phylogenie 2.1.8__tar.gz → 2.1.10__tar.gz

{phylogenie-2.1.8 → phylogenie-2.1.10}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: phylogenie
-Version: 2.1.8
+Version: 2.1.10
 Summary: Generate phylogenetic datasets with minimal setup effort
 Author: Gabriele Marino
 Author-email: gabmarino.8601@gmail.com

phylogenie-2.1.10/phylogenie/plot.py

@@ -0,0 +1,78 @@
+from enum import Enum
+
+import matplotlib.colors as mcolors
+import matplotlib.patches as mpatches
+import matplotlib.pyplot as plt
+from matplotlib.axes import Axes
+
+from phylogenie import Tree
+from phylogenie.tree import Tree
+from phylogenie.utils import get_times
+
+
+class Coloring(str, Enum):
+    DISCRETE = "discrete"
+    CONTINUOUS = "continuous"
+
+
+def plot_tree(
+    tree: Tree,
+    ax: Axes | None = None,
+    color_by: str | None = None,
+    default_color: str = "black",
+    coloring: str | Coloring | None = None,
+    cmap: str | None = None,
+    show_legend: bool = True,
+) -> Axes:
+    if ax is None:
+        ax = plt.gca()
+
+    xs = get_times(tree)
+    ys = {node: i for i, node in enumerate(tree.inorder_traversal())}
+
+    if color_by is not None:
+        features = set(node.get(color_by) for node in tree)
+        if coloring is None and any(isinstance(f, float) for f in features):
+            coloring = Coloring.CONTINUOUS
+        elif coloring is None:
+            coloring = Coloring.DISCRETE
+        if coloring == Coloring.DISCRETE:
+            if any(isinstance(f, float) for f in features):
+                raise ValueError(
+                    "Discrete coloring selected but feature values are not all categorical."
+                )
+            cmap = "tab20" if cmap is None else cmap
+            colormap = plt.get_cmap(cmap, len(features))
+            feature_colors = {
+                f: mcolors.to_hex(colormap(i)) for i, f in enumerate(features)
+            }
+            colors = {node: feature_colors[node.get(color_by)] for node in tree}
+            legend_handles = [
+                mpatches.Patch(color=feature_colors[f], label=str(f)) for f in features
+            ]
+            if show_legend:
+                ax.legend(handles=legend_handles, title=color_by)  # pyright: ignore
+        elif coloring in {Coloring.CONTINUOUS}:
+            cmap = "viridis" if cmap is None else cmap
+            values = list(map(float, features))
+            norm = mcolors.Normalize(vmin=min(values), vmax=max(values))
+            colormap = plt.get_cmap(cmap)
+            colors = {node: colormap(norm(float(node.get(color_by)))) for node in tree}
+        else:
+            raise ValueError(
+                f"Unknown coloring method: {coloring}. Choices are {list(Coloring)}."
+            )
+    else:
+        colors = {node: default_color for node in tree}
+
+    for node in tree:
+        x1, y1 = xs[node.name], ys[node]
+        if node.parent is None:
+            ax.hlines(y=y1, xmin=0, xmax=x1, color=colors[node])  # pyright: ignore
+            continue
+        x0, y0 = xs[node.parent.name], ys[node.parent]
+        ax.vlines(x=x0, ymin=y0, ymax=y1, color=colors[node])  # pyright: ignore
+        ax.hlines(y=y1, xmin=x0, xmax=x1, color=colors[node])  # pyright: ignore
+
+    ax.set_yticks([])  # pyright: ignore
+    return ax

{phylogenie-2.1.8 → phylogenie-2.1.10}/phylogenie/tree.py

@@ -22,6 +22,14 @@ class Tree:
     def features(self) -> dict[str, Any]:
         return self._features.copy()
 
+    @property
+    def time_to_parent(self) -> float:
+        if self.parent is None and self.branch_length is None:
+            return 0.0
+        if self.branch_length is None:
+            raise ValueError(f"Branch length of node {self.name} is not set.")
+        return self.branch_length
+
     def add_child(self, child: "Tree") -> "Tree":
         child._parent = self
         self._children.append(child)
@@ -69,14 +77,9 @@ class Tree:
     def get_leaves(self) -> tuple["Tree", ...]:
         return tuple(node for node in self if not node.children)
 
-    def parse_branch_length(self) -> float:
-        if self.branch_length is None:
-            raise ValueError(f"Branch length of node {self.name} is not set.")
-        return self.branch_length
-
     def get_time(self) -> float:
         parent_time = 0 if self.parent is None else self.parent.get_time()
-        return self.parse_branch_length() + parent_time
+        return self.time_to_parent + parent_time
 
     def set(self, key: str, value: Any) -> None:
         self._features[key] = value

{phylogenie-2.1.8 → phylogenie-2.1.10}/phylogenie/utils.py

@@ -14,7 +14,7 @@ def get_times(tree: Tree) -> dict[str, float]:
     times: dict[str, float] = {}
     for node in tree:
         parent_time = 0 if node.parent is None else times[node.parent.name]
-        times[node.name] = node.parse_branch_length() + parent_time
+        times[node.name] = node.time_to_parent + parent_time
     return times
 
 

{phylogenie-2.1.8 → phylogenie-2.1.10}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "phylogenie"
-version = "2.1.8"
+version = "2.1.10"
 description = "Generate phylogenetic datasets with minimal setup effort"
 authors = ["Gabriele Marino <gabmarino.8601@gmail.com>"]
 readme = "README.md"

phylogenie-2.1.8/phylogenie/plot.py

@@ -1,39 +0,0 @@
-import matplotlib.colors as mcolors
-import matplotlib.pyplot as plt
-
-from phylogenie import Tree
-from phylogenie.tree import Tree
-from phylogenie.utils import get_times
-
-
-def plot_tree(
-    tree: Tree,
-    ax: plt.Axes | None = None,  # pyright: ignore
-    color_by: str | None = None,
-    default_color: str = "black",
-    cmap: str = "tab20",
-) -> plt.Axes:  # pyright: ignore
-    if ax is None:
-        ax = plt.gca()
-
-    xs = get_times(tree)
-    ys = {node.name: i for i, node in enumerate(tree.inorder_traversal())}
-    if color_by is not None:
-        features = set(node.get(color_by) for node in tree)
-        feature_colors = {
-            f: mcolors.to_hex(plt.get_cmap(cmap, len(features))(i))
-            for i, f in enumerate(features)
-        }
-        colors = {node.name: feature_colors[node.get(color_by)] for node in tree}
-    else:
-        colors = {node.name: default_color for node in tree}
-
-    for node in tree:
-        if node.parent is None:
-            continue
-        x0, y0 = xs[node.parent.name], ys[node.parent.name]
-        x1, y1 = xs[node.name], ys[node.name]
-        ax.plot([x0, x0], [y0, y1], color=colors[node.name])  # pyright: ignore
-        ax.plot([x0, x1], [y1, y1], color=colors[node.name])  # pyright: ignore
-    ax.set_yticks([])  # pyright: ignore
-    return ax