From 59b1b494297d5c2cd7ac55c94c32ac46298acfc0 Mon Sep 17 00:00:00 2001
From: Merit Kayastha <90002479+mkayasth@users.noreply.github.com>
Date: Fri, 10 May 2024 01:04:55 -0400
Subject: [PATCH] Update tree_maker.py

---
 .../neighborJoining/tree_maker.py             | 28 +++++++++++++------
 1 file changed, 19 insertions(+), 9 deletions(-)

diff --git a/fullSequenceAnalysis/neighborJoining/tree_maker.py b/fullSequenceAnalysis/neighborJoining/tree_maker.py
index b1461ea..056e174 100644
--- a/fullSequenceAnalysis/neighborJoining/tree_maker.py
+++ b/fullSequenceAnalysis/neighborJoining/tree_maker.py
@@ -3,23 +3,33 @@
 from Bio import Phylo
 import matplotlib.pyplot as plt
 
-# Parse the Newick string to create a Phylo tree object.
+# Parsing the Newick string to create a Phylo tree object.
 tree = Phylo.read("fullSequence-output/tree.txt", "newick")
 
-# Set up a matplotlib figure.
-fig = plt.figure(figsize=(15, 10), dpi=100)
+
+fig = plt.figure(figsize=(20, 15), dpi=300)
 axes = fig.add_subplot(1, 1, 1)
 
+# formatting the branch labels to 3 significant figures.
+def format_branch_length(clade):
+    if clade.branch_length is not None:
+        return f"{clade.branch_length:.3g}"
+
+
+Phylo.draw(tree, do_show=False, axes=axes, branch_labels=format_branch_length)
 
-Phylo.draw(tree, do_show=False, axes=axes, branch_labels=lambda c: c.branch_length)
 
-axes.set_title('Phylogenetic Tree', fontsize=24)
+axes.set_title('Phylogenetic Tree', fontsize=26)
 
-# setting style.
+# Setting style for the tree lines.
 for line in axes.get_lines():
-	line.set_linewidth(3)
-plt.setp(axes.get_xticklabels(), fontsize=20)
-plt.setp(axes.get_yticklabels(), fontsize=20)
+    line.set_linewidth(3)
+
+for lbl in axes.findobj(match=lambda obj: isinstance(obj, plt.Text)):
+    lbl.set_fontsize(16)
+    
+
+
 
 # Saving the figure to a JPEG file.
 plt.savefig("fullSequence-output/tree.jpg", format='jpg', dpi=300)