Refactor codes

src/pycirclize/circos.py

@@ -412,7 +412,6 @@ def initialize_from_bed(
         circos : Circos
             Circos instance initialized from BED file
         """
-        sector2clockwise = {} if sector2clockwise is None else sector2clockwise
         records = Bed(bed_file).records
         sectors = {rec.chr: rec.size for rec in records}
         sector2start_pos = {rec.chr: rec.start for rec in records}

src/pycirclize/tree.py

@@ -185,7 +185,7 @@ def load_tree(data: str | Path | Tree, format: str) -> Tree:
             # Load tree string
             return Phylo.read(io.StringIO(data), format=format)
         elif isinstance(data, Tree):
-            return data
+            return deepcopy(data)
         else:
             raise ValueError(f"{data=} is invalid input tree data!!")
 
@@ -255,26 +255,23 @@ def marker(
         """
         target_node_name = self._search_target_node_name(query)
 
+        # Set markers (x, r) coordinates (include descendent nodes)
         x: list[float] = []
         r: list[float] = []
         rmin, rmax = self.track.r_plot_lim
-        if descendent:
-            clade: Clade = next(self.tree.find_clades(target_node_name))
-            descendent_nodes: list[Clade] = list(clade.find_clades())
-            for descendent_node in descendent_nodes:
-                node_x, node_r = self.name2xr[str(descendent_node.name)]
-                if descendent_node.is_terminal() and self._align_leaf_label:
-                    node_r = rmax if self._outer else rmin
-                x.append(node_x)
-                r.append(node_r)
-        else:
-            node_x, node_r = self.name2xr[target_node_name]
-            target_node: Clade = next(self.tree.find_clades(target_node_name))
-            if target_node.is_terminal() and self._align_leaf_label:
+        clade: Clade = next(self.tree.find_clades(target_node_name))
+        descendent_nodes: list[Clade] = list(clade.find_clades())
+        for descendent_node in descendent_nodes:
+            node_x, node_r = self.name2xr[str(descendent_node.name)]
+            if descendent_node.is_terminal() and self._align_leaf_label:
                 node_r = rmax if self._outer else rmin
             x.append(node_x)
             r.append(node_r)
 
+        # If `descendent=False`, remove descendent nodes (x, r) coordinate
+        if not descendent:
+            x, r = [x[0]], [r[0]]
+
         self.track.scatter(
             x, r, s=size**2, vmin=rmin, vmax=rmax, marker=marker, **kwargs
         )
@@ -535,10 +532,7 @@ def _calc_name2rect(self) -> dict[str, Rectangle]:
             parent_xr = self.name2xr[str(parent_node.name)]
             upper_r = (xr[1] + parent_xr[1]) / 2
             r_plot_lim = self.track.r_plot_lim
-            if self._align_leaf_label:
-                lower_r = max(r_plot_lim) if self._outer else min(r_plot_lim)
-            else:
-                lower_r = max(r_list) if self._outer else min(r_list)
+            lower_r = max(r_plot_lim) if self._outer else min(r_plot_lim)
             rmin, rmax = min(upper_r, lower_r), max(upper_r, lower_r)
 
             # Set rectangle
@@ -581,8 +575,6 @@ def _plot_tree_label(self) -> None:
         """Plot tree label"""
         text_kws = dict(size=self._leaf_label_size, orientation="vertical")
         for node in self.tree.get_terminals():
-            if self._leaf_label_size <= 0:
-                continue
             # Set label text (x, r) position
             label = str(node.name)
             x, r = self.name2xr[label]
@@ -599,4 +591,6 @@ def _plot_tree_label(self) -> None:
             _text_kws.update(params)
             _text_kws.update(self._node2label_props[label])
 
-            self.track.text(label, x, r, **_text_kws)  # type: ignore
+            # Plot label if text size > 0
+            if float(_text_kws["size"]) > 0:
+                self.track.text(label, x, r, **_text_kws)  # type: ignore