pylocuszoom 1.0.0__py3-none-any.whl → 1.1.0__py3-none-any.whl

pylocuszoom/plotter.py

@@ -17,6 +17,7 @@ import numpy as np
 import pandas as pd
 import requests
 
+from ._plotter_utils import DEFAULT_GENOMEWIDE_THRESHOLD
 from .backends import BackendType, get_backend
 from .backends.hover import HoverConfig, HoverDataBuilder
 from .colors import (
@@ -29,7 +30,6 @@ from .colors import (
     get_eqtl_color,
     get_ld_bin,
     get_ld_color_palette,
-    get_phewas_category_palette,
 )
 from .config import PlotConfig, StackedPlotConfig
 from .ensembl import get_genes_for_region
@@ -38,24 +38,23 @@ from .finemapping import (
     get_credible_sets,
     prepare_finemapping_for_plotting,
 )
-from .forest import validate_forest_df
 from .gene_track import (
     assign_gene_positions,
     plot_gene_track_generic,
 )
 from .ld import calculate_ld, find_plink
 from .logging import enable_logging, logger
-from .phewas import validate_phewas_df
+from .manhattan_plotter import ManhattanPlotter
 from .recombination import (
     RECOMB_COLOR,
     download_canine_recombination_maps,
     get_default_data_dir,
     get_recombination_rate_for_region,
 )
+from .stats_plotter import StatsPlotter
 from .utils import normalize_chrom, validate_genes_df, validate_gwas_df
 
-# Default significance threshold: 5e-8 (genome-wide significance)
-DEFAULT_GENOMEWIDE_THRESHOLD = 5e-8
+# Precomputed significance line value (used for plotting)
 DEFAULT_GENOMEWIDE_LINE = -np.log10(DEFAULT_GENOMEWIDE_THRESHOLD)
 
 
@@ -140,6 +139,7 @@ class LocusZoomPlotter:
             genome_build if genome_build else self._default_build(species)
         )
         self._backend = get_backend(backend)
+        self._backend_name = backend  # Store for delegation to child plotters
         self.plink_path = plink_path or find_plink()
         self.recomb_data_dir = recomb_data_dir
         self.genomewide_threshold = genomewide_threshold
@@ -149,6 +149,27 @@ 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."""
@@ -214,6 +235,22 @@ class LocusZoomPlotter:
         except FileNotFoundError:
             return None
 
+    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.
+
+        Args:
+            df: DataFrame with p-value column (should be a copy).
+            p_col: Name of p-value column.
+
+        Returns:
+            DataFrame with neglog10p column added.
+        """
+        # Use shared utility - note: df should already be a copy at call sites
+        df["neglog10p"] = -np.log10(df[p_col].clip(lower=1e-300))
+        return df
+
     def plot(
         self,
         gwas_df: pd.DataFrame,
@@ -249,7 +286,8 @@ class LocusZoomPlotter:
             label_top_n: Number of top SNPs to label.
             show_recombination: Whether to show recombination rate overlay.
             figsize: Figure size as (width, height) in inches.
-            lead_pos: Position of lead/index SNP to highlight.
+            lead_pos: Position of lead SNP to highlight. For stacked plots with
+                multiple regions, use plot_stacked() with lead_positions (plural).
             ld_reference_file: Path to PLINK binary fileset for LD calculation.
             ld_col: Column name for pre-computed LD (R^2) values.
             genes_df: Gene annotations with chr, start, end, gene_name.
@@ -332,7 +370,7 @@ class LocusZoomPlotter:
         if clipped_count > 0:
             logger.debug(f"Clipping {clipped_count} p-values below 1e-300 to 1e-300")
 
-        df["neglog10p"] = -np.log10(df[p_col].clip(lower=1e-300))
+        df = self._transform_pvalues(df, p_col)
 
         # Calculate LD if reference file provided
         if ld_reference_file and lead_pos and ld_col is None:
@@ -401,7 +439,12 @@ class LocusZoomPlotter:
         # Format axes
         self._backend.set_ylabel(ax, r"$-\log_{10}$ P")
         self._backend.set_xlim(ax, start, end)
-        self._backend.hide_spines(ax, ["top", "right"])
+        # When recombination overlay is present, keep right spine for secondary y-axis
+        has_recomb = recomb_df is not None and not recomb_df.empty
+        if has_recomb and self._backend.supports_secondary_axis:
+            self._backend.hide_spines(ax, ["top"])
+        else:
+            self._backend.hide_spines(ax, ["top", "right"])
 
         # Add LD legend (all backends)
         if ld_col is not None and ld_col in df.columns:
@@ -605,24 +648,28 @@ class LocusZoomPlotter:
             region_recomb["pos"],
             region_recomb["rate"],
             color=RECOMB_COLOR,
-            linewidth=1.5,
-            alpha=0.7,
+            linewidth=2.5,
+            alpha=0.8,
             yaxis_name=secondary_y,
         )
 
-        # Set y-axis limits and label
+        # Set y-axis limits and label - scale to fit data with headroom
         max_rate = region_recomb["rate"].max()
         self._backend.set_secondary_ylim(
-            secondary_ax, 0, max(max_rate * 1.2, 20), yaxis_name=secondary_y
+            secondary_ax, 0, max(max_rate * 1.3, 10), yaxis_name=secondary_y
         )
         self._backend.set_secondary_ylabel(
             secondary_ax,
             "Recombination rate (cM/Mb)",
-            color=RECOMB_COLOR,
+            color="black",  # Use black for readability (line/fill color remains light blue)
             fontsize=9,
             yaxis_name=secondary_y,
         )
 
+        # Hide top spine on the secondary axis (matplotlib twin axis has its own frame)
+        if isinstance(twin_result, Axes):
+            secondary_ax.spines["top"].set_visible(False)
+
     def _plot_finemapping(
         self,
         ax: Any,
@@ -770,7 +817,8 @@ class LocusZoomPlotter:
             figsize: Figure size as (width, height) in inches.
             ld_reference_file: Single PLINK fileset (broadcast to all panels).
             ld_col: Column name for pre-computed LD (R^2) values.
-            lead_positions: List of lead SNP positions (one per panel).
+            lead_positions: List of lead SNP positions, one per region. For single
+                region plots, use plot() with lead_pos (singular).
             panel_labels: List of panel labels (one per panel).
             ld_reference_files: List of PLINK filesets (one per panel).
             genes_df: Gene annotations for bottom track.
@@ -929,24 +977,34 @@ class LocusZoomPlotter:
         for i, (gwas_df, lead_pos) in enumerate(zip(gwas_dfs, lead_positions)):
             ax = axes[i]
             df = gwas_df.copy()
-            df["neglog10p"] = -np.log10(df[p_col].clip(lower=1e-300))
+            df = self._transform_pvalues(df, p_col)
 
             # Use pre-computed LD or calculate from reference
             panel_ld_col = ld_col
             if ld_reference_files and ld_reference_files[i] and lead_pos and not ld_col:
-                lead_snp_row = df[df[pos_col] == lead_pos]
-                if not lead_snp_row.empty and rs_col in df.columns:
-                    lead_snp_id = lead_snp_row[rs_col].iloc[0]
-                    ld_df = calculate_ld(
-                        bfile_path=ld_reference_files[i],
-                        lead_snp=lead_snp_id,
-                        window_kb=max((end - start) // 1000, 500),
-                        plink_path=self.plink_path,
-                        species=self.species,
+                # Check if rs_col exists before attempting LD calculation
+                if rs_col not in df.columns:
+                    logger.warning(
+                        f"Cannot calculate LD for panel {i + 1}: column '{rs_col}' "
+                        f"not found in GWAS data. "
+                        f"Provide rs_col parameter or add SNP IDs to DataFrame."
                     )
-                    if not ld_df.empty:
-                        df = df.merge(ld_df, left_on=rs_col, right_on="SNP", how="left")
-                        panel_ld_col = "R2"
+                else:
+                    lead_snp_row = df[df[pos_col] == lead_pos]
+                    if not lead_snp_row.empty:
+                        lead_snp_id = lead_snp_row[rs_col].iloc[0]
+                        ld_df = calculate_ld(
+                            bfile_path=ld_reference_files[i],
+                            lead_snp=lead_snp_id,
+                            window_kb=max((end - start) // 1000, 500),
+                            plink_path=self.plink_path,
+                            species=self.species,
+                        )
+                        if not ld_df.empty:
+                            df = df.merge(
+                                ld_df, left_on=rs_col, right_on="SNP", how="left"
+                            )
+                            panel_ld_col = "R2"
 
             # Plot association
             self._plot_association(
@@ -1041,8 +1099,16 @@ class LocusZoomPlotter:
             eqtl_data = eqtl_df.copy()
 
             # Filter by gene if specified
-            if eqtl_gene and "gene" in eqtl_data.columns:
-                eqtl_data = eqtl_data[eqtl_data["gene"] == eqtl_gene]
+            eqtl_gene_filtered = False
+            if eqtl_gene:
+                if "gene" in eqtl_data.columns:
+                    eqtl_data = eqtl_data[eqtl_data["gene"] == eqtl_gene]
+                    eqtl_gene_filtered = True
+                else:
+                    logger.warning(
+                        f"eqtl_gene='{eqtl_gene}' specified but eQTL data has no 'gene' column; "
+                        "showing all eQTL data unfiltered"
+                    )
 
             # Filter by region (position and chromosome)
             if "pos" in eqtl_data.columns:
@@ -1057,9 +1123,7 @@ class LocusZoomPlotter:
                 eqtl_data = eqtl_data[mask]
 
             if not eqtl_data.empty:
-                eqtl_data["neglog10p"] = -np.log10(
-                    eqtl_data["p_value"].clip(lower=1e-300)
-                )
+                eqtl_data = self._transform_pvalues(eqtl_data, "p_value")
 
                 # Build hover data using HoverDataBuilder
                 eqtl_extra_cols = {}
@@ -1119,7 +1183,8 @@ class LocusZoomPlotter:
                     )
                 else:
                     # No effect sizes - plot as diamonds
-                    label = f"eQTL ({eqtl_gene})" if eqtl_gene else "eQTL"
+                    # Only show gene in label if filtering was actually applied
+                    label = f"eQTL ({eqtl_gene})" if eqtl_gene_filtered else "eQTL"
                     self._backend.scatter(
                         ax,
                         eqtl_data["pos"],
@@ -1179,143 +1244,17 @@ class LocusZoomPlotter:
         significance_threshold: float = 5e-8,
         figsize: Tuple[float, float] = (10, 8),
     ) -> Any:
-        """Create a PheWAS (Phenome-Wide Association Study) plot.
-
-        Shows associations of a single variant across multiple phenotypes,
-        with phenotypes grouped by category and colored accordingly.
-
-        Args:
-            phewas_df: DataFrame with phenotype associations.
-            variant_id: Variant identifier (e.g., "rs12345") for plot title.
-            phenotype_col: Column name for phenotype names.
-            p_col: Column name for p-values.
-            category_col: Column name for phenotype categories.
-            effect_col: Optional column name for effect direction (beta/OR).
-            significance_threshold: P-value threshold for significance line.
-            figsize: Figure size as (width, height).
-
-        Returns:
-            Figure object (type depends on backend).
-
-        Example:
-            >>> fig = plotter.plot_phewas(
-            ...     phewas_df,
-            ...     variant_id="rs12345",
-            ...     category_col="category",
-            ... )
-        """
-        validate_phewas_df(phewas_df, phenotype_col, p_col, category_col)
-
-        df = phewas_df.copy()
-        df["neglog10p"] = -np.log10(df[p_col].clip(lower=1e-300))
-
-        # Sort by category then by p-value for consistent ordering
-        if category_col in df.columns:
-            df = df.sort_values([category_col, p_col])
-            categories = df[category_col].unique().tolist()
-            palette = get_phewas_category_palette(categories)
-        else:
-            df = df.sort_values(p_col)
-            categories = []
-            palette = {}
-
-        # Create figure
-        fig, axes = self._backend.create_figure(
-            n_panels=1,
-            height_ratios=[1.0],
+        """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,
         )
-        ax = axes[0]
-
-        # Assign y-positions (one per phenotype)
-        df["y_pos"] = range(len(df))
-
-        # Plot points by category
-        if categories:
-            for cat in categories:
-                # Handle NaN category: NaN == NaN is False in pandas
-                if pd.isna(cat):
-                    cat_data = df[df[category_col].isna()]
-                else:
-                    cat_data = df[df[category_col] == cat]
-                # Use upward triangles for positive effects, circles otherwise
-                if effect_col and effect_col in cat_data.columns:
-                    # Vectorized: split by effect sign, 2 scatter calls per category
-                    pos_data = cat_data[cat_data[effect_col] >= 0]
-                    neg_data = cat_data[cat_data[effect_col] < 0]
-
-                    if not pos_data.empty:
-                        self._backend.scatter(
-                            ax,
-                            pos_data["neglog10p"],
-                            pos_data["y_pos"],
-                            colors=palette[cat],
-                            sizes=60,
-                            marker="^",
-                            edgecolor="black",
-                            linewidth=0.5,
-                            zorder=2,
-                        )
-                    if not neg_data.empty:
-                        self._backend.scatter(
-                            ax,
-                            neg_data["neglog10p"],
-                            neg_data["y_pos"],
-                            colors=palette[cat],
-                            sizes=60,
-                            marker="v",
-                            edgecolor="black",
-                            linewidth=0.5,
-                            zorder=2,
-                        )
-                else:
-                    self._backend.scatter(
-                        ax,
-                        cat_data["neglog10p"],
-                        cat_data["y_pos"],
-                        colors=palette[cat],
-                        sizes=60,
-                        marker="o",
-                        edgecolor="black",
-                        linewidth=0.5,
-                        zorder=2,
-                    )
-        else:
-            self._backend.scatter(
-                ax,
-                df["neglog10p"],
-                df["y_pos"],
-                colors="#4169E1",
-                sizes=60,
-                edgecolor="black",
-                linewidth=0.5,
-                zorder=2,
-            )
-
-        # Add significance threshold line
-        sig_line = -np.log10(significance_threshold)
-        self._backend.axvline(
-            ax, x=sig_line, color="red", linestyle="--", linewidth=1, alpha=0.7
-        )
-
-        # Set axis labels and limits
-        self._backend.set_xlabel(ax, r"$-\log_{10}$ P")
-        self._backend.set_ylabel(ax, "Phenotype")
-        self._backend.set_ylim(ax, -0.5, len(df) - 0.5)
-
-        # Set y-tick labels to phenotype names
-        self._backend.set_yticks(
-            ax,
-            positions=df["y_pos"].tolist(),
-            labels=df[phenotype_col].tolist(),
-            fontsize=8,
-        )
-
-        self._backend.set_title(ax, f"PheWAS: {variant_id}")
-        self._backend.hide_spines(ax, ["top", "right"])
-        self._backend.finalize_layout(fig)
-
-        return fig
 
     def plot_forest(
         self,
@@ -1330,116 +1269,143 @@ class LocusZoomPlotter:
         effect_label: str = "Effect Size",
         figsize: Tuple[float, float] = (8, 6),
     ) -> Any:
-        """Create a forest plot showing effect sizes with confidence intervals.
-
-        Args:
-            forest_df: DataFrame with effect sizes and confidence intervals.
-            variant_id: Variant identifier for plot title.
-            study_col: Column name for study/phenotype names.
-            effect_col: Column name for effect sizes.
-            ci_lower_col: Column name for lower confidence interval.
-            ci_upper_col: Column name for upper confidence interval.
-            weight_col: Optional column for study weights (affects marker size).
-            null_value: Reference value for null effect (0 for beta, 1 for OR).
-            effect_label: X-axis label.
-            figsize: Figure size as (width, height).
-
-        Returns:
-            Figure object (type depends on backend).
-
-        Example:
-            >>> fig = plotter.plot_forest(
-            ...     forest_df,
-            ...     variant_id="rs12345",
-            ...     effect_label="Odds Ratio",
-            ...     null_value=1.0,
-            ... )
-        """
-        validate_forest_df(forest_df, study_col, effect_col, ci_lower_col, ci_upper_col)
-
-        df = forest_df.copy()
-
-        # Create figure
-        fig, axes = self._backend.create_figure(
-            n_panels=1,
-            height_ratios=[1.0],
+        """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,
         )
-        ax = axes[0]
-
-        # Assign y-positions (reverse so first study is at top)
-        df["y_pos"] = range(len(df) - 1, -1, -1)
-
-        # Calculate marker sizes from weights
-        if weight_col and weight_col in df.columns:
-            # Scale weights to marker sizes (min 40, max 200)
-            weights = df[weight_col]
-            min_size, max_size = 40, 200
-            weight_range = weights.max() - weights.min()
-            if weight_range > 0:
-                sizes = min_size + (weights - weights.min()) / weight_range * (
-                    max_size - min_size
-                )
-            else:
-                sizes = (min_size + max_size) / 2
-        else:
-            sizes = 80
-
-        # Calculate error bar extents
-        xerr_lower = df[effect_col] - df[ci_lower_col]
-        xerr_upper = df[ci_upper_col] - df[effect_col]
 
-        # Plot error bars (confidence intervals)
-        self._backend.errorbar_h(
-            ax,
-            x=df[effect_col],
-            y=df["y_pos"],
-            xerr_lower=xerr_lower,
-            xerr_upper=xerr_upper,
-            color="black",
-            linewidth=1.5,
-            capsize=3,
-            zorder=2,
+    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,
         )
 
-        # Plot effect size markers
-        self._backend.scatter(
-            ax,
-            df[effect_col],
-            df["y_pos"],
-            colors="#4169E1",
-            sizes=sizes,
-            marker="s",  # square markers typical for forest plots
-            edgecolor="black",
-            linewidth=0.5,
-            zorder=3,
+    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,
         )
 
-        # Add null effect line
-        self._backend.axvline(
-            ax, x=null_value, color="grey", linestyle="--", linewidth=1, alpha=0.7
+    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,
         )
 
-        # Set axis labels and limits
-        self._backend.set_xlabel(ax, effect_label)
-        self._backend.set_ylim(ax, -0.5, len(df) - 0.5)
-
-        # Ensure x-axis includes the null value with some padding
-        x_min = min(df[ci_lower_col].min(), null_value)
-        x_max = max(df[ci_upper_col].max(), null_value)
-        x_padding = (x_max - x_min) * 0.1
-        self._backend.set_xlim(ax, x_min - x_padding, x_max + x_padding)
-
-        # Set y-tick labels to study names
-        self._backend.set_yticks(
-            ax,
-            positions=df["y_pos"].tolist(),
-            labels=df[study_col].tolist(),
-            fontsize=10,
+    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,
         )
 
-        self._backend.set_title(ax, f"Forest Plot: {variant_id}")
-        self._backend.hide_spines(ax, ["top", "right"])
-        self._backend.finalize_layout(fig)
-
-        return fig
+    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,
+        )