pylocuszoom 1.1.2__py3-none-any.whl → 1.2.0__py3-none-any.whl

pylocuszoom/__init__.py

@@ -89,6 +89,7 @@ from .finemapping import (
     filter_finemapping_by_region,
     get_credible_sets,
     get_top_pip_variants,
+    plot_finemapping,
     prepare_finemapping_for_plotting,
     validate_finemapping_df,
 )
@@ -144,6 +145,7 @@ from .plotter import LocusZoomPlotter
 from .recombination import (
     add_recombination_overlay,
     download_canine_recombination_maps,
+    ensure_recomb_maps,
     get_recombination_rate_for_region,
     load_recombination_map,
 )
@@ -182,6 +184,7 @@ __all__ = [
     "add_snp_labels",
     # Recombination
     "add_recombination_overlay",
+    "ensure_recomb_maps",
     "get_recombination_rate_for_region",
     "load_recombination_map",
     # eQTL
@@ -198,6 +201,7 @@ __all__ = [
     "filter_by_credible_set",
     "get_credible_sets",
     "get_top_pip_variants",
+    "plot_finemapping",
     "prepare_finemapping_for_plotting",
     "FinemappingValidationError",
     # Logging

pylocuszoom/finemapping.py

@@ -4,18 +4,20 @@ Provides utilities for loading, validating, and preparing statistical
 fine-mapping results (SuSiE, FINEMAP, etc.) for visualization.
 """
 
-from typing import List, Optional
+from typing import Any, List, Optional
 
 import pandas as pd
 
+from .backends.base import PlotBackend
+from .backends.hover import HoverConfig, HoverDataBuilder
+from .colors import PIP_LINE_COLOR, get_credible_set_color
 from .exceptions import FinemappingValidationError, ValidationError
 from .logging import logger
 from .utils import filter_by_region
 from .validation import DataFrameValidator
 
-# Required columns for fine-mapping data
+# Required columns for fine-mapping data (default column names)
 REQUIRED_FINEMAPPING_COLS = ["pos", "pip"]
-OPTIONAL_FINEMAPPING_COLS = ["rs", "cs", "cs_id", "effect", "se"]
 
 
 def validate_finemapping_df(
@@ -207,3 +209,109 @@ def calculate_credible_set_coverage(
         coverage[cs_id] = cs_data[pip_col].sum()
 
     return coverage
+
+
+def plot_finemapping(
+    backend: PlotBackend,
+    ax: Any,
+    df: pd.DataFrame,
+    pos_col: str = "pos",
+    pip_col: str = "pip",
+    cs_col: Optional[str] = "cs",
+    show_credible_sets: bool = True,
+    pip_threshold: float = 0.0,
+) -> None:
+    """Plot fine-mapping results (PIP line with credible set coloring).
+
+    Renders posterior inclusion probabilities as a line plot, with optional
+    scatter points colored by credible set membership.
+
+    Args:
+        backend: Plotting backend implementing PlotBackend protocol.
+        ax: Axes or panel to plot on.
+        df: Fine-mapping DataFrame with pos and pip columns.
+        pos_col: Column name for position.
+        pip_col: Column name for posterior inclusion probability.
+        cs_col: Column name for credible set assignment (optional).
+        show_credible_sets: Whether to color points by credible set.
+        pip_threshold: Minimum PIP to display as scatter point.
+    """
+    # Build hover data using HoverDataBuilder
+    extra_cols = {pip_col: "PIP"}
+    if cs_col and cs_col in df.columns:
+        extra_cols[cs_col] = "Credible Set"
+    hover_config = HoverConfig(
+        pos_col=pos_col if pos_col in df.columns else None,
+        extra_cols=extra_cols,
+    )
+    hover_builder = HoverDataBuilder(hover_config)
+
+    # Sort by position for line plotting
+    df = df.sort_values(pos_col)
+
+    # Plot PIP as line
+    backend.line(
+        ax,
+        df[pos_col],
+        df[pip_col],
+        color=PIP_LINE_COLOR,
+        linewidth=1.5,
+        alpha=0.8,
+        zorder=1,
+    )
+
+    # Check if credible sets are available
+    has_cs = cs_col is not None and cs_col in df.columns and show_credible_sets
+    credible_sets = get_credible_sets(df, cs_col) if has_cs else []
+
+    if credible_sets:
+        # Plot points colored by credible set
+        for cs_id in credible_sets:
+            cs_data = df[df[cs_col] == cs_id]
+            color = get_credible_set_color(cs_id)
+            backend.scatter(
+                ax,
+                cs_data[pos_col],
+                cs_data[pip_col],
+                colors=color,
+                sizes=50,
+                marker="o",
+                edgecolor="black",
+                linewidth=0.5,
+                zorder=3,
+                hover_data=hover_builder.build_dataframe(cs_data),
+            )
+        # Plot variants not in any credible set (only if threshold is set)
+        if pip_threshold > 0:
+            non_cs_data = df[(df[cs_col].isna()) | (df[cs_col] == 0)]
+            non_cs_data = non_cs_data[non_cs_data[pip_col] >= pip_threshold]
+            if not non_cs_data.empty:
+                backend.scatter(
+                    ax,
+                    non_cs_data[pos_col],
+                    non_cs_data[pip_col],
+                    colors="#BEBEBE",
+                    sizes=30,
+                    marker="o",
+                    edgecolor="black",
+                    linewidth=0.3,
+                    zorder=2,
+                    hover_data=hover_builder.build_dataframe(non_cs_data),
+                )
+    else:
+        # No credible sets - show all points above threshold
+        if pip_threshold > 0:
+            high_pip = df[df[pip_col] >= pip_threshold]
+            if not high_pip.empty:
+                backend.scatter(
+                    ax,
+                    high_pip[pos_col],
+                    high_pip[pip_col],
+                    colors=PIP_LINE_COLOR,
+                    sizes=50,
+                    marker="o",
+                    edgecolor="black",
+                    linewidth=0.5,
+                    zorder=3,
+                    hover_data=hover_builder.build_dataframe(high_pip),
+                )

pylocuszoom/plotter.py

@@ -15,7 +15,6 @@ from typing import Any, List, Optional, Tuple
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
-import requests
 
 from ._plotter_utils import DEFAULT_GENOMEWIDE_THRESHOLD
 from .backends import BackendType, get_backend
@@ -25,7 +24,6 @@ from .colors import (
     EQTL_POSITIVE_BINS,
     LD_BINS,
     LEAD_SNP_COLOR,
-    PIP_LINE_COLOR,
     get_credible_set_color,
     get_eqtl_color,
     get_ld_bin,
@@ -36,6 +34,7 @@ from .ensembl import get_genes_for_region
 from .eqtl import validate_eqtl_df
 from .finemapping import (
     get_credible_sets,
+    plot_finemapping,
     prepare_finemapping_for_plotting,
 )
 from .gene_track import (
@@ -44,14 +43,11 @@ from .gene_track import (
 )
 from .ld import calculate_ld, find_plink
 from .logging import enable_logging, logger
-from .manhattan_plotter import ManhattanPlotter
 from .recombination import (
     RECOMB_COLOR,
-    download_canine_recombination_maps,
-    get_default_data_dir,
+    ensure_recomb_maps,
     get_recombination_rate_for_region,
 )
-from .stats_plotter import StatsPlotter
 from .utils import normalize_chrom, validate_genes_df, validate_gwas_df
 
 # Precomputed significance line value (used for plotting)
@@ -149,27 +145,6 @@ class LocusZoomPlotter:
         # Cache for loaded data
         self._recomb_cache = {}
 
-    @property
-    def _manhattan_plotter(self) -> ManhattanPlotter:
-        """Lazy-load ManhattanPlotter with shared configuration."""
-        if not hasattr(self, "_manhattan_plotter_instance"):
-            self._manhattan_plotter_instance = ManhattanPlotter(
-                species=self.species,
-                backend=self._backend_name,
-                genomewide_threshold=self.genomewide_threshold,
-            )
-        return self._manhattan_plotter_instance
-
-    @property
-    def _stats_plotter(self) -> StatsPlotter:
-        """Lazy-load StatsPlotter with shared configuration."""
-        if not hasattr(self, "_stats_plotter_instance"):
-            self._stats_plotter_instance = StatsPlotter(
-                backend=self._backend_name,
-                genomewide_threshold=self.genomewide_threshold,
-            )
-        return self._stats_plotter_instance
-
     @staticmethod
     def _default_build(species: str) -> Optional[str]:
         """Get default genome build for species."""
@@ -177,37 +152,14 @@ class LocusZoomPlotter:
         return builds.get(species)
 
     def _ensure_recomb_maps(self) -> Optional[Path]:
-        """Ensure recombination maps are downloaded.
+        """Ensure recombination maps are available.
 
-        Returns path to recombination map directory, or None if not available.
+        Delegates to the recombination module's ensure_recomb_maps function.
+
+        Returns:
+            Path to recombination map directory, or None if not available.
         """
-        if self.species == "canine":
-            if self.recomb_data_dir:
-                return Path(self.recomb_data_dir)
-            # Check if already downloaded
-            default_dir = get_default_data_dir()
-            if (
-                default_dir.exists()
-                and len(list(default_dir.glob("chr*_recomb.tsv"))) >= 39
-            ):  # 38 autosomes + X
-                return default_dir
-            # Download
-            try:
-                return download_canine_recombination_maps()
-            except (requests.RequestException, OSError, IOError) as e:
-                # Expected network/file errors - graceful fallback
-                logger.warning(f"Could not download recombination maps: {e}")
-                return None
-            except Exception as e:
-                # JUSTIFICATION: Download failure should not prevent plotting.
-                # We catch broadly here because graceful degradation is acceptable
-                # for optional recombination map downloads. Error-level logging
-                # ensures the issue is visible.
-                logger.error(f"Unexpected error downloading recombination maps: {e}")
-                return None
-        elif self.recomb_data_dir:
-            return Path(self.recomb_data_dir)
-        return None
+        return ensure_recomb_maps(species=self.species, data_dir=self.recomb_data_dir)
 
     def _get_recomb_for_region(
         self, chrom: int, start: int, end: int
@@ -238,7 +190,7 @@ class LocusZoomPlotter:
     def _transform_pvalues(self, df: pd.DataFrame, p_col: str) -> pd.DataFrame:
         """Add neglog10p column with -log10 transformed p-values.
 
-        Delegates to shared utility function. Assumes df is already a copy.
+        Modifies df in place. Callers should pass a copy to avoid side effects.
 
         Args:
             df: DataFrame with p-value column (should be a copy).
@@ -670,107 +622,6 @@ class LocusZoomPlotter:
         if isinstance(twin_result, Axes):
             secondary_ax.spines["top"].set_visible(False)
 
-    def _plot_finemapping(
-        self,
-        ax: Any,
-        df: pd.DataFrame,
-        pos_col: str = "pos",
-        pip_col: str = "pip",
-        cs_col: Optional[str] = "cs",
-        show_credible_sets: bool = True,
-        pip_threshold: float = 0.0,
-    ) -> None:
-        """Plot fine-mapping results (PIP line with credible set coloring).
-
-        Args:
-            ax: Matplotlib axes object.
-            df: Fine-mapping DataFrame with pos and pip columns.
-            pos_col: Column name for position.
-            pip_col: Column name for posterior inclusion probability.
-            cs_col: Column name for credible set assignment (optional).
-            show_credible_sets: Whether to color points by credible set.
-            pip_threshold: Minimum PIP to display as scatter point.
-        """
-        # Build hover data using HoverDataBuilder
-        extra_cols = {pip_col: "PIP"}
-        if cs_col and cs_col in df.columns:
-            extra_cols[cs_col] = "Credible Set"
-        hover_config = HoverConfig(
-            pos_col=pos_col if pos_col in df.columns else None,
-            extra_cols=extra_cols,
-        )
-        hover_builder = HoverDataBuilder(hover_config)
-
-        # Sort by position for line plotting
-        df = df.sort_values(pos_col)
-
-        # Plot PIP as line
-        self._backend.line(
-            ax,
-            df[pos_col],
-            df[pip_col],
-            color=PIP_LINE_COLOR,
-            linewidth=1.5,
-            alpha=0.8,
-            zorder=1,
-        )
-
-        # Check if credible sets are available
-        has_cs = cs_col is not None and cs_col in df.columns and show_credible_sets
-        credible_sets = get_credible_sets(df, cs_col) if has_cs else []
-
-        if credible_sets:
-            # Plot points colored by credible set
-            for cs_id in credible_sets:
-                cs_data = df[df[cs_col] == cs_id]
-                color = get_credible_set_color(cs_id)
-                self._backend.scatter(
-                    ax,
-                    cs_data[pos_col],
-                    cs_data[pip_col],
-                    colors=color,
-                    sizes=50,
-                    marker="o",
-                    edgecolor="black",
-                    linewidth=0.5,
-                    zorder=3,
-                    hover_data=hover_builder.build_dataframe(cs_data),
-                )
-            # Plot variants not in any credible set
-            non_cs_data = df[(df[cs_col].isna()) | (df[cs_col] == 0)]
-            if not non_cs_data.empty and pip_threshold > 0:
-                non_cs_data = non_cs_data[non_cs_data[pip_col] >= pip_threshold]
-                if not non_cs_data.empty:
-                    self._backend.scatter(
-                        ax,
-                        non_cs_data[pos_col],
-                        non_cs_data[pip_col],
-                        colors="#BEBEBE",
-                        sizes=30,
-                        marker="o",
-                        edgecolor="black",
-                        linewidth=0.3,
-                        zorder=2,
-                        hover_data=hover_builder.build_dataframe(non_cs_data),
-                    )
-        else:
-            # No credible sets - show all points above threshold
-            if pip_threshold > 0:
-                high_pip = df[df[pip_col] >= pip_threshold]
-                if not high_pip.empty:
-                    self._backend.scatter(
-                        ax,
-                        high_pip[pos_col],
-                        high_pip[pip_col],
-                        colors=PIP_LINE_COLOR,
-                        sizes=50,
-                        marker="o",
-                        edgecolor="black",
-                        linewidth=0.5,
-                        zorder=3,
-                        hover_data=hover_builder.build_dataframe(high_pip),
-                    )
-
     def plot_stacked(
         self,
         gwas_dfs: List[pd.DataFrame],
@@ -1070,7 +921,8 @@ class LocusZoomPlotter:
             )
 
             if not fm_data.empty:
-                self._plot_finemapping(
+                plot_finemapping(
+                    self._backend,
                     ax,
                     fm_data,
                     pos_col="pos",
@@ -1232,180 +1084,3 @@ class LocusZoomPlotter:
         self._backend.finalize_layout(fig, hspace=0.1)
 
         return fig
-
-    def plot_phewas(
-        self,
-        phewas_df: pd.DataFrame,
-        variant_id: str,
-        phenotype_col: str = "phenotype",
-        p_col: str = "p_value",
-        category_col: str = "category",
-        effect_col: Optional[str] = None,
-        significance_threshold: float = 5e-8,
-        figsize: Tuple[float, float] = (10, 8),
-    ) -> Any:
-        """Create a PheWAS plot. See StatsPlotter.plot_phewas for docs."""
-        return self._stats_plotter.plot_phewas(
-            phewas_df=phewas_df,
-            variant_id=variant_id,
-            phenotype_col=phenotype_col,
-            p_col=p_col,
-            category_col=category_col,
-            effect_col=effect_col,
-            significance_threshold=significance_threshold,
-            figsize=figsize,
-        )
-
-    def plot_forest(
-        self,
-        forest_df: pd.DataFrame,
-        variant_id: str,
-        study_col: str = "study",
-        effect_col: str = "effect",
-        ci_lower_col: str = "ci_lower",
-        ci_upper_col: str = "ci_upper",
-        weight_col: Optional[str] = None,
-        null_value: float = 0.0,
-        effect_label: str = "Effect Size",
-        figsize: Tuple[float, float] = (8, 6),
-    ) -> Any:
-        """Create a forest plot. See StatsPlotter.plot_forest for docs."""
-        return self._stats_plotter.plot_forest(
-            forest_df=forest_df,
-            variant_id=variant_id,
-            study_col=study_col,
-            effect_col=effect_col,
-            ci_lower_col=ci_lower_col,
-            ci_upper_col=ci_upper_col,
-            weight_col=weight_col,
-            null_value=null_value,
-            effect_label=effect_label,
-            figsize=figsize,
-        )
-
-    def plot_manhattan(
-        self,
-        df: pd.DataFrame,
-        chrom_col: str = "chrom",
-        pos_col: str = "pos",
-        p_col: str = "p",
-        custom_chrom_order: Optional[List[str]] = None,
-        category_col: Optional[str] = None,
-        category_order: Optional[List[str]] = None,
-        significance_threshold: Optional[float] = DEFAULT_GENOMEWIDE_THRESHOLD,
-        figsize: Tuple[float, float] = (12, 5),
-        title: Optional[str] = None,
-    ) -> Any:
-        """Create a Manhattan plot. See ManhattanPlotter.plot_manhattan for docs."""
-        return self._manhattan_plotter.plot_manhattan(
-            df=df,
-            chrom_col=chrom_col,
-            pos_col=pos_col,
-            p_col=p_col,
-            custom_chrom_order=custom_chrom_order,
-            category_col=category_col,
-            category_order=category_order,
-            significance_threshold=significance_threshold,
-            figsize=figsize,
-            title=title,
-        )
-
-    def plot_qq(
-        self,
-        df: pd.DataFrame,
-        p_col: str = "p",
-        show_confidence_band: bool = True,
-        show_lambda: bool = True,
-        figsize: Tuple[float, float] = (6, 6),
-        title: Optional[str] = None,
-    ) -> Any:
-        """Create a QQ plot. See ManhattanPlotter.plot_qq for docs."""
-        return self._manhattan_plotter.plot_qq(
-            df=df,
-            p_col=p_col,
-            show_confidence_band=show_confidence_band,
-            show_lambda=show_lambda,
-            figsize=figsize,
-            title=title,
-        )
-
-    def plot_manhattan_stacked(
-        self,
-        gwas_dfs: List[pd.DataFrame],
-        chrom_col: str = "chrom",
-        pos_col: str = "pos",
-        p_col: str = "p",
-        custom_chrom_order: Optional[List[str]] = None,
-        significance_threshold: Optional[float] = DEFAULT_GENOMEWIDE_THRESHOLD,
-        panel_labels: Optional[List[str]] = None,
-        figsize: Tuple[float, float] = (12, 8),
-        title: Optional[str] = None,
-    ) -> Any:
-        """Create stacked Manhattan plots. See ManhattanPlotter.plot_manhattan_stacked for docs."""
-        return self._manhattan_plotter.plot_manhattan_stacked(
-            gwas_dfs=gwas_dfs,
-            chrom_col=chrom_col,
-            pos_col=pos_col,
-            p_col=p_col,
-            custom_chrom_order=custom_chrom_order,
-            significance_threshold=significance_threshold,
-            panel_labels=panel_labels,
-            figsize=figsize,
-            title=title,
-        )
-
-    def plot_manhattan_qq(
-        self,
-        df: pd.DataFrame,
-        chrom_col: str = "chrom",
-        pos_col: str = "pos",
-        p_col: str = "p",
-        custom_chrom_order: Optional[List[str]] = None,
-        significance_threshold: Optional[float] = DEFAULT_GENOMEWIDE_THRESHOLD,
-        show_confidence_band: bool = True,
-        show_lambda: bool = True,
-        figsize: Tuple[float, float] = (14, 5),
-        title: Optional[str] = None,
-    ) -> Any:
-        """Create side-by-side Manhattan and QQ plots. See ManhattanPlotter.plot_manhattan_qq for docs."""
-        return self._manhattan_plotter.plot_manhattan_qq(
-            df=df,
-            chrom_col=chrom_col,
-            pos_col=pos_col,
-            p_col=p_col,
-            custom_chrom_order=custom_chrom_order,
-            significance_threshold=significance_threshold,
-            show_confidence_band=show_confidence_band,
-            show_lambda=show_lambda,
-            figsize=figsize,
-            title=title,
-        )
-
-    def plot_manhattan_qq_stacked(
-        self,
-        gwas_dfs: List[pd.DataFrame],
-        chrom_col: str = "chrom",
-        pos_col: str = "pos",
-        p_col: str = "p",
-        custom_chrom_order: Optional[List[str]] = None,
-        significance_threshold: Optional[float] = DEFAULT_GENOMEWIDE_THRESHOLD,
-        show_confidence_band: bool = True,
-        show_lambda: bool = True,
-        panel_labels: Optional[List[str]] = None,
-        figsize: Tuple[float, float] = (14, 8),
-        title: Optional[str] = None,
-    ) -> Any:
-        """Create stacked Manhattan+QQ plots. See ManhattanPlotter.plot_manhattan_qq_stacked for docs."""
-        return self._manhattan_plotter.plot_manhattan_qq_stacked(
-            gwas_dfs=gwas_dfs,
-            chrom_col=chrom_col,
-            pos_col=pos_col,
-            p_col=p_col,
-            custom_chrom_order=custom_chrom_order,
-            significance_threshold=significance_threshold,
-            show_confidence_band=show_confidence_band,
-            show_lambda=show_lambda,
-            panel_labels=panel_labels,
-            figsize=figsize,
-            title=title,
-        )

pylocuszoom/recombination.py

@@ -395,6 +395,45 @@ def get_recombination_rate_for_region(
     return region_df[["pos", "rate"]]
 
 
+def ensure_recomb_maps(
+    species: str = "canine",
+    data_dir: Optional[str] = None,
+) -> Optional[Path]:
+    """Ensure recombination maps are available, downloading if needed.
+
+    Args:
+        species: Species name ('canine', 'feline', etc.).
+        data_dir: Directory for recombination maps. Uses default if None.
+
+    Returns:
+        Path to recombination maps directory, or None if species not supported
+        or download fails.
+    """
+    if species != "canine":
+        logger.debug(f"No built-in recombination maps for species: {species}")
+        return None
+
+    if data_dir is not None:
+        output_path = Path(data_dir)
+    else:
+        output_path = get_default_data_dir()
+
+    # Check if maps already exist
+    if output_path.exists():
+        existing_files = list(output_path.glob("chr*_recomb.tsv"))
+        if len(existing_files) >= 39:  # 38 autosomes + X
+            logger.debug(f"Recombination maps already exist at {output_path}")
+            return output_path
+
+    # Download maps with error handling
+    logger.info("Downloading canine recombination maps...")
+    try:
+        return download_canine_recombination_maps(output_dir=str(output_path))
+    except Exception as e:
+        logger.warning(f"Could not download recombination maps: {e}")
+        return None
+
+
 def add_recombination_overlay(
     ax: Axes,
     recomb_df: pd.DataFrame,

{pylocuszoom-1.1.2.dist-info → pylocuszoom-1.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pylocuszoom
-Version: 1.1.2
+Version: 1.2.0
 Summary: Publication-ready regional association plots with LD coloring, gene tracks, and recombination overlays
 Project-URL: Homepage, https://github.com/michael-denyer/pylocuszoom
 Project-URL: Documentation, https://github.com/michael-denyer/pylocuszoom#readme
@@ -35,6 +35,7 @@ Requires-Dist: tqdm>=4.60.0
 Provides-Extra: all
 Requires-Dist: pyspark>=3.0.0; extra == 'all'
 Provides-Extra: dev
+Requires-Dist: hypothesis>=6.0.0; extra == 'dev'
 Requires-Dist: pytest-cov>=4.0.0; extra == 'dev'
 Requires-Dist: pytest-randomly>=3.0.0; extra == 'dev'
 Requires-Dist: pytest-xdist>=3.0.0; extra == 'dev'
@@ -320,13 +321,16 @@ fig = plotter.plot_stacked(
 Visualize associations of a single variant across multiple phenotypes:
 
 ```python
+from pylocuszoom import StatsPlotter
+
 phewas_df = pd.DataFrame({
     "phenotype": ["Height", "BMI", "T2D", "CAD", "HDL"],
     "p_value": [1e-15, 0.05, 1e-8, 1e-3, 1e-10],
     "category": ["Anthropometric", "Anthropometric", "Metabolic", "Cardiovascular", "Lipids"],
 })
 
-fig = plotter.plot_phewas(
+stats_plotter = StatsPlotter()
+fig = stats_plotter.plot_phewas(
     phewas_df,
     variant_id="rs12345",
     category_col="category",
@@ -341,6 +345,8 @@ fig = plotter.plot_phewas(
 Create forest plots for meta-analysis visualization:
 
 ```python
+from pylocuszoom import StatsPlotter
+
 forest_df = pd.DataFrame({
     "study": ["Study A", "Study B", "Study C", "Meta-analysis"],
     "effect": [0.45, 0.52, 0.38, 0.46],
@@ -349,7 +355,8 @@ forest_df = pd.DataFrame({
     "weight": [25, 35, 20, 100],
 })
 
-fig = plotter.plot_forest(
+stats_plotter = StatsPlotter()
+fig = stats_plotter.plot_forest(
     forest_df,
     variant_id="rs12345",
     weight_col="weight",
@@ -364,9 +371,9 @@ fig = plotter.plot_forest(
 Create genome-wide Manhattan plots showing associations across all chromosomes:
 
 ```python
-from pylocuszoom import LocusZoomPlotter
+from pylocuszoom import ManhattanPlotter
 
-plotter = LocusZoomPlotter(species="human")
+plotter = ManhattanPlotter(species="human")
 
 fig = plotter.plot_manhattan(
     gwas_df,
@@ -397,9 +404,9 @@ fig = plotter.plot_manhattan(
 Create quantile-quantile plots to assess p-value distribution:
 
 ```python
-from pylocuszoom import LocusZoomPlotter
+from pylocuszoom import ManhattanPlotter
 
-plotter = LocusZoomPlotter()
+plotter = ManhattanPlotter()
 
 fig = plotter.plot_qq(
     gwas_df,
@@ -419,9 +426,9 @@ fig.savefig("qq_plot.png", dpi=150)
 Compare multiple GWAS results in vertically stacked Manhattan plots:
 
 ```python
-from pylocuszoom import LocusZoomPlotter
+from pylocuszoom import ManhattanPlotter
 
-plotter = LocusZoomPlotter()
+plotter = ManhattanPlotter()
 
 fig = plotter.plot_manhattan_stacked(
     [gwas_study1, gwas_study2, gwas_study3],
@@ -444,9 +451,9 @@ fig.savefig("manhattan_stacked.png", dpi=150)
 Create combined Manhattan and QQ plots in a single figure:
 
 ```python
-from pylocuszoom import LocusZoomPlotter
+from pylocuszoom import ManhattanPlotter
 
-plotter = LocusZoomPlotter()
+plotter = ManhattanPlotter()
 
 fig = plotter.plot_manhattan_qq(
     gwas_df,

{pylocuszoom-1.1.2.dist-info → pylocuszoom-1.2.0.dist-info}/RECORD

@@ -1,11 +1,11 @@
-pylocuszoom/__init__.py,sha256=WWoPLRzx-ptSs6WU5ABz1-HzK5o06RV-KXqtDeQKPgQ,6108
+pylocuszoom/__init__.py,sha256=l_P-moa2FZkrqvpyRj_PT97Q70X7l29bCjzNB5NI_mM,6204
 pylocuszoom/_plotter_utils.py,sha256=ELdSOcKk2KvOo_AxEWHeutmmUS4zZMaDMmQfpQUWaF0,1541
 pylocuszoom/colors.py,sha256=B28rfhWwGZ-e6Q-F43iXxC6NZpjUo0yWk4S_-vp9ZvU,7686
 pylocuszoom/config.py,sha256=qjIEodI-RY71RVyQ5QmE6WXcPXU4Re_xEWiDlkEww3g,13266
 pylocuszoom/ensembl.py,sha256=w2msgBoIrY79iHI3hURSbevvdFHxHyWF9Z78hXtAaBc,14296
 pylocuszoom/eqtl.py,sha256=9hGcFARABQRCMN3rco0pVlFJdmlh4SLBBKSgOvdIH_U,5924
 pylocuszoom/exceptions.py,sha256=nd-rWMUodW62WVV4TfcYVPQcb66xV6v9FA-_4xHb5VY,926
-pylocuszoom/finemapping.py,sha256=VYQs4o4dVREXicueT1anzuENiFZk6YXb6HpbwyF0FD0,5828
+pylocuszoom/finemapping.py,sha256=S3ulQj3fkaDM3n4I8EBymbWym_kTD5NEqfIEj93Mdjk,9630
 pylocuszoom/forest.py,sha256=K-wBinxBOqIzsNMtZJ587e_oMhUXIXEqmEzVTUbmHSY,1161
 pylocuszoom/gene_track.py,sha256=Sh0JCSdLNAAH0NQEiDVMvyXjm63PiCMq3gLvewcagvo,17277
 pylocuszoom/labels.py,sha256=l4PHAR_err75Z9kTmb3a2h0eunkFj6UjzhKBUgmZTDc,3623
@@ -15,10 +15,10 @@ pylocuszoom/logging.py,sha256=nZHEkbnjp8zoyWj_S-Hy9UQvUYLoMoxyiOWRozBT2dg,4987
 pylocuszoom/manhattan.py,sha256=sNhPnsfsIqe1ls74D-kKMFyF_ZmaYB9Ul8qf4UMWnF0,8022
 pylocuszoom/manhattan_plotter.py,sha256=1QQxaXEh5YG4x6ZIxpdhdfQPI2KuO_525qYKI7c32n4,27584
 pylocuszoom/phewas.py,sha256=6g2LmwA5kmxYlHgPxJvuXIMerEqfqgsrth110Y3CgVU,968
-pylocuszoom/plotter.py,sha256=mMOQxyLU3d1XJGpDJUuy71fAFm6IAnQfMZQXHgN6Mzk,54689
+pylocuszoom/plotter.py,sha256=Z24UWRRdp9E-nJx2urKmM_jz-i0OZ9BOwSmJJestdS4,42362
 pylocuszoom/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 pylocuszoom/qq.py,sha256=GPIFHXYCLvhP4IUgjcU3QELLREH8r1AEYXMord8gtEo,3650
-pylocuszoom/recombination.py,sha256=e11IlFRXKILEAP-vgMcbFK28zbAQ5jY-fESsisogq0o,14570
+pylocuszoom/recombination.py,sha256=M-wDBdGbC5qGDHPFoGzBTPmTdiRD7bpRskyxBAKxTUY,15878
 pylocuszoom/schemas.py,sha256=XxeivyRm5LGDwJw4GToxzOSdyx1yXvFYk3xgeFJ6VW0,11858
 pylocuszoom/stats_plotter.py,sha256=67bgU-TXGnmVTxfTRWT3-PFemVVy6lTu4-ZlxUnwHS4,11171
 pylocuszoom/utils.py,sha256=Z2P__Eau3ilF2ftuAZBm11EZ1NqCFQzfr4br9jCiJmg,6887
@@ -30,7 +30,7 @@ pylocuszoom/backends/hover.py,sha256=Hjm_jcxJL8dDxO_Ye7jeWAUcHKlbH6oO8ZfGJ2MzIFM
 pylocuszoom/backends/matplotlib_backend.py,sha256=9WAFLWcclj2-4WKi6bE6IPJfQ_HNoIekOE45ibBGPa0,22824
 pylocuszoom/backends/plotly_backend.py,sha256=VDEZMdP7nOeFYLli-YOc_2DG00ZA6VVRNUcvT5PU0HM,39084
 pylocuszoom/reference_data/__init__.py,sha256=qqHqAUt1jebGlCN3CjqW3Z-_coHVNo5K3a3bb9o83hA,109
-pylocuszoom-1.1.2.dist-info/METADATA,sha256=dkrVAdEcwo5yQku8yUfX7Dlpiv3u01FzdHrZ23c3WyM,22289
-pylocuszoom-1.1.2.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-pylocuszoom-1.1.2.dist-info/licenses/LICENSE.md,sha256=U2y_hv8RcN5lECA3uK88irU3ODUE1TDAPictcmnP0Q4,698
-pylocuszoom-1.1.2.dist-info/RECORD,,
+pylocuszoom-1.2.0.dist-info/METADATA,sha256=O0SkzFPHNYqOrjh0zUfL_73UvE2z2NzzH1nKYECchw4,22488
+pylocuszoom-1.2.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+pylocuszoom-1.2.0.dist-info/licenses/LICENSE.md,sha256=U2y_hv8RcN5lECA3uK88irU3ODUE1TDAPictcmnP0Q4,698
+pylocuszoom-1.2.0.dist-info/RECORD,,