bio-analyze-plot 0.1.0a0__py3-none-any.whl

bio_analyze_plot/__init__.py

@@ -0,0 +1,35 @@
+"""
+zh: 生物信息学绘图工具包。
+en: Bioinformatics plotting toolkit.
+"""
+
+from .plots import (
+    BarPlot,
+    BasePlot,
+    BoxPlot,
+    ChromosomePlot,
+    GSEAPlot,
+    HeatmapPlot,
+    LinePlot,
+    PCAPlot,
+    PiePlot,
+    ScatterPlot,
+    VolcanoPlot,
+)
+from .theme import PlotTheme, set_theme
+
+__all__ = [
+    "BarPlot",
+    "BasePlot",
+    "BoxPlot",
+    "ChromosomePlot",
+    "GSEAPlot",
+    "HeatmapPlot",
+    "LinePlot",
+    "PCAPlot",
+    "PiePlot",
+    "ScatterPlot",
+    "VolcanoPlot",
+    "PlotTheme",
+    "set_theme",
+]

bio_analyze_plot/cli.py

@@ -0,0 +1,578 @@
+from __future__ import annotations
+
+from pathlib import Path
+
+import pandas as pd
+import typer
+
+from bio_analyze_core.cli_i18n import detect_language, localize_app
+
+from .plots.bar import BarPlot
+from .plots.box import BoxPlot
+from .plots.chromosome import ChromosomePlot
+from .plots.gsea import GSEAPlot
+from .plots.heatmap import HeatmapPlot
+from .plots.line import LinePlot
+from .plots.pca import PCAPlot
+from .plots.pie import PiePlot
+from .plots.scatter import ScatterPlot
+from .plots.volcano import VolcanoPlot
+
+
+def read_data(input_path: Path, sheet: str | None = None) -> pd.DataFrame:
+    """
+    zh: 从 CSV、TSV 或 Excel 文件读取数据。
+    en: Read data from CSV, TSV, or Excel file.
+
+    Args:
+        input_path (Path):
+            zh: 输入文件路径
+            en: Input file path
+        sheet (str | None, optional):
+            zh: Excel 工作表名称
+            en: Excel sheet name
+
+    Returns:
+        pd.DataFrame:
+            zh: 读取的数据
+            en: Loaded data
+    """
+    suffix = input_path.suffix.lower()
+    if suffix in [".csv"]:
+        return pd.read_csv(input_path)
+    elif suffix in [".tsv", ".txt"]:
+        return pd.read_csv(input_path, sep="\t")
+    elif suffix in [".xlsx", ".xls"]:
+        if sheet:
+            return pd.read_excel(input_path, sheet_name=sheet)
+        return pd.read_excel(input_path)
+    else:
+        # 默认为 csv
+        return pd.read_csv(input_path)
+
+
+def get_app() -> typer.Typer:
+    app = typer.Typer(help="zh: 绘图工具\nen: Publication-ready plotting tools.")
+
+    @app.command("volcano")
+    def _volcano(
+        input_file: Path = typer.Argument(
+            ..., help="zh: 输入文件路径 (CSV, TSV 或 Excel)。\nen: Input file path (CSV, TSV, or Excel)."
+        ),
+        output: Path = typer.Option(
+            ...,
+            "-o",
+            "--output",
+            help="zh: 输出文件路径 (例如 volcano.png)。\nen: Output file path (e.g. volcano.png).",
+        ),
+        x: str = typer.Option(
+            "log2FoldChange", help="zh: log2 fold change 列名。\nen: Column name for log2 fold change."
+        ),
+        y: str = typer.Option("pvalue", help="zh: p-value 列名。\nen: Column name for p-value."),
+        theme: str = typer.Option(
+            "nature",
+            help="zh: 绘图主题 (nature, science, default) 或自定义主题路径 (.json/.py)。\nen: Plot theme (nature, science, default) or path to custom theme (.json/.py).",
+        ),
+        fc_cutoff: float = typer.Option(1.0, help="zh: Fold change 截断值。\nen: Fold change cutoff."),
+        p_cutoff: float = typer.Option(0.05, help="zh: P-value 截断值。\nen: P-value cutoff."),
+        title: str = typer.Option(None, help="zh: 图表标题。\nen: Plot title."),
+        sheet: str = typer.Option(None, help="zh: Excel 工作表名称。\nen: Sheet name for Excel files."),
+    ) -> None:
+        """
+        zh: 从数据生成火山图。
+        en: Generate volcano plot from data.
+        """
+        df = read_data(input_file, sheet=sheet)
+        plotter = VolcanoPlot(theme=theme)
+        plotter.plot(
+            data=df,
+            x=x,
+            y=y,
+            fc_cutoff=fc_cutoff,
+            p_cutoff=p_cutoff,
+            title=title,
+            output=str(output),
+        )
+        typer.echo(f"Saved volcano plot to {output}")
+
+    @app.command("line")
+    def _line(
+        input_file: Path = typer.Argument(
+            ..., help="zh: 输入文件路径 (CSV, TSV 或 Excel)。\nen: Input file path (CSV, TSV, or Excel)."
+        ),
+        output: Path = typer.Option(..., "-o", "--output", help="zh: 输出文件路径。\nen: Output file path."),
+        x: str = typer.Option(..., help="zh: X 轴列名。\nen: Column name for X-axis."),
+        y: str = typer.Option(..., help="zh: Y 轴列名。\nen: Column name for Y-axis."),
+        hue: str = typer.Option(None, help="zh: 分组列名 (hue)。\nen: Grouping column name (hue)."),
+        theme: str = typer.Option(
+            "nature",
+            help="zh: 绘图主题 (nature, science, default) 或自定义主题路径 (.json/.py)。\nen: Plot theme (nature, science, default) or path to custom theme (.json/.py).",
+        ),
+        title: str = typer.Option(None, help="zh: 图表标题。\nen: Plot title."),
+        sheet: str = typer.Option(None, help="zh: Excel 工作表名称。\nen: Sheet name for Excel files."),
+        error_bar_type: str = typer.Option(None, help="zh: 误差棒类型: SD, SE, CI。\nen: Error bar type: SD, SE, CI."),
+        error_bar_ci: float = typer.Option(
+            95, help="zh: 置信区间大小 (默认: 95)。\nen: Confidence interval size (default: 95)."
+        ),
+        error_bar_capsize: float = typer.Option(
+            3.0, help="zh: 误差棒帽大小 (以点为单位)。\nen: Error bar capsize (in points)."
+        ),
+        markers: bool = typer.Option(
+            False, help="zh: 为数据点使用默认标记。\nen: Use default markers for data points."
+        ),
+        marker_style: str = typer.Option(
+            None,
+            help="zh: 指定标记符号 (逗号分隔, 例如 'o,s')。覆盖 --markers。\nen: Specific marker symbols (comma-separated, e.g. 'o,s'). Overrides --markers.",
+        ),
+        dashes: bool = typer.Option(True, help="zh: 为线条使用虚线样式。\nen: Use dashes for lines."),
+        smooth: bool = typer.Option(False, help="zh: 启用平滑曲线拟合。\nen: Enable smooth curve fitting."),
+        smooth_points: int = typer.Option(300, help="zh: 插值点数。\nen: Number of points for interpolation."),
+    ) -> None:
+        """
+        zh: 生成折线图。
+        en: Generate line plot.
+        """
+        df = read_data(input_file, sheet=sheet)
+
+        # Parse markers
+        markers_arg = markers
+        if marker_style:
+            if "," in marker_style:
+                markers_arg = [m.strip() for m in marker_style.split(",")]
+            else:
+                markers_arg = marker_style
+
+        plotter = LinePlot(theme=theme)
+        plotter.plot(
+            data=df,
+            x=x,
+            y=y,
+            hue=hue,
+            title=title,
+            output=str(output),
+            error_bar_type=error_bar_type,
+            error_bar_ci=error_bar_ci,
+            error_bar_capsize=error_bar_capsize,
+            markers=markers_arg,
+            dashes=dashes,
+            smooth=smooth,
+            smooth_points=smooth_points,
+        )
+        typer.echo(f"Saved line plot to {output}")
+
+    @app.command("bar")
+    def _bar(
+        input_file: Path = typer.Argument(
+            ..., help="zh: 输入文件路径 (CSV, TSV 或 Excel)。\nen: Input file path (CSV, TSV, or Excel)."
+        ),
+        output: Path = typer.Option(..., "-o", "--output", help="zh: 输出文件路径。\nen: Output file path."),
+        x: str = typer.Option(..., help="zh: X 轴列名。\nen: Column name for X-axis."),
+        y: str = typer.Option(..., help="zh: Y 轴列名。\nen: Column name for Y-axis."),
+        hue: str = typer.Option(None, help="zh: 分组列名 (hue)。\nen: Grouping column name (hue)."),
+        theme: str = typer.Option(
+            "nature",
+            help="zh: 绘图主题 (nature, science, default) 或自定义主题路径 (.json/.py)。\nen: Plot theme (nature, science, default) or path to custom theme (.json/.py).",
+        ),
+        title: str = typer.Option(None, help="zh: 图表标题。\nen: Plot title."),
+        error_bar_type: str = typer.Option(None, help="zh: 误差棒类型: SD, SE, CI。\nen: Error bar type: SD, SE, CI."),
+        error_bar_ci: float = typer.Option(
+            95, help="zh: 置信区间大小 (默认: 95)。\nen: Confidence interval size (default: 95)."
+        ),
+        error_bar_max: str = typer.Option(
+            None, help="zh: 误差棒上限列名。\nen: Column name for error bar upper limit."
+        ),
+        error_bar_min: str = typer.Option(
+            None, help="zh: 误差棒下限列名。\nen: Column name for error bar lower limit."
+        ),
+        error_bar_capsize: float = typer.Option(0.1, help="zh: 误差棒帽大小。\nen: Error bar capsize."),
+        significance: list[str] = typer.Option(
+            None, help="zh: 显著性检验配对 (例如 'A,B' 'C,D')。\nen: Pairs for significance testing (e.g. 'A,B' 'C,D')."
+        ),
+        test: str = typer.Option("t-test_ind", help="zh: 统计检验方法。\nen: Statistical test method."),
+        text_format: str = typer.Option("star", help="zh: 显著性标注格式。\nen: Significance annotation format."),
+        sheet: str = typer.Option(None, help="zh: Excel 工作表名称。\nen: Sheet name for Excel files."),
+    ) -> None:
+        """
+        zh: 生成柱状图。
+        en: Generate bar plot.
+        """
+        df = read_data(input_file, sheet=sheet)
+
+        # 解析显著性对
+        sig_pairs = []
+        if significance:
+            for pair_str in significance:
+                parts = pair_str.split(",")
+                if len(parts) == 2:
+                    sig_pairs.append((parts[0].strip(), parts[1].strip()))
+
+        plotter = BarPlot(theme=theme)
+        plotter.plot(
+            data=df,
+            x=x,
+            y=y,
+            hue=hue,
+            title=title,
+            output=str(output),
+            error_bar_type=error_bar_type,
+            error_bar_ci=error_bar_ci,
+            error_bar_max=error_bar_max,
+            error_bar_min=error_bar_min,
+            error_bar_capsize=error_bar_capsize,
+            significance=sig_pairs if sig_pairs else None,
+            test=test,
+            text_format=text_format,
+        )
+        typer.echo(f"Saved bar plot to {output}")
+
+    @app.command("box")
+    def _box(
+        input_file: Path = typer.Argument(
+            ..., help="zh: 输入文件路径 (CSV, TSV 或 Excel)。\nen: Input file path (CSV, TSV, or Excel)."
+        ),
+        output: Path = typer.Option(..., "-o", "--output", help="zh: 输出文件路径。\nen: Output file path."),
+        x: str = typer.Option(..., help="zh: X 轴列名。\nen: Column name for X-axis."),
+        y: str = typer.Option(..., help="zh: Y 轴列名。\nen: Column name for Y-axis."),
+        hue: str = typer.Option(None, help="zh: 分组列名 (hue)。\nen: Grouping column name (hue)."),
+        theme: str = typer.Option(
+            "nature",
+            help="zh: 绘图主题 (nature, science, default) 或自定义主题路径 (.json/.py)。\nen: Plot theme (nature, science, default) or path to custom theme (.json/.py).",
+        ),
+        title: str = typer.Option(None, help="zh: 图表标题。\nen: Plot title."),
+        significance: list[str] = typer.Option(
+            None, help="zh: 显著性检验配对 (例如 'A,B' 'C,D')。\nen: Pairs for significance testing (e.g. 'A,B' 'C,D')."
+        ),
+        test: str = typer.Option("t-test_ind", help="zh: 统计检验方法。\nen: Statistical test method."),
+        text_format: str = typer.Option("star", help="zh: 显著性标注格式。\nen: Significance annotation format."),
+        add_swarm: bool = typer.Option(False, help="zh: 叠加蜂群图点。\nen: Overlay swarmplot points."),
+        swarm_color: str = typer.Option(".25", help="zh: 蜂群图点颜色。\nen: Swarmplot point color."),
+        swarm_size: float = typer.Option(3.0, help="zh: 蜂群图点大小。\nen: Swarmplot point size."),
+        sheet: str = typer.Option(None, help="zh: Excel 工作表名称。\nen: Sheet name for Excel files."),
+    ) -> None:
+        """
+        zh: 生成箱线图。
+        en: Generate box plot.
+        """
+        df = read_data(input_file, sheet=sheet)
+
+        # 解析显著性对
+        sig_pairs = []
+        if significance:
+            for pair_str in significance:
+                parts = pair_str.split(",")
+                if len(parts) == 2:
+                    sig_pairs.append((parts[0].strip(), parts[1].strip()))
+
+        plotter = BoxPlot(theme=theme)
+        plotter.plot(
+            data=df,
+            x=x,
+            y=y,
+            hue=hue,
+            title=title,
+            output=str(output),
+            significance=sig_pairs if sig_pairs else None,
+            test=test,
+            text_format=text_format,
+            add_swarm=add_swarm,
+            swarm_color=swarm_color,
+            swarm_size=swarm_size,
+        )
+        typer.echo(f"Saved box plot to {output}")
+
+    @app.command("heatmap")
+    def _heatmap(
+        input_file: Path = typer.Argument(
+            ..., help="zh: 输入文件路径 (CSV, TSV 或 Excel)。\nen: Input file path (CSV, TSV, or Excel)."
+        ),
+        output: Path = typer.Option(..., "-o", "--output", help="zh: 输出文件路径。\nen: Output file path."),
+        index_col: str = typer.Option(None, help="zh: 用作行索引的列。\nen: Column to use as row index."),
+        cluster_rows: bool = typer.Option(True, help="zh: 是否聚类行。\nen: Whether to cluster rows."),
+        cluster_cols: bool = typer.Option(True, help="zh: 是否聚类列。\nen: Whether to cluster columns."),
+        z_score: int = typer.Option(
+            None,
+            help="zh: 标准化 (0: 行, 1: 列)。None 禁用。\nen: 0 (rows) or 1 (columns) for standardization. None to disable.",
+        ),
+        cmap: str = typer.Option(
+            None, help="zh: 颜色映射名称 (例如 'vlag', 'coolwarm')。\nen: Colormap name (e.g. 'vlag', 'coolwarm')."
+        ),
+        center: float = typer.Option(None, help="zh: 颜色映射居中的值。\nen: Value at which to center the colormap."),
+        theme: str = typer.Option(
+            "nature",
+            help="zh: 绘图主题 (nature, science, default) 或自定义主题路径 (.json/.py)。\nen: Plot theme (nature, science, default) or path to custom theme (.json/.py).",
+        ),
+        title: str = typer.Option(None, help="zh: 图表标题。\nen: Plot title."),
+        sheet: str = typer.Option(None, help="zh: Excel 工作表名称。\nen: Sheet name for Excel files."),
+    ) -> None:
+        """
+        zh: 生成热图/聚类图。
+        en: Generate heatmap/clustermap.
+        """
+        df = read_data(input_file, sheet=sheet)
+
+        # 准备传递给 plot 的 kwargs，过滤掉 None 的值以允许使用默认值/主题值
+        kwargs = {}
+        if cmap is not None:
+            kwargs["cmap"] = cmap
+        if center is not None:
+            kwargs["center"] = center
+
+        plotter = HeatmapPlot(theme=theme)
+        plotter.plot(
+            data=df,
+            index_col=index_col,
+            cluster_rows=cluster_rows,
+            cluster_cols=cluster_cols,
+            z_score=z_score,
+            title=title,
+            output=str(output),
+            **kwargs,
+        )
+        typer.echo(f"Saved heatmap to {output}")
+
+    @app.command("pca")
+    def _pca(
+        input_file: Path = typer.Argument(
+            ..., help="zh: 输入文件路径 (CSV, TSV 或 Excel)。\nen: Input file path (CSV, TSV, or Excel)."
+        ),
+        output: Path = typer.Option(..., "-o", "--output", help="zh: 输出文件路径。\nen: Output file path."),
+        hue: str = typer.Option(None, help="zh: 分组列名 (hue)。\nen: Grouping column name (hue)."),
+        style: str = typer.Option(None, help="zh: 标记样式列名。\nen: Column name for marker style."),
+        size: str = typer.Option(None, help="zh: 标记大小列名。\nen: Column name for marker size."),
+        index_col: str = typer.Option(
+            None, help="zh: 用作索引的列 (例如基因名)。\nen: Column to use as index (e.g. gene names)."
+        ),
+        transpose: bool = typer.Option(
+            True,
+            help="zh: 转置输入数据 (默认: True, 假设 Genes x Samples)。\nen: Transpose input data (default: True, assumes Genes x Samples).",
+        ),
+        theme: str = typer.Option(
+            "nature",
+            help="zh: 绘图主题 (nature, science, default) 或自定义主题路径 (.json/.py)。\nen: Plot theme (nature, science, default) or path to custom theme (.json/.py).",
+        ),
+        title: str = typer.Option(None, help="zh: 图表标题。\nen: Plot title."),
+        cluster: bool = typer.Option(False, help="zh: 执行 KMeans 聚类。\nen: Perform KMeans clustering."),
+        n_clusters: int = typer.Option(3, help="zh: KMeans 聚类的簇数。\nen: Number of clusters for KMeans."),
+        add_ellipse: bool = typer.Option(
+            False, help="zh: 为每个分组绘制置信椭圆。\nen: Draw confidence ellipses for each group."
+        ),
+        ellipse_std: float = typer.Option(
+            2.0, help="zh: 置信椭圆的标准差。\nen: Standard deviation for confidence ellipses."
+        ),
+        sheet: str = typer.Option(None, help="zh: Excel 工作表名称。\nen: Sheet name for Excel files."),
+    ) -> None:
+        """
+        zh: 生成 PCA 图。
+        en: Generate PCA plot.
+        """
+        df = read_data(input_file, sheet=sheet)
+        plotter = PCAPlot(theme=theme)
+        plotter.plot(
+            data=df,
+            hue=hue,
+            style=style,
+            size=size,
+            index_col=index_col,
+            transpose=transpose,
+            title=title,
+            cluster=cluster,
+            n_clusters=n_clusters,
+            add_ellipse=add_ellipse,
+            ellipse_std=ellipse_std,
+            output=str(output),
+        )
+        typer.echo(f"Saved PCA plot to {output}")
+
+    @app.command("scatter")
+    def _scatter(
+        input_file: Path = typer.Argument(
+            ..., help="zh: 输入文件路径 (CSV, TSV 或 Excel)。\nen: Input file path (CSV, TSV, or Excel)."
+        ),
+        output: Path = typer.Option(..., "-o", "--output", help="zh: 输出文件路径。\nen: Output file path."),
+        x: str = typer.Option(..., help="zh: X 轴列名。\nen: Column name for X-axis."),
+        y: str = typer.Option(..., help="zh: Y 轴列名。\nen: Column name for Y-axis."),
+        hue: str = typer.Option(None, help="zh: 分组列名 (hue)。\nen: Grouping column name (hue)."),
+        style: str = typer.Option(None, help="zh: 标记样式列名。\nen: Column name for marker style."),
+        size: str = typer.Option(None, help="zh: 标记大小列名。\nen: Column name for marker size."),
+        theme: str = typer.Option(
+            "nature",
+            help="zh: 绘图主题 (nature, science, default) 或自定义主题路径 (.json/.py)。\nen: Plot theme (nature, science, default) or path to custom theme (.json/.py).",
+        ),
+        title: str = typer.Option(None, help="zh: 图表标题。\nen: Plot title."),
+        add_ellipse: bool = typer.Option(
+            False, help="zh: 为每个分组绘制置信椭圆。\nen: Draw confidence ellipses for each group."
+        ),
+        ellipse_std: float = typer.Option(
+            2.0, help="zh: 置信椭圆的标准差。\nen: Standard deviation for confidence ellipses."
+        ),
+        sheet: str = typer.Option(None, help="zh: Excel 工作表名称。\nen: Sheet name for Excel files."),
+    ) -> None:
+        """
+        zh: 生成散点图。
+        en: Generate scatter plot.
+        """
+        df = read_data(input_file, sheet=sheet)
+        plotter = ScatterPlot(theme=theme)
+        plotter.plot(
+            data=df,
+            x=x,
+            y=y,
+            hue=hue,
+            style=style,
+            size=size,
+            title=title,
+            output=str(output),
+            add_ellipse=add_ellipse,
+            ellipse_std=ellipse_std,
+        )
+        typer.echo(f"Saved scatter plot to {output}")
+
+    @app.command("pie")
+    def _pie(
+        input_file: Path = typer.Argument(
+            ..., help="zh: 输入文件路径 (CSV, TSV 或 Excel)。\nen: Input file path (CSV, TSV, or Excel)."
+        ),
+        output: Path = typer.Option(..., "-o", "--output", help="zh: 输出文件路径。\nen: Output file path."),
+        x: str = typer.Option(..., help="zh: 标签列名 (分类变量)。\nen: Column name for labels (categorical)."),
+        y: str = typer.Option(..., help="zh: 数值列名。\nen: Column name for values (numerical)."),
+        theme: str = typer.Option(
+            "nature",
+            help="zh: 绘图主题 (nature, science, default) 或自定义主题路径 (.json/.py)。\nen: Plot theme (nature, science, default) or path to custom theme (.json/.py).",
+        ),
+        title: str = typer.Option(None, help="zh: 图表标题。\nen: Plot title."),
+        autopct: str = typer.Option("%1.1f%%", help="zh: 百分比格式。\nen: Percentage format."),
+        startangle: float = typer.Option(90, help="zh: 起始角度。\nen: Start angle."),
+        explode: str = typer.Option(
+            None,
+            help="zh: 扇区偏移。可以是列名或逗号分隔的数值。\nen: Explode slices. Can be a column name or comma-separated values.",
+        ),
+        shadow: bool = typer.Option(False, help="zh: 显示阴影。\nen: Show shadow."),
+        sheet: str = typer.Option(None, help="zh: Excel 工作表名称。\nen: Sheet name for Excel files."),
+    ) -> None:
+        """
+        zh: 生成饼图。
+        en: Generate pie chart.
+        """
+        df = read_data(input_file, sheet=sheet)
+
+        explode_arg = None
+        if explode:
+            if explode in df.columns:
+                explode_arg = explode
+            else:
+                try:
+                    explode_arg = [float(v.strip()) for v in explode.split(",")]
+                except ValueError:
+                    explode_arg = None
+                    typer.echo(f"Warning: Invalid explode format '{explode}'. Ignored.")
+
+        plotter = PiePlot(theme=theme)
+        plotter.plot(
+            data=df,
+            x=x,
+            y=y,
+            title=title,
+            autopct=autopct,
+            startangle=startangle,
+            explode=explode_arg,
+            shadow=shadow,
+            output=str(output),
+        )
+        typer.echo(f"Saved pie chart to {output}")
+
+    @app.command("gsea")
+    def _gsea(
+        input_file: Path = typer.Argument(
+            ..., help="zh: 输入文件路径 (CSV, TSV 或 Excel)。\nen: Input file path (CSV, TSV, or Excel)."
+        ),
+        output: Path = typer.Option(..., "-o", "--output", help="zh: 输出文件路径。\nen: Output file path."),
+        rank: str = typer.Option("rank", help="zh: 排名列名 (X 轴)。\nen: Column name for rank (x-axis)."),
+        score: str = typer.Option(
+            "running_es", help="zh: 运行富集得分列名 (Y 轴)。\nen: Column name for running ES (y-axis)."
+        ),
+        hit: str = typer.Option(
+            "hit", help="zh: 命中状态列名 (0/1 或布尔值)。\nen: Column name for hit status (0/1 or boolean)."
+        ),
+        metric: str = typer.Option(
+            None, help="zh: 排名指标列名 (Y 轴底部)。\nen: Column name for ranking metric (y-axis bottom)."
+        ),
+        theme: str = typer.Option(
+            "nature",
+            help="zh: 绘图主题 (nature, science, default) 或自定义主题路径 (.json/.py)。\nen: Plot theme (nature, science, default) or path to custom theme (.json/.py).",
+        ),
+        title: str = typer.Option(None, help="zh: 图表标题。\nen: Plot title."),
+        sheet: str = typer.Option(None, help="zh: Excel 工作表名称。\nen: Sheet name for Excel files."),
+        color: str = typer.Option("#4DAF4A", help="zh: 富集得分曲线颜色。\nen: Color for enrichment score line."),
+        hit_color: str = typer.Option("black", help="zh: 命中线条颜色。\nen: Color for hit lines."),
+        nes: float = typer.Option(None, help="zh: 标准化富集得分 (NES)。\nen: Normalized Enrichment Score."),
+        pvalue: float = typer.Option(None, help="zh: P-value。\nen: P-value."),
+        fdr: float = typer.Option(None, help="zh: FDR q-value。\nen: FDR q-value."),
+        show_border: bool = typer.Option(True, help="zh: 显示顶部和右侧边框。\nen: Show top and right borders."),
+    ) -> None:
+        """
+        zh: 生成 GSEA 富集图。
+        en: Generate GSEA enrichment plot.
+        """
+        df = read_data(input_file, sheet=sheet)
+        plotter = GSEAPlot(theme=theme)
+        plotter.plot(
+            data=df,
+            rank=rank,
+            score=score,
+            hit=hit,
+            metric=metric,
+            title=title,
+            output=str(output),
+            color=color,
+            hit_color=hit_color,
+            nes=nes,
+            pvalue=pvalue,
+            fdr=fdr,
+            show_border=show_border,
+        )
+        typer.echo(f"Saved GSEA plot to {output}")
+
+    @app.command("chromosome")
+    def _chromosome(
+        input_file: Path = typer.Argument(
+            ..., help="zh: 输入文件路径 (CSV, TSV 或 Excel)。\nen: Input file path (CSV, TSV, or Excel)."
+        ),
+        output: Path = typer.Option(..., "-o", "--output", help="zh: 输出文件路径。\nen: Output file path."),
+        chrom_col: str = typer.Option("chrom", help="zh: 染色体列名。\nen: Column name for chromosome."),
+        pos_col: str = typer.Option("pos", help="zh: 位置列名。\nen: Column name for position."),
+        pos_counts_col: str = typer.Option(
+            "pos_counts", help="zh: 正链计数列名。\nen: Column name for positive strand counts."
+        ),
+        neg_counts_col: str = typer.Option(
+            "neg_counts", help="zh: 负链计数列名。\nen: Column name for negative strand counts."
+        ),
+        theme: str = typer.Option(
+            "nature",
+            help="zh: 绘图主题 (nature, science, default) 或自定义主题路径 (.json/.py)。\nen: Plot theme (nature, science, default) or path to custom theme (.json/.py).",
+        ),
+        title: str = typer.Option(None, help="zh: 图表标题。\nen: Plot title."),
+        sheet: str = typer.Option(None, help="zh: Excel 工作表名称。\nen: Sheet name for Excel files."),
+        max_chroms: int = typer.Option(
+            24, help="zh: 显示的最大染色体数量。\nen: Maximum number of chromosomes to display."
+        ),
+    ) -> None:
+        """
+        zh: 生成染色体覆盖度分布图。
+        en: Generate chromosome coverage distribution plot.
+        """
+        df = read_data(input_file, sheet=sheet)
+        plotter = ChromosomePlot(theme=theme)
+        plotter.plot(
+            data=df,
+            chrom_col=chrom_col,
+            pos_col=pos_col,
+            pos_counts_col=pos_counts_col,
+            neg_counts_col=neg_counts_col,
+            max_chroms=max_chroms,
+            title=title,
+            output=str(output),
+        )
+        typer.echo(f"Saved chromosome plot to {output}")
+
+    localize_app(app, detect_language())
+    return app

bio_analyze_plot/plots/__init__.py

@@ -0,0 +1,30 @@
+"""
+zh: 图表类集合。
+en: Collection of chart classes.
+"""
+
+from .bar import BarPlot
+from .base import BasePlot
+from .box import BoxPlot
+from .chromosome import ChromosomePlot
+from .gsea import GSEAPlot
+from .heatmap import HeatmapPlot
+from .line import LinePlot
+from .pca import PCAPlot
+from .pie import PiePlot
+from .scatter import ScatterPlot
+from .volcano import VolcanoPlot
+
+__all__ = [
+    "BarPlot",
+    "BasePlot",
+    "BoxPlot",
+    "ChromosomePlot",
+    "GSEAPlot",
+    "HeatmapPlot",
+    "LinePlot",
+    "PCAPlot",
+    "PiePlot",
+    "ScatterPlot",
+    "VolcanoPlot",
+]