feat(letsplot): implement tree-phylogenetic

plots/tree-phylogenetic/implementations/python/letsplot.py

@@ -1,9 +1,10 @@
-""" pyplots.ai
+""" anyplot.ai
 tree-phylogenetic: Phylogenetic Tree Diagram
-Library: letsplot 4.8.2 | Python 3.13.11
-Quality: 91/100 | Created: 2025-12-31
+Library: letsplot 4.9.0 | Python 3.13.13
+Quality: 93/100 | Updated: 2026-05-15
 """
 
+import os
 import re
 
 import pandas as pd
@@ -12,8 +13,16 @@
 
 LetsPlot.setup_html()
 
+THEME = os.getenv("ANYPLOT_THEME", "light")
+PAGE_BG = "#FAF8F1" if THEME == "light" else "#1A1A17"
+ELEVATED_BG = "#FFFDF6" if THEME == "light" else "#242420"
+INK = "#1A1A17" if THEME == "light" else "#F0EFE8"
+INK_SOFT = "#4A4A44" if THEME == "light" else "#B8B7B0"
+GRID_COLOR = "rgba(26,26,23,0.10)" if THEME == "light" else "rgba(240,239,232,0.10)"
+
+OKABE_ITO = ["#009E73", "#D55E00", "#0072B2", "#CC79A7", "#E69F00", "#56B4E9", "#F0E442"]
+
 
-# Simple Newick parser for phylogenetic tree
 def parse_newick(newick_str):
     """Parse Newick format string into tree structure."""
     newick_str = newick_str.strip().rstrip(";")
@@ -23,9 +32,7 @@ def parse_node(s, parent_id=None, depth=0):
         nodes = []
         s = s.strip()
 
-        # Check if this is a leaf node (no parentheses)
         if "(" not in s:
-            # Leaf: name:length or just name
             match = re.match(r"([^:]*):?([\d.]*)", s)
             name = match.group(1) if match else s
             length = float(match.group(2)) if match and match.group(2) else 0.1
@@ -34,9 +41,7 @@ def parse_node(s, parent_id=None, depth=0):
                 {"id": node_id[0], "name": name, "length": length, "parent": parent_id, "depth": depth, "children": []}
             ]
 
-        # Internal node: find matching parentheses
         if s.startswith("("):
-            # Find the matching closing parenthesis
             level = 0
             children_str = ""
             remaining = ""
@@ -50,7 +55,6 @@ def parse_node(s, parent_id=None, depth=0):
                         remaining = s[i + 1 :]
                         break
 
-            # Parse branch length for this internal node
             match = re.match(r":?([\d.]*)", remaining)
             length = float(match.group(1)) if match and match.group(1) else 0.1
 
@@ -66,7 +70,6 @@ def parse_node(s, parent_id=None, depth=0):
             }
             nodes.append(current_node)
 
-            # Split children by comma at level 0
             children = []
             level = 0
             current = ""
@@ -83,7 +86,6 @@ def parse_node(s, parent_id=None, depth=0):
             if current.strip():
                 children.append(current.strip())
 
-            # Parse each child
             for child_str in children:
                 child_nodes = parse_node(child_str, current_id, depth + 1)
                 nodes.extend(child_nodes)
@@ -94,18 +96,14 @@ def parse_node(s, parent_id=None, depth=0):
     return parse_node(newick_str)
 
 
-# Primate phylogenetic tree (based on mitochondrial DNA)
 newick = "((((Human:0.1,Chimpanzee:0.12):0.08,Gorilla:0.2):0.15,(Orangutan:0.25,Gibbon:0.28):0.1):0.2,(Macaque:0.35,(Baboon:0.3,Mandrill:0.32):0.05):0.15)"
 
 nodes = parse_newick(newick)
 
-# Build node dictionary for easy lookup
 node_dict = {n["id"]: n for n in nodes}
 
 
-# Calculate x positions (cumulative branch length from root)
 def calc_x_positions(node_dict):
-    # Find root (node with no parent)
     root = [n for n in node_dict.values() if n["parent"] is None][0]
 
     def assign_x(node_id, parent_x=0):
@@ -117,17 +115,13 @@ def assign_x(node_id, parent_x=0):
     assign_x(root["id"], 0)
 
 
-# Calculate y positions (spacing for leaves, centered for internal nodes)
 def calc_y_positions(node_dict):
-    # Get leaves in order
     leaves = [n for n in node_dict.values() if not n["children"]]
     leaves.sort(key=lambda n: n["id"])
 
-    # Assign y positions to leaves
     for i, leaf in enumerate(leaves):
         leaf["y"] = i
 
-    # Calculate y for internal nodes (average of children)
     def get_y(node_id):
         node = node_dict[node_id]
         if "y" in node:
@@ -143,72 +137,68 @@ def get_y(node_id):
 calc_x_positions(node_dict)
 calc_y_positions(node_dict)
 
-# Build segments for the tree (horizontal and vertical lines)
 segments = []
 for node in node_dict.values():
     if node["parent"] is not None:
         parent = node_dict[node["parent"]]
-        # Horizontal segment from parent x to node x at node y
         segments.append({"x": parent["x"], "xend": node["x"], "y": node["y"], "yend": node["y"], "type": "horizontal"})
-        # Vertical segment at parent x from parent y to node y
         segments.append(
             {"x": parent["x"], "xend": parent["x"], "y": parent["y"], "yend": node["y"], "type": "vertical"}
         )
 
 df_segments = pd.DataFrame(segments)
 
-# Get leaf labels
 leaves = [n for n in node_dict.values() if not n["children"]]
 df_labels = pd.DataFrame([{"x": n["x"] + 0.02, "y": n["y"], "label": n["name"]} for n in leaves])
 
-# Get internal node points
 df_nodes = pd.DataFrame([{"x": n["x"], "y": n["y"]} for n in node_dict.values()])
 
-# Define clade colors for visualization
 clade_colors = {
-    "Human": "#306998",
-    "Chimpanzee": "#306998",
-    "Gorilla": "#306998",
-    "Orangutan": "#FFD43B",
-    "Gibbon": "#FFD43B",
-    "Macaque": "#22C55E",
-    "Baboon": "#22C55E",
-    "Mandrill": "#22C55E",
+    "Human": OKABE_ITO[0],
+    "Chimpanzee": OKABE_ITO[0],
+    "Gorilla": OKABE_ITO[0],
+    "Orangutan": OKABE_ITO[1],
+    "Gibbon": OKABE_ITO[1],
+    "Macaque": OKABE_ITO[2],
+    "Baboon": OKABE_ITO[2],
+    "Mandrill": OKABE_ITO[2],
 }
 
 df_labels["color"] = df_labels["label"].map(clade_colors)
 
-# Create the phylogenetic tree plot
+anyplot_theme = theme(
+    plot_background=element_rect(fill=PAGE_BG, color=PAGE_BG),
+    panel_background=element_rect(fill=PAGE_BG, color=PAGE_BG),
+    panel_grid_major_x=element_line(color=GRID_COLOR, size=0.3),
+    panel_grid_major_y=element_blank(),
+    panel_grid_minor=element_blank(),
+    axis_title_x=element_text(size=20, color=INK),
+    axis_title_y=element_blank(),
+    axis_text_x=element_text(size=16, color=INK_SOFT),
+    axis_text_y=element_blank(),
+    axis_ticks_y=element_blank(),
+    axis_line_y=element_blank(),
+    plot_title=element_text(size=24, face="bold", color=INK),
+    legend_background=element_rect(fill=ELEVATED_BG, color=INK_SOFT),
+    legend_text=element_text(size=16, color=INK_SOFT),
+)
+
 plot = (
     ggplot()
-    + geom_segment(aes(x="x", y="y", xend="xend", yend="yend"), data=df_segments, color="#306998", size=1.5)
-    + geom_point(aes(x="x", y="y"), data=df_nodes, color="#306998", size=4)
+    + geom_segment(aes(x="x", y="y", xend="xend", yend="yend"), data=df_segments, color=OKABE_ITO[0], size=1.5)
+    + geom_point(aes(x="x", y="y"), data=df_nodes, color=OKABE_ITO[0], size=4)
     + geom_point(aes(x="x", y="y", color="color"), data=df_labels, size=6, show_legend=False)
-    + geom_text(aes(x="x", y="y", label="label"), data=df_labels, hjust=0, size=14, family="sans-serif")
+    + geom_text(aes(x="x", y="y", label="label"), data=df_labels, hjust=0, size=14, color=INK_SOFT, family="sans-serif")
     + scale_color_identity()
     + scale_x_continuous(limits=[0, 0.85])
     + labs(
-        title="Primate Evolution · tree-phylogenetic · letsplot · pyplots.ai",
+        title="Primate Evolution · tree-phylogenetic · letsplot · anyplot.ai",
         x="Evolutionary Distance (substitutions per site)",
-        y="",
     )
     + theme_minimal()
-    + theme(
-        plot_title=element_text(size=24, face="bold"),
-        axis_title_x=element_text(size=20),
-        axis_title_y=element_blank(),
-        axis_text_x=element_text(size=16),
-        axis_text_y=element_blank(),
-        axis_ticks_y=element_blank(),
-        panel_grid_major_y=element_blank(),
-        panel_grid_minor=element_blank(),
-        panel_grid_major_x=element_line(color="#E5E5E5", size=0.5),
-    )
+    + anyplot_theme
     + ggsize(1600, 900)
 )
 
-# Save as PNG (scale 3x for 4800x2700)
-ggsave(plot, "plot.png", path=".", scale=3)
-
-# Save as HTML for interactivity
-ggsave(plot, "plot.html", path=".")
+ggsave(plot, f"plot-{THEME}.png", path=".", scale=3)
+ggsave(plot, f"plot-{THEME}.html", path=".")