pylocuszoom 0.2.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

pylocuszoom/backends/matplotlib_backend.py

@@ -9,7 +9,7 @@ import matplotlib.pyplot as plt
 import pandas as pd
 from matplotlib.axes import Axes
 from matplotlib.figure import Figure
-from matplotlib.patches import Rectangle
+from matplotlib.patches import Polygon, Rectangle
 from matplotlib.ticker import FuncFormatter, MaxNLocator
 
 
@@ -55,13 +55,8 @@ class MatplotlibBackend:
             figsize=figsize,
             height_ratios=height_ratios,
             sharex=sharex,
-            gridspec_kw={"hspace": 0},
         )
 
-        # Ensure axes is always a list
-        if n_panels == 1:
-            axes = [axes]
-
         return fig, list(axes)
 
     def scatter(
@@ -139,11 +134,17 @@ class MatplotlibBackend:
         color: str = "grey",
         linestyle: str = "--",
         linewidth: float = 1.0,
+        alpha: float = 1.0,
         zorder: int = 1,
     ) -> Any:
         """Add a horizontal line across the axes."""
         return ax.axhline(
-            y=y, color=color, linestyle=linestyle, linewidth=linewidth, zorder=zorder
+            y=y,
+            color=color,
+            linestyle=linestyle,
+            linewidth=linewidth,
+            alpha=alpha,
+            zorder=zorder,
         )
 
     def add_text(
@@ -187,6 +188,27 @@ class MatplotlibBackend:
         ax.add_patch(rect)
         return rect
 
+    def add_polygon(
+        self,
+        ax: Axes,
+        points: List[List[float]],
+        facecolor: str = "blue",
+        edgecolor: str = "black",
+        linewidth: float = 0.5,
+        zorder: int = 2,
+    ) -> Any:
+        """Add a polygon patch to axes."""
+        polygon = Polygon(
+            points,
+            closed=True,
+            facecolor=facecolor,
+            edgecolor=edgecolor,
+            linewidth=linewidth,
+            zorder=zorder,
+        )
+        ax.add_patch(polygon)
+        return polygon
+
     def set_xlim(self, ax: Axes, left: float, right: float) -> None:
         """Set x-axis limits."""
         ax.set_xlim(left, right)
@@ -268,6 +290,110 @@ class MatplotlibBackend:
         """Close the figure and free resources."""
         plt.close(fig)
 
+    def add_eqtl_legend(
+        self,
+        ax: Axes,
+        eqtl_positive_bins: List[Tuple[float, float, str, str]],
+        eqtl_negative_bins: List[Tuple[float, float, str, str]],
+    ) -> None:
+        """Add eQTL effect size legend using matplotlib Line2D markers."""
+        from matplotlib.lines import Line2D
+
+        legend_elements = []
+
+        # Positive effects (upward triangles)
+        for _, _, label, color in eqtl_positive_bins:
+            legend_elements.append(
+                Line2D(
+                    [0],
+                    [0],
+                    marker="^",
+                    color="w",
+                    markerfacecolor=color,
+                    markeredgecolor="black",
+                    markersize=7,
+                    label=label,
+                )
+            )
+
+        # Negative effects (downward triangles)
+        for _, _, label, color in eqtl_negative_bins:
+            legend_elements.append(
+                Line2D(
+                    [0],
+                    [0],
+                    marker="v",
+                    color="w",
+                    markerfacecolor=color,
+                    markeredgecolor="black",
+                    markersize=7,
+                    label=label,
+                )
+            )
+
+        ax.legend(
+            handles=legend_elements,
+            loc="upper right",
+            fontsize=8,
+            frameon=True,
+            framealpha=0.9,
+            title="eQTL effect",
+            title_fontsize=9,
+            handlelength=1.2,
+            handleheight=1.0,
+            labelspacing=0.3,
+        )
+
+    def add_finemapping_legend(
+        self,
+        ax: Axes,
+        credible_sets: List[int],
+        get_color_func: Any,
+    ) -> None:
+        """Add fine-mapping credible set legend using matplotlib Line2D markers."""
+        from matplotlib.lines import Line2D
+
+        if not credible_sets:
+            return
+
+        legend_elements = []
+        for cs_id in credible_sets:
+            color = get_color_func(cs_id)
+            legend_elements.append(
+                Line2D(
+                    [0],
+                    [0],
+                    marker="o",
+                    color="w",
+                    markerfacecolor=color,
+                    markeredgecolor="black",
+                    markersize=7,
+                    label=f"CS{cs_id}",
+                )
+            )
+
+        ax.legend(
+            handles=legend_elements,
+            loc="upper right",
+            fontsize=8,
+            frameon=True,
+            framealpha=0.9,
+            title="Credible sets",
+            title_fontsize=9,
+            handlelength=1.2,
+            handleheight=1.0,
+            labelspacing=0.3,
+        )
+
+    def add_simple_legend(
+        self,
+        ax: Axes,
+        label: str,
+        loc: str = "upper right",
+    ) -> None:
+        """Add simple legend for labeled scatter data."""
+        ax.legend(loc=loc, fontsize=9)
+
     def finalize_layout(
         self,
         fig: Figure,