scmcp-shared 0.4.0__py3-none-any.whl → 0.6.0__py3-none-any.whl

scmcp_shared/schema/pl.py

@@ -1,258 +1,220 @@
-from typing import Optional, Union, List, Literal, Any, Collection, Tuple, Sequence, Mapping
-from pydantic import (
-    Field,
-    ValidationInfo,
-    computed_field,
-    field_validator,
-    model_validator,
-    BaseModel
-)
+from typing import Optional, Union, List, Literal, Tuple, Mapping
+from pydantic import Field, field_validator, BaseModel
+
 
 # 创建 Mixin 类处理特定功能
 class LegendMixin:
     """处理图例相关的字段"""
-    
+
     legend_fontsize: Optional[Union[int, float, str]] = Field(
-        default=None,
-        description="Numeric size in pt or string describing the size."
+        default=None, description="Numeric size in pt or string describing the size."
     )
-    
+
     legend_fontweight: Union[int, str] = Field(
-        default='bold',
-        description="Legend font weight. A numeric value in range 0-1000 or a string."
+        default="bold",
+        description="Legend font weight. A numeric value in range 0-1000 or a string.",
     )
-    
+
     legend_loc: str = Field(
-        default='right margin',
-        description="Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter."
+        default="right margin",
+        description="Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter.",
     )
-    
+
     legend_fontoutline: Optional[int] = Field(
-        default=None,
-        description="Line width of the legend font outline in pt."
+        default=None, description="Line width of the legend font outline in pt."
     )
 
 
 class ColorMappingMixin:
     """处理颜色映射相关的字段"""
-    
+
     color_map: Optional[str] = Field(
-        default=None,
-        description="Color map to use for continuous variables."
+        default=None, description="Color map to use for continuous variables."
     )
-    
+
     palette: Optional[Union[str, List[str], Mapping[str, str]]] = Field(
         default=None,
-        description="Colors to use for plotting categorical annotation groups."
+        description="Colors to use for plotting categorical annotation groups.",
     )
-    
+
     vmax: Optional[Union[str, float, List[Union[str, float]]]] = Field(
         default=None,
-        description="The value representing the upper limit of the color scale."
+        description="The value representing the upper limit of the color scale.",
     )
-    
+
     vmin: Optional[Union[str, float, List[Union[str, float]]]] = Field(
         default=None,
-        description="The value representing the lower limit of the color scale."
+        description="The value representing the lower limit of the color scale.",
     )
-    
+
     vcenter: Optional[Union[str, float, List[Union[str, float]]]] = Field(
         default=None,
-        description="The value representing the center of the color scale."
+        description="The value representing the center of the color scale.",
     )
 
 
 class FigureSizeMixin:
     """处理图形大小相关的字段"""
-    
+
     figsize: Optional[Tuple[float, float]] = Field(
-        default=None,
-        description="Figure size. Format is (width, height)."
+        default=None, description="Figure size. Format is (width, height)."
     )
 
 
 # 基础可视化模型，包含所有可视化工具共享的字段
-class BaseVisualizationParams(BaseModel, LegendMixin, ColorMappingMixin, FigureSizeMixin):
-    """基础可视化模型，包含所有可视化工具共享的字段"""    
+class BaseVisualizationParam(
+    BaseModel, LegendMixin, ColorMappingMixin, FigureSizeMixin
+):
+    adata: str = Field(..., description="The AnnData object variable name.")
+    """基础可视化模型，包含所有可视化工具共享的字段"""
     pass
 
+
 # 基础嵌入可视化模型，包含所有嵌入可视化工具共享的字段
-class BaseEmbeddingParams(BaseVisualizationParams):
+class BaseEmbeddingParam(BaseVisualizationParam):
     """基础嵌入可视化模型，包含所有嵌入可视化工具共享的字段"""
-    
+
     color: Optional[Union[str, List[str]]] = Field(
         default=None,
-        description="Keys for annotations of observations/cells or variables/genes."
+        description="Keys for annotations of observations/cells or variables/genes.",
     )
-    
+
     gene_symbols: Optional[str] = Field(
         default=None,
-        description="Column name in .var DataFrame that stores gene symbols."
+        description="Column name in .var DataFrame that stores gene symbols.",
     )
-    
+
     use_raw: Optional[bool] = Field(
         default=None,
-        description="Use .raw attribute of adata for coloring with gene expression."
+        description="Use .raw attribute of adata for coloring with gene expression.",
     )
-    
+
     sort_order: bool = Field(
         default=True,
-        description="For continuous annotations used as color parameter, plot data points with higher values on top of others."
-    )
-    
-    edges: bool = Field(
-        default=False,
-        description="Show edges between nodes."
-    )
-    
-    edges_width: float = Field(
-        default=0.1,
-        description="Width of edges."
+        description="For continuous annotations used as color parameter, plot data points with higher values on top of others.",
     )
-    
+
+    edges: bool = Field(default=False, description="Show edges between nodes.")
+
+    edges_width: float = Field(default=0.1, description="Width of edges.")
+
     edges_color: Union[str, List[float], List[str]] = Field(
-        default='grey',
-        description="Color of edges."
+        default="grey", description="Color of edges."
     )
-    
+
     neighbors_key: Optional[str] = Field(
-        default=None,
-        description="Where to look for neighbors connectivities."
+        default=None, description="Where to look for neighbors connectivities."
     )
-    
-    arrows: bool = Field(
-        default=False,
-        description="Show arrows."
-    )
-    
+
+    arrows: bool = Field(default=False, description="Show arrows.")
+
     groups: Optional[Union[str, List[str]]] = Field(
         default=None,
-        description="Restrict to a few categories in categorical observation annotation."
+        description="Restrict to a few categories in categorical observation annotation.",
     )
-    
+
     components: Optional[Union[str, List[str]]] = Field(
         default=None,
-        description="For instance, ['1,2', '2,3']. To plot all available components use components='all'."
+        description="For instance, ['1,2', '2,3']. To plot all available components use components='all'.",
     )
-    
+
     dimensions: Optional[Union[Tuple[int, int], List[Tuple[int, int]]]] = Field(
         default=None,
-        description="0-indexed dimensions of the embedding to plot as integers. E.g. [(0, 1), (1, 2)]."
+        description="0-indexed dimensions of the embedding to plot as integers. E.g. [(0, 1), (1, 2)].",
     )
-    
+
     layer: Optional[str] = Field(
         default=None,
-        description="Name of the AnnData object layer that wants to be plotted."
+        description="Name of the AnnData object layer that wants to be plotted.",
     )
-    
-    projection: Literal['2d', '3d'] = Field(
-        default='2d',
-        description="Projection of plot."
+
+    projection: Literal["2d", "3d"] = Field(
+        default="2d", description="Projection of plot."
     )
-    
+
     size: Optional[Union[float, List[float]]] = Field(
-        default=None,
-        description="Point size. If None, is automatically computed."
+        default=None, description="Point size. If None, is automatically computed."
     )
-    
+
     frameon: Optional[bool] = Field(
-        default=None,
-        description="Draw a frame around the scatter plot."
+        default=None, description="Draw a frame around the scatter plot."
     )
-    
+
     add_outline: Optional[bool] = Field(
-        default=False,
-        description="Add outline to scatter plot points."
+        default=False, description="Add outline to scatter plot points."
     )
-    
-    ncols: int = Field(
-        default=4,
-        description="Number of columns for multiple plots."
-    )
-    
+
+    ncols: int = Field(default=4, description="Number of columns for multiple plots.")
+
     marker: Union[str, List[str]] = Field(
-        default='.',
-        description="Matplotlib marker style for points."
+        default=".", description="Matplotlib marker style for points."
     )
 
 
-# 重构 ScatterParams 作为基础散点图模型
-class BaseScatterParams(BaseVisualizationParams):
+# 重构 ScatterParam 作为基础散点图模型
+class BaseScatterParam(BaseVisualizationParam):
     """基础散点图模型"""
-    
-    x: Optional[str] = Field(
-        default=None,
-        description="x coordinate."
-    )    
-    
-    y: Optional[str] = Field(
-        default=None,
-        description="y coordinate."
-    )
-    
+
+    x: Optional[str] = Field(default=None, description="x coordinate.")
+
+    y: Optional[str] = Field(default=None, description="y coordinate.")
+
     color: Optional[Union[str, List[str]]] = Field(
         default=None,
-        description="Keys for annotations of observations/cells or variables/genes, or a hex color specification."
+        description="Keys for annotations of observations/cells or variables/genes, or a hex color specification.",
     )
-    
+
     use_raw: Optional[bool] = Field(
         default=None,
-        description="Whether to use raw attribute of adata. Defaults to True if .raw is present."
+        description="Whether to use raw attribute of adata. Defaults to True if .raw is present.",
     )
-    
+
     layers: Optional[Union[str, List[str]]] = Field(
         default=None,
-        description="Use the layers attribute of adata if present: specify the layer for x, y and color."
+        description="Use the layers attribute of adata if present: specify the layer for x, y and color.",
     )
-    
+
     basis: Optional[str] = Field(
-        default=None,
-        description="Basis to use for embedding."
+        default=None, description="Basis to use for embedding."
     )
 
 
-# 使用继承关系重构 EnhancedScatterParams
-class EnhancedScatterParams(BaseScatterParams):
+# 使用继承关系重构 EnhancedScatterParam
+class EnhancedScatterParam(BaseScatterParam):
     """Input schema for the enhanced scatter plotting tool."""
-    
+
     sort_order: bool = Field(
         default=True,
-        description="For continuous annotations used as color parameter, plot data points with higher values on top of others."
+        description="For continuous annotations used as color parameter, plot data points with higher values on top of others.",
     )
-    
+
     alpha: Optional[float] = Field(
-        default=None,
-        description="Alpha value for the plot.",
-        ge=0,
-        le=1
+        default=None, description="Alpha value for the plot.", ge=0, le=1
     )
-    
+
     groups: Optional[Union[str, List[str]]] = Field(
         default=None,
-        description="Restrict to a few categories in categorical observation annotation."
+        description="Restrict to a few categories in categorical observation annotation.",
     )
-    
+
     components: Optional[Union[str, List[str]]] = Field(
         default=None,
-        description="For instance, ['1,2', '2,3']. To plot all available components use components='all'."
+        description="For instance, ['1,2', '2,3']. To plot all available components use components='all'.",
     )
-    
-    projection: Literal['2d', '3d'] = Field(
-        default='2d',
-        description="Projection of plot."
+
+    projection: Literal["2d", "3d"] = Field(
+        default="2d", description="Projection of plot."
     )
-    
+
     right_margin: Optional[float] = Field(
-        default=None,
-        description="Adjust the width of the right margin."
+        default=None, description="Adjust the width of the right margin."
     )
-    
+
     left_margin: Optional[float] = Field(
-        default=None,
-        description="Adjust the width of the left margin."
+        default=None, description="Adjust the width of the left margin."
     )
-    
-    @field_validator('alpha')
+
+    @field_validator("alpha")
     def validate_alpha(cls, v: Optional[float]) -> Optional[float]:
         """Validate alpha is between 0 and 1"""
         if v is not None and (v < 0 or v > 1):
@@ -261,150 +223,136 @@ class EnhancedScatterParams(BaseScatterParams):
 
 
 # 创建基础统计可视化模型
-class BaseStatPlotParams(BaseVisualizationParams):
+class BaseStatPlotParam(BaseVisualizationParam):
     """基础统计可视化模型，包含统计图表共享的字段"""
-    
+
     groupby: Optional[str] = Field(
-        default=None,
-        description="The key of the observation grouping to consider."
-    )
-    
-    log: bool = Field(
-        default=False,
-        description="Plot on logarithmic axis."
+        default=None, description="The key of the observation grouping to consider."
     )
-    
+
+    log: bool = Field(default=False, description="Plot on logarithmic axis.")
+
     use_raw: Optional[bool] = Field(
-        default=None,
-        description="Use raw attribute of adata if present."
+        default=None, description="Use raw attribute of adata if present."
     )
-    
+
     var_names: Optional[Union[str, List[str]]] = Field(
         default=None,
-        description="var_names should be a valid subset of adata.var_names."
+        description="var_names should be a valid subset of adata.var_names.",
     )
-    
+
     layer: Optional[str] = Field(
         default=None,
-        description="Name of the AnnData object layer that wants to be plotted."
+        description="Name of the AnnData object layer that wants to be plotted.",
     )
-    
+
     gene_symbols: Optional[str] = Field(
         default=None,
-        description="Column name in .var DataFrame that stores gene symbols."
+        description="Column name in .var DataFrame that stores gene symbols.",
     )
-    
+
     # 添加共享的小提琴图相关字段
     stripplot: bool = Field(
-        default=True,
-        description="Add a stripplot on top of the violin plot."
+        default=True, description="Add a stripplot on top of the violin plot."
     )
-    
+
     jitter: Union[float, bool] = Field(
         default=True,
-        description="Add jitter to the stripplot (only when stripplot is True)."
-    )
-    
-    size: int = Field(
-        default=1,
-        description="Size of the jitter points.",
-        gt=0
+        description="Add jitter to the stripplot (only when stripplot is True).",
     )
-    
+
+    size: int = Field(default=1, description="Size of the jitter points.", gt=0)
+
     order: Optional[List[str]] = Field(
-        default=None,
-        description="Order in which to show the categories."
+        default=None, description="Order in which to show the categories."
     )
-    
-    scale: Literal['area', 'count', 'width'] = Field(
-        default='width',
-        description="The method used to scale the width of each violin."
+
+    scale: Literal["area", "count", "width"] = Field(
+        default="width",
+        description="The method used to scale the width of each violin.",
     )
-    
-    @field_validator('size')
+
+    @field_validator("size")
     def validate_size(cls, v: int) -> int:
         """Validate size is positive"""
         if v <= 0:
             raise ValueError("size must be a positive integer")
         return v
 
-# 添加缺失的 BaseMatrixParams 类
-class BaseMatrixParams(BaseVisualizationParams):
+
+# 添加缺失的 BaseMatrixParam 类
+class BaseMatrixParam(BaseVisualizationParam):
     """基础矩阵可视化模型，包含所有矩阵可视化工具共享的字段"""
-    
+
     var_names: Union[List[str], Mapping[str, List[str]]] = Field(
         default=None,
-        description="var_names should be a valid subset of adata.var_names or a mapping where the key is used as label to group the values."
-    )    
+        description="var_names should be a valid subset of adata.var_names or a mapping where the key is used as label to group the values.",
+    )
     groupby: Union[str, List[str]] = Field(
         ...,  # Required field
-        description="The key of the observation grouping to consider."
+        description="The key of the observation grouping to consider.",
     )
     use_raw: Optional[bool] = Field(
-        default=None,
-        description="Use raw attribute of adata if present."
-    )
-    log: bool = Field(
-        default=False,
-        description="Plot on logarithmic axis."
+        default=None, description="Use raw attribute of adata if present."
     )
+    log: bool = Field(default=False, description="Plot on logarithmic axis.")
     dendrogram: Union[bool, str] = Field(
         default=False,
-        description="If True or a valid dendrogram key, a dendrogram based on the hierarchical clustering between the groupby categories is added."
+        description="If True or a valid dendrogram key, a dendrogram based on the hierarchical clustering between the groupby categories is added.",
     )
-    
+
     gene_symbols: Optional[str] = Field(
         default=None,
-        description="Column name in .var DataFrame that stores gene symbols."
+        description="Column name in .var DataFrame that stores gene symbols.",
     )
-    
+
     var_group_positions: Optional[List[Tuple[int, int]]] = Field(
         default=None,
-        description="Use this parameter to highlight groups of var_names with brackets or color blocks between the given start and end positions."
+        description="Use this parameter to highlight groups of var_names with brackets or color blocks between the given start and end positions.",
     )
-    
+
     var_group_labels: Optional[List[str]] = Field(
         default=None,
-        description="Labels for each of the var_group_positions that want to be highlighted."
+        description="Labels for each of the var_group_positions that want to be highlighted.",
     )
-    
+
     layer: Optional[str] = Field(
         default=None,
-        description="Name of the AnnData object layer that wants to be plotted."
+        description="Name of the AnnData object layer that wants to be plotted.",
     )
 
 
-# 重构 HeatmapParams
-class HeatmapParams(BaseMatrixParams):
+# 重构 HeatmapParam
+class HeatmapParam(BaseMatrixParam):
     """Input schema for the heatmap plotting tool."""
-    
+
     num_categories: int = Field(
         default=7,
         description="Only used if groupby observation is not categorical. This value determines the number of groups into which the groupby observation should be subdivided.",
-        gt=0
+        gt=0,
     )
-    
+
     var_group_rotation: Optional[float] = Field(
         default=None,
-        description="Label rotation degrees. By default, labels larger than 4 characters are rotated 90 degrees."
+        description="Label rotation degrees. By default, labels larger than 4 characters are rotated 90 degrees.",
     )
-    
-    standard_scale: Optional[Literal['var', 'obs']] = Field(
+
+    standard_scale: Optional[Literal["var", "obs"]] = Field(
         default=None,
-        description="Whether or not to standardize that dimension between 0 and 1."
+        description="Whether or not to standardize that dimension between 0 and 1.",
     )
-    
+
     swap_axes: bool = Field(
         default=False,
-        description="By default, the x axis contains var_names and the y axis the groupby categories. By setting swap_axes then x are the groupby categories and y the var_names."
+        description="By default, the x axis contains var_names and the y axis the groupby categories. By setting swap_axes then x are the groupby categories and y the var_names.",
     )
-    
+
     show_gene_labels: Optional[bool] = Field(
         default=None,
-        description="By default gene labels are shown when there are 50 or less genes. Otherwise the labels are removed."
+        description="By default gene labels are shown when there are 50 or less genes. Otherwise the labels are removed.",
     )
-    
-    @field_validator('num_categories')
+
+    @field_validator("num_categories")
     def validate_num_categories(cls, v: int) -> int:
         """Validate num_categories is positive"""
         if v <= 0:
@@ -412,64 +360,56 @@ class HeatmapParams(BaseMatrixParams):
         return v
 
 
-# 重构 TracksplotParams
-class TracksplotParams(BaseMatrixParams):
+# 重构 TracksplotParam
+class TracksplotParam(BaseMatrixParam):
     """Input schema for the tracksplot plotting tool."""
-    # 所有需要的字段已经在 BaseMatrixParams 中定义
 
+    # 所有需要的字段已经在 BaseMatrixParam 中定义
 
-# 重构 ViolinParams
-class ViolinParams(BaseStatPlotParams):
+
+# 重构 ViolinParam
+class ViolinParam(BaseStatPlotParam):
     """Input schema for the violin plotting tool."""
-    
+
     keys: Union[str, List[str]] = Field(
         ...,  # Required field
-        description="Keys for accessing variables of adata.var or adata.obs. or variables of adata.obsm when obsm_key is not None."
+        description="Keys for accessing variables of adata.var or adata.obs. or variables of adata.obsm when obsm_key is not None.",
     )
     use_obsm: str = Field(
-        default=None,
-        description="using data of adata.obsm instead of adata.X"
+        default=None, description="using data of adata.obsm instead of adata.X"
     )
     stripplot: bool = Field(
-        default=True,
-        description="Add a stripplot on top of the violin plot."
+        default=True, description="Add a stripplot on top of the violin plot."
     )
     jitter: Union[float, bool] = Field(
         default=True,
-        description="Add jitter to the stripplot (only when stripplot is True)."
-    )
-    size: int = Field(
-        default=1,
-        description="Size of the jitter points.",
-        gt=0
+        description="Add jitter to the stripplot (only when stripplot is True).",
     )
-    scale: Literal['area', 'count', 'width'] = Field(
-        default='width',
-        description="The method used to scale the width of each violin."
+    size: int = Field(default=1, description="Size of the jitter points.", gt=0)
+    scale: Literal["area", "count", "width"] = Field(
+        default="width",
+        description="The method used to scale the width of each violin.",
     )
     order: Optional[List[str]] = Field(
-        default=None,
-        description="Order in which to show the categories."
+        default=None, description="Order in which to show the categories."
     )
     multi_panel: Optional[bool] = Field(
         default=None,
-        description="Display keys in multiple panels also when groupby is not None."
+        description="Display keys in multiple panels also when groupby is not None.",
     )
     xlabel: str = Field(
-        default='',
-        description="Label of the x axis. Defaults to groupby if rotation is None, otherwise, no label is shown."
-    )    
+        default="",
+        description="Label of the x axis. Defaults to groupby if rotation is None, otherwise, no label is shown.",
+    )
     ylabel: Optional[Union[str, List[str]]] = Field(
-        default=None,
-        description="Label of the y axis."
+        default=None, description="Label of the y axis."
     )
-    
+
     rotation: Optional[float] = Field(
-        default=None,
-        description="Rotation of xtick labels."
+        default=None, description="Rotation of xtick labels."
     )
-    
-    @field_validator('size')
+
+    @field_validator("size")
     def validate_size(cls, v: int) -> int:
         """Validate size is positive"""
         if v <= 0:
@@ -477,45 +417,44 @@ class ViolinParams(BaseStatPlotParams):
         return v
 
 
-# 重构 MatrixplotParams
-class MatrixplotParams(BaseMatrixParams):
+# 重构 MatrixplotParam
+class MatrixplotParam(BaseMatrixParam):
     """Input schema for the matrixplot plotting tool."""
-    
+
     num_categories: int = Field(
         default=7,
         description="Only used if groupby observation is not categorical. This value determines the number of groups into which the groupby observation should be subdivided.",
-        gt=0
+        gt=0,
     )
-    
+
     cmap: Optional[str] = Field(
-        default='viridis',
-        description="String denoting matplotlib color map."
+        default="viridis", description="String denoting matplotlib color map."
     )
-    
+
     colorbar_title: Optional[str] = Field(
-        default='Mean expression\nin group',
-        description="Title for the color bar. New line character (\\n) can be used."
+        default="Mean expression\nin group",
+        description="Title for the color bar. New line character (\\n) can be used.",
     )
-    
+
     var_group_rotation: Optional[float] = Field(
         default=None,
-        description="Label rotation degrees. By default, labels larger than 4 characters are rotated 90 degrees."
+        description="Label rotation degrees. By default, labels larger than 4 characters are rotated 90 degrees.",
     )
-    
-    standard_scale: Optional[Literal['var', 'group']] = Field(
+
+    standard_scale: Optional[Literal["var", "group"]] = Field(
         default=None,
-        description="Whether or not to standardize the given dimension between 0 and 1."
+        description="Whether or not to standardize the given dimension between 0 and 1.",
     )
-    
+
     swap_axes: bool = Field(
         default=False,
-        description="By default, the x axis contains var_names and the y axis the groupby categories. By setting swap_axes then x are the groupby categories and y the var_names."
+        description="By default, the x axis contains var_names and the y axis the groupby categories. By setting swap_axes then x are the groupby categories and y the var_names.",
     )
     use_obsm: str = Field(
-        default=None,
-        description="using data of adata.obsm instead of adata.X"
+        default=None, description="using data of adata.obsm instead of adata.X"
     )
-    @field_validator('num_categories')
+
+    @field_validator("num_categories")
     def validate_num_categories(cls, v: int) -> int:
         """Validate num_categories is positive"""
         if v <= 0:
@@ -523,164 +462,141 @@ class MatrixplotParams(BaseMatrixParams):
         return v
 
 
-# 重构 DotplotParams
-class DotplotParams(BaseMatrixParams):
+# 重构 DotplotParam
+class DotplotParam(BaseMatrixParam):
     """Input schema for the dotplot plotting tool."""
-    
+
     expression_cutoff: float = Field(
         default=0.0,
-        description="Expression cutoff that is used for binarizing the gene expression."
+        description="Expression cutoff that is used for binarizing the gene expression.",
     )
-    
+
     mean_only_expressed: bool = Field(
         default=False,
-        description="If True, gene expression is averaged only over the cells expressing the given genes."
+        description="If True, gene expression is averaged only over the cells expressing the given genes.",
     )
-    
-    standard_scale: Optional[Literal['var', 'group']] = Field(
+
+    standard_scale: Optional[Literal["var", "group"]] = Field(
         default=None,
-        description="Whether or not to standardize that dimension between 0 and 1."
+        description="Whether or not to standardize that dimension between 0 and 1.",
     )
-    
+
     swap_axes: bool = Field(
         default=False,
-        description="By default, the x axis contains var_names and the y axis the groupby categories. By setting swap_axes then x are the groupby categories and y the var_names."
+        description="By default, the x axis contains var_names and the y axis the groupby categories. By setting swap_axes then x are the groupby categories and y the var_names.",
     )
-    
+
     dot_max: Optional[float] = Field(
-        default=None,
-        description="The maximum size of the dots."
+        default=None, description="The maximum size of the dots."
     )
-    
+
     dot_min: Optional[float] = Field(
-        default=None,
-        description="The minimum size of the dots."
+        default=None, description="The minimum size of the dots."
     )
-    
+
     smallest_dot: Optional[float] = Field(
-        default=None,
-        description="The smallest dot size."
+        default=None, description="The smallest dot size."
     )
     var_group_rotation: Optional[float] = Field(
         default=None,
-        description="Label rotation degrees. By default, labels larger than 4 characters are rotated 90 degrees."
+        description="Label rotation degrees. By default, labels larger than 4 characters are rotated 90 degrees.",
     )
-    
+
     colorbar_title: Optional[str] = Field(
-        default='Mean expression\nin group',
-        description="Title for the color bar. New line character (\\n) can be used."
+        default="Mean expression\nin group",
+        description="Title for the color bar. New line character (\\n) can be used.",
     )
-    
+
     size_title: Optional[str] = Field(
-        default='Fraction of cells\nin group (%)',
-        description="Title for the size legend. New line character (\\n) can be used."
+        default="Fraction of cells\nin group (%)",
+        description="Title for the size legend. New line character (\\n) can be used.",
     )
 
 
-# 重构 RankGenesGroupsParams
-class RankGenesGroupsParams(BaseVisualizationParams):
+# 重构 RankGenesGroupsParam
+class RankGenesGroupsParam(BaseVisualizationParam):
     """Input schema for the rank_genes_groups plotting tool."""
-    
-    n_genes: int = Field(
-        default=20,
-        description="Number of genes to show.",
-        gt=0
-    )
-    
+
+    n_genes: int = Field(default=20, description="Number of genes to show.", gt=0)
+
     gene_symbols: Optional[str] = Field(
         default=None,
-        description="Column name in `.var` DataFrame that stores gene symbols."
+        description="Column name in `.var` DataFrame that stores gene symbols.",
     )
-    
+
     groupby: Optional[str] = Field(
-        default=None,
-        description="The key of the observation grouping to consider."
+        default=None, description="The key of the observation grouping to consider."
     )
-    
+
     groups: Optional[Union[str, List[str]]] = Field(
-        default=None,
-        description="Subset of groups, e.g. ['g1', 'g2', 'g3']."
+        default=None, description="Subset of groups, e.g. ['g1', 'g2', 'g3']."
     )
-    
+
     key: Optional[str] = Field(
-        default='rank_genes_groups',
-        description="Key used to store the rank_genes_groups parameters."
-    )
-    
-    fontsize: int = Field(
-        default=8,
-        description="Fontsize for gene names."
-    )
-    
-    ncols: int = Field(
-        default=4,
-        description="Number of columns."
+        default="rank_genes_groups",
+        description="Key used to store the rank_genes_groups parameters.",
     )
-    
+
+    fontsize: int = Field(default=8, description="Fontsize for gene names.")
+
+    ncols: int = Field(default=4, description="Number of columns.")
+
     sharey: bool = Field(
         default=True,
-        description="Controls if the y-axis of each panels should be shared."
+        description="Controls if the y-axis of each panels should be shared.",
     )
-    
-    @field_validator('n_genes', 'fontsize')
+
+    @field_validator("n_genes", "fontsize")
     def validate_positive_int(cls, v: int) -> int:
         """Validate positive integers"""
         if v <= 0:
-            raise ValueError(f"Value must be a positive integer")
+            raise ValueError("Value must be a positive integer")
         return v
 
 
 # 重构 ClusterMapModel
-class ClusterMapParams(BaseModel):
+class ClusterMapParam(BaseModel):
     """Input schema for the clustermap plotting tool."""
 
     obs_keys: Optional[str] = Field(
         default=None,
-        description="key column in adata.obs, categorical annotation to plot with a different color map."
+        description="key column in adata.obs, categorical annotation to plot with a different color map.",
     )
     use_raw: Optional[bool] = Field(
         default=None,
-        description="Whether to use `raw` attribute of `adata`. Defaults to `True` if `.raw` is present."
+        description="Whether to use `raw` attribute of `adata`. Defaults to `True` if `.raw` is present.",
     )
 
 
-
-# 重构 StackedViolinParams
-class StackedViolinParams(BaseStatPlotParams):
+# 重构 StackedViolinParam
+class StackedViolinParam(BaseStatPlotParam):
     """Input schema for the stacked_violin plotting tool."""
-    
+
     stripplot: bool = Field(
-        default=True,
-        description="Add a stripplot on top of the violin plot."
+        default=True, description="Add a stripplot on top of the violin plot."
     )
-    
+
     jitter: Union[float, bool] = Field(
         default=True,
-        description="Add jitter to the stripplot (only when stripplot is True)."
-    )
-    
-    size: int = Field(
-        default=1,
-        description="Size of the jitter points.",
-        gt=0
+        description="Add jitter to the stripplot (only when stripplot is True).",
     )
-    
+
+    size: int = Field(default=1, description="Size of the jitter points.", gt=0)
+
     order: Optional[List[str]] = Field(
-        default=None,
-        description="Order in which to show the categories."
+        default=None, description="Order in which to show the categories."
     )
-    
-    scale: Literal['area', 'count', 'width'] = Field(
-        default='width',
-        description="The method used to scale the width of each violin."
+
+    scale: Literal["area", "count", "width"] = Field(
+        default="width",
+        description="The method used to scale the width of each violin.",
     )
-    
+
     swap_axes: bool = Field(
-        default=False,
-        description="Swap axes such that observations are on the x-axis."
+        default=False, description="Swap axes such that observations are on the x-axis."
     )
-    
-    @field_validator('size')
+
+    @field_validator("size")
     def validate_size(cls, v: int) -> int:
         """Validate size is positive"""
         if v <= 0:
@@ -688,62 +604,58 @@ class StackedViolinParams(BaseStatPlotParams):
         return v
 
 
-# 重构 TrackingParams
-class TrackingParams(BaseVisualizationParams):
+# 重构 TrackingParam
+class TrackingParam(BaseVisualizationParam):
     """Input schema for the tracking plotting tool."""
-    
+
     groupby: str = Field(
         ...,  # Required field
-        description="The key of the observation grouping to consider."
+        description="The key of the observation grouping to consider.",
     )
-    
+
     min_group_size: int = Field(
         default=1,
         description="Minimal number of cells in a group for the group to be considered.",
-        gt=0
+        gt=0,
     )
-    
+
     min_split_size: int = Field(
         default=1,
         description="Minimal number of cells in a split for the split to be shown.",
-        gt=0
+        gt=0,
     )
-    
-    @field_validator('min_group_size', 'min_split_size')
+
+    @field_validator("min_group_size", "min_split_size")
     def validate_positive_int(cls, v: int) -> int:
         """Validate positive integers"""
         if v <= 0:
-            raise ValueError(f"Value must be a positive integer")
+            raise ValueError("Value must be a positive integer")
         return v
 
 
-# 重构 EmbeddingDensityParams
-class EmbeddingDensityParams(BaseEmbeddingParams):
+# 重构 EmbeddingDensityParam
+class EmbeddingDensityParam(BaseEmbeddingParam):
     """Input schema for the embedding_density plotting tool."""
-    
+
     basis: str = Field(
         ...,  # Required field
-        description="Basis to use for embedding."
+        description="Basis to use for embedding.",
     )
-    
+
     key: Optional[str] = Field(
         default=None,
-        description="Key for annotation of observations/cells or variables/genes."
+        description="Key for annotation of observations/cells or variables/genes.",
     )
-    
+
     convolve: Optional[float] = Field(
-        default=None,
-        description="Sigma for Gaussian kernel used for convolution."
+        default=None, description="Sigma for Gaussian kernel used for convolution."
     )
-    
+
     alpha: float = Field(
-        default=0.5,
-        description="Alpha value for the plot.",
-        ge=0,
-        le=1
+        default=0.5, description="Alpha value for the plot.", ge=0, le=1
     )
-    
-    @field_validator('alpha')
+
+    @field_validator("alpha")
     def validate_alpha(cls, v: float) -> float:
         """Validate alpha is between 0 and 1"""
         if v < 0 or v > 1:
@@ -751,51 +663,48 @@ class EmbeddingDensityParams(BaseEmbeddingParams):
         return v
 
 
-class PCAParams(BaseEmbeddingParams):
+class PCAParam(BaseEmbeddingParam):
     """Input schema for the PCA plotting tool."""
-    
+
     annotate_var_explained: bool = Field(
-        default=False,
-        description="Annotate the explained variance."
+        default=False, description="Annotate the explained variance."
     )
 
 
 # 重构 UMAP 模型
-class UMAPParams(BaseEmbeddingParams):
+class UMAPParam(BaseEmbeddingParam):
     """Input schema for the UMAP plotting tool."""
-    # 所有需要的字段已经在 BaseEmbeddingParams 中定义
+
+    # 所有需要的字段已经在 BaseEmbeddingParam 中定义
 
 
 # 重构 TSNE 模型
-class TSNEParams(BaseEmbeddingParams):
+class TSNEParam(BaseEmbeddingParam):
     """Input schema for the TSNE plotting tool."""
-    # 所有需要的字段已经在 BaseEmbeddingParams 中定义
 
-# 重构 DiffusionMapParams
-class DiffusionMapParams(BaseEmbeddingParams):
+    # 所有需要的字段已经在 BaseEmbeddingParam 中定义
+
+
+# 重构 DiffusionMapParam
+class DiffusionMapParam(BaseEmbeddingParam):
     """Input schema for the diffusion map plotting tool."""
-    # 所有需要的字段已经在 BaseEmbeddingParams 中定义
 
-class HighestExprGenesParams(BaseVisualizationParams):
+    # 所有需要的字段已经在 BaseEmbeddingParam 中定义
+
+
+class HighestExprGenesParam(BaseVisualizationParam):
     """Input schema for the highest_expr_genes plotting tool."""
-    
-    n_top: int = Field(
-        default=30,
-        description="Number of top genes to plot.",
-        gt=0
-    )
-    
+
+    n_top: int = Field(default=30, description="Number of top genes to plot.", gt=0)
+
     gene_symbols: Optional[str] = Field(
         default=None,
-        description="Key for field in .var that stores gene symbols if you do not want to use .var_names."
-    )
-    
-    log: bool = Field(
-        default=False,
-        description="Plot x-axis in log scale."
+        description="Key for field in .var that stores gene symbols if you do not want to use .var_names.",
     )
-    
-    @field_validator('n_top')
+
+    log: bool = Field(default=False, description="Plot x-axis in log scale.")
+
+    @field_validator("n_top")
     def validate_n_top(cls, v: int) -> int:
         """Validate n_top is positive"""
         if v <= 0:
@@ -803,145 +712,132 @@ class HighestExprGenesParams(BaseVisualizationParams):
         return v
 
 
-class HighlyVariableGenesParams(BaseVisualizationParams):
+class HighlyVariableGenesParam(BaseVisualizationParam):
     """Input schema for the highly_variable_genes plotting tool."""
-    
-    log: bool = Field(
-        default=False,
-        description="Plot on logarithmic axes."
-    )
-    
+
+    log: bool = Field(default=False, description="Plot on logarithmic axes.")
+
     highly_variable_genes: bool = Field(
-        default=True,
-        description="Whether to plot highly variable genes or all genes."
+        default=True, description="Whether to plot highly variable genes or all genes."
     )
 
-class PCAVarianceRatioParams(BaseVisualizationParams):
+
+class PCAVarianceRatioParam(BaseVisualizationParam):
     """Input schema for the pca_variance_ratio plotting tool."""
-    
-    n_pcs: int = Field(
-        default=30,
-        description="Number of PCs to show.",
-        gt=0
-    )
-    
-    log: bool = Field(
-        default=False,
-        description="Plot on logarithmic scale."
-    )
-    
-    @field_validator('n_pcs')
+
+    n_pcs: int = Field(default=30, description="Number of PCs to show.", gt=0)
+
+    log: bool = Field(default=False, description="Plot on logarithmic scale.")
+
+    @field_validator("n_pcs")
     def validate_n_pcs(cls, v: int) -> int:
         """Validate n_pcs is positive"""
         if v <= 0:
             raise ValueError("n_pcs must be a positive integer")
         return v
 
+
 # ... existing code ...
 
-class RankGenesGroupsDotplotParams(BaseMatrixParams):
+
+class RankGenesGroupsDotplotParam(BaseMatrixParam):
     """Input schema for the rank_genes_groups_dotplot plotting tool."""
-    
+
     groups: Optional[Union[str, List[str]]] = Field(
-        default=None,
-        description="The groups for which to show the gene ranking."
-    )    
+        default=None, description="The groups for which to show the gene ranking."
+    )
     n_genes: Optional[int] = Field(
         default=None,
-        description="Number of genes to show. This can be a negative number to show down regulated genes. Ignored if var_names is passed."
+        description="Number of genes to show. This can be a negative number to show down regulated genes. Ignored if var_names is passed.",
     )
-    values_to_plot: Optional[Literal['scores', 'logfoldchanges', 'pvals', 'pvals_adj', 'log10_pvals', 'log10_pvals_adj']] = Field(
+    values_to_plot: Optional[
+        Literal[
+            "scores",
+            "logfoldchanges",
+            "pvals",
+            "pvals_adj",
+            "log10_pvals",
+            "log10_pvals_adj",
+        ]
+    ] = Field(
         default=None,
-        description="Instead of the mean gene value, plot the values computed by sc.rank_genes_groups."
+        description="Instead of the mean gene value, plot the values computed by sc.rank_genes_groups.",
     )
     min_logfoldchange: Optional[float] = Field(
         default=None,
-        description="Value to filter genes in groups if their logfoldchange is less than the min_logfoldchange."
+        description="Value to filter genes in groups if their logfoldchange is less than the min_logfoldchange.",
     )
     key: Optional[str] = Field(
-        default=None,
-        description="Key used to store the ranking results in adata.uns."
+        default=None, description="Key used to store the ranking results in adata.uns."
     )
     var_names: Union[List[str], Mapping[str, List[str]]] = Field(
         default=None,
-        description="Genes to plot. Sometimes is useful to pass a specific list of var names (e.g. genes) to check their fold changes or p-values"
-    )        
-    @field_validator('n_genes')
+        description="Genes to plot. Sometimes is useful to pass a specific list of var names (e.g. genes) to check their fold changes or p-values",
+    )
+
+    @field_validator("n_genes")
     def validate_n_genes(cls, v: Optional[int]) -> Optional[int]:
         """Validate n_genes"""
         # n_genes can be positive or negative, so no validation needed
         return v
 
 
-
-class EmbeddingParams(BaseEmbeddingParams):
+class EmbeddingParam(BaseEmbeddingParam):
     """Input schema for the embedding plotting tool."""
-    
+
     basis: str = Field(
         ...,  # Required field
-        description="Name of the obsm basis to use."
+        description="Name of the obsm basis to use.",
     )
     use_obsm: str = Field(
-        default=None,
-        description="using data of adata.obsm instead of adata.X"
+        default=None, description="using data of adata.obsm instead of adata.X"
     )
     mask_obs: Optional[str] = Field(
         default=None,
-        description="A boolean array or a string mask expression to subset observations."
+        description="A boolean array or a string mask expression to subset observations.",
     )
-    
+
     arrows_kwds: Optional[dict] = Field(
         default=None,
-        description="Passed to matplotlib's quiver function for drawing arrows."
+        description="Passed to matplotlib's quiver function for drawing arrows.",
     )
-    
+
     scale_factor: Optional[float] = Field(
-        default=None,
-        description="Scale factor for the plot."
+        default=None, description="Scale factor for the plot."
     )
-    
+
     cmap: Optional[str] = Field(
         default=None,
-        description="Color map to use for continuous variables. Overrides color_map."
+        description="Color map to use for continuous variables. Overrides color_map.",
     )
-    
+
     na_color: str = Field(
-        default="lightgray",
-        description="Color to use for null or masked values."
+        default="lightgray", description="Color to use for null or masked values."
     )
-    
+
     na_in_legend: bool = Field(
-        default=True,
-        description="Whether to include null values in the legend."
+        default=True, description="Whether to include null values in the legend."
     )
-    
+
     outline_width: Tuple[float, float] = Field(
-        default=(0.3, 0.05),
-        description="Width of the outline for highlighted points."
+        default=(0.3, 0.05), description="Width of the outline for highlighted points."
     )
-    
+
     outline_color: Tuple[str, str] = Field(
         default=("black", "white"),
-        description="Color of the outline for highlighted points."
+        description="Color of the outline for highlighted points.",
     )
-    
+
     colorbar_loc: Optional[str] = Field(
-        default="right",
-        description="Location of the colorbar."
+        default="right", description="Location of the colorbar."
     )
-    
-    hspace: float = Field(
-        default=0.25,
-        description="Height space between panels."
-    )
-    
+
+    hspace: float = Field(default=0.25, description="Height space between panels.")
+
     wspace: Optional[float] = Field(
-        default=None,
-        description="Width space between panels."
+        default=None, description="Width space between panels."
     )
-    
+
     title: Optional[Union[str, List[str]]] = Field(
-        default=None,
-        description="Title for the plot."
+        default=None, description="Title for the plot."
     )
-