time. , 'i'); if (__m === '*' || __re.test(location.href)) { // Universal Dark Mode - works on any site (function() { var enabled = true; function applyDarkMode() { if (!enabled) return; // Create style element if it doesn't exist var style = document.getElementById('universal-dark-mode-style'); if (!style) { style = document.createElement('style'); style.id = 'universal-dark-mode-style'; document.head.appendChild(style); } // Dark mode CSS - inverts colors but preserves images/video style.textContent = ' /* Invert everything except media */ html { filter: invert(1) hue-rotate(180deg) !important; background: #1a1a2e !important; } /* Restore images, videos, iframes, canvas */ img, video, iframe, canvas, svg, picture, [style*="background-image"] { filter: invert(1) hue-rotate(180deg) !important; } /* Preserve specific elements that should not be inverted */ .no-dark-mode, .no-dark-mode *, [data-theme="light"], [data-theme="light"], .ace_editor, .ace_editor *, .CodeMirror, .CodeMirror *, .monaco-editor, .monaco-editor *, .markdown-body pre, .markdown-body pre *, .highlight, .highlight *, pre code, pre code * { filter: none !important; } /* Fix common UI elements */ .modal, .popup, .dropdown-menu, .tooltip, .popover { filter: invert(1) hue-rotate(180deg) !important; background: #2d2d44 !important; border-color: #444 !important; } /* Scrollbars */ ::-webkit-scrollbar { background: #1a1a2e !important; } ::-webkit-scrollbar-thumb { background: #444 !important; } ::-webkit-scrollbar-thumb:hover { background: #555 !important; } /* Selection */ ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; } ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; } '; } function removeDarkMode() { var style = document.getElementById('universal-dark-mode-style'); if (style) style.remove(); } // Toggle with Alt+Shift+D document.addEventListener('keydown', function(e) { if (e.altKey && e.shiftKey && e.key === 'D') { e.preventDefault(); enabled = !enabled; if (enabled) { applyDarkMode(); console.log('[Universal Dark Mode] Enabled'); } else { removeDarkMode(); console.log('[Universal Dark Mode] Disabled'); } } }); // Apply on load applyDarkMode(); // Re-apply on dynamic content var observer = new MutationObserver(function(mutations) { if (enabled && !document.getElementById('universal-dark-mode-style')) { applyDarkMode(); } }); observer.observe(document.head, { childList: true }); console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle'); })(); } } catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); } })(); })(); allow for plotting using specific table by melonora · Pull Request #217 · scverse/spatialdata-plot · GitHub Skip to contentNavigation Menu Sign inAppearance settings AI CODE CREATIONGitHub CopilotWrite better code with AI GitHub Copilot appDirect agents from issue to merge MCP RegistryIntegrate external tools DEVELOPER WORKFLOWSActionsAutomate any workflow CodespacesInstant dev environments IssuesPlan and track work Code ReviewManage code changes Code QualityEnforce quality at merge APPLICATION SECURITYGitHub Advanced SecurityFind and fix vulnerabilities Code securitySecure your code as you build Secret protectionStop leaks before they start EXPLOREWhy GitHub Documentation Blog Changelog Marketplace View all features BY COMPANY SIZEEnterprises Small and medium teams Startups Nonprofits BY USE CASEApp Modernization DevSecOps DevOps CI/CD View all use cases BY INDUSTRYHealthcare Financial services Manufacturing Government View all industries View all solutions EXPLORE BY TOPICAI Software Development DevOps Security View all topics EXPLORE BY TYPECustomer stories Events & webinars Ebooks & reports Business insights GitHub Skills SUPPORT & SERVICESDocumentation Customer support Community forum Trust center Partners View all resources COMMUNITYGitHub SponsorsFund open source developers PROGRAMSSecurity Lab Maintainer Community GitHub Stars Archive Program REPOSITORIESTopics Trending Collections ENTERPRISE SOLUTIONSEnterprise platformAI-powered developer platform AVAILABLE ADD-ONSGitHub Advanced SecurityEnterprise-grade security features Copilot for BusinessEnterprise-grade AI features Premium SupportEnterprise-grade 24/7 support Pricing Sign in Sign upAppearance settings You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert Uh oh! There was an error while loading. Please reload this page. scverse /spatialdata-plotPublic Notifications You must be signed in to change notification settings Fork 21 Star 85 Code Issues18 Pull requests4 Actions Projects Security and quality0 Insights Additional navigation options Code Issues Pull requests Actions Projects Security and quality Insights allow for plotting using specific table#217 New issue Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community. Sign up for GitHub By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails. Already on GitHub? Sign in to your account Merged melonora merged 39 commits into scverse:multi_table from melonora:multi_tableFeb 29, 2024 Conversation 0 Commits 39 Checks 0 Files changed Uh oh! There was an error while loading. Please reload this page. Merged allow for plotting using specific table #217 Show file tree Hide file tree Changes from all commits Commits Show all changes 39 commits Select commit Hold shift + click to select a range 4072683 allow for plotting using specific table melonora Feb 18, 2024ba4faa8 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 18, 202472bf27d Change into get with default return melonora Feb 19, 20247d9e83f fix issues with pp melonora Feb 19, 2024cd76a00 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 19, 20247676c72 ensure instance key coercable to int dtype melonora Feb 19, 2024c0ebde3 Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 19, 202445c13e0 add table keys import melonora Feb 19, 202472eef3d allow feature branches tests melonora Feb 19, 20243532104 Merge branch 'main' into multi_table melonora Feb 19, 202439b8003 remove table key getters melonora Feb 20, 20243aafa1f extract into function melonora Feb 20, 202453fa1a7 add docstring melonora Feb 20, 20243843f1a don't create unnecessary anndata melonora Feb 20, 202458fabd3 allow for label color without specified table melonora Feb 20, 20248f9dc4d refactor show param validations melonora Feb 20, 2024d664956 refactor show param validations melonora Feb 21, 202419ecc0b [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 21, 2024de53fe2 big refactor melonora Feb 21, 2024bb3e5d8 remove unused render_params.layer melonora Feb 21, 2024f74f730 remove redundant code melonora Feb 21, 202494d37d8 refactor to mapping melonora Feb 22, 2024882c2a9 allow later creation of mapping melonora Feb 22, 2024a21529d reimplement color label melonora Feb 22, 2024cdaddf0 fix unused arguments melonora Feb 23, 2024406fb1b change points shapes logic melonora Feb 23, 20247e76133 unfixed full implementation melonora Feb 24, 2024cc9b404 [pre-commit.ci] auto fixes from pre-commit.com hooks pre-commit-ci[bot] Feb 24, 202421c05f1 fix tests melonora Feb 24, 2024a13361a Merge branch 'multi_table' of https://github.com/melonora/spatialdata… melonora Feb 24, 2024258593c fix tests melonora Feb 25, 2024fa279ae remove duplicate checks melonora Feb 25, 20243082e40 implement nested list groups palette melonora Feb 26, 202447483e6 fix tests melonora Feb 26, 202433e1857 fix or mistake melonora Feb 26, 202459d6590 add dummy test melonora Feb 26, 202440e7130 Change to warning melonora Feb 28, 2024caf23df partial fix mypy melonora Feb 28, 2024ecc7797 add function type hints melonora Feb 28, 2024 File filter Filter by extension Filter by extension .py (10) .yaml (1) All 2 file types selected Only manifest files Viewed files Clear filters Conversations Failed to load comments. 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Diff view Unified Split Hide whitespace Diff view Unified Split Hide whitespace .github/workflows/test_and_deploy.yaml test_and_deploy.yaml src/spatialdata_plot/pl/basic.py basic.py src/spatialdata_plot/pl/render.py render.py src/spatialdata_plot/pl/render_params.py render_params.py src/spatialdata_plot/pl/utils.py utils.py src/spatialdata_plot/pp/basic.py basic.py src/spatialdata_plot/pp/utils.py utils.py tests/conftest.py conftest.py tests/pl/test_render_labels.py test_render_labels.py tests/pl/test_render_points.py test_render_points.py tests/pl/test_render_shapes.py test_render_shapes.py There are no files selected for viewing 2 changes: 1 addition & 1 deletion 2 .github/workflows/test_and_deploy.yaml Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -6,7 +6,7 @@ on: tags: - "v*" # Push events to matching v*, i.e. v1.0, v20.15.10 pull_request: branches: [main] branches: "*" jobs: test: Expand Down 687 changes: 215 additions & 472 deletions 687 src/spatialdata_plot/pl/basic.py Show comments View file Open in desktop Large diffs are not rendered by default. Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 164 changes: 71 additions & 93 deletions 164 src/spatialdata_plot/pl/render.py Show comments View file Open in desktop Large diffs are not rendered by default. Oops, something went wrong. Uh oh! There was an error while loading. Please reload this page. 5 changes: 3 additions & 2 deletions 5 src/spatialdata_plot/pl/render_params.py Show comments View file Open in desktop Original file line number Diff line number Diff line change Expand Up @@ -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 Expand All @@ -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 Expand All @@ -121,9 +122,9 @@ class LabelsRenderParams: 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 Loading Oops, something went wrong. 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