From 16cfa8b13f29dac4307d9c68db616dbe418c94f6 Mon Sep 17 00:00:00 2001
From: ChanceChallacombe <chance.challacombe@gmail.com>
Date: Mon, 7 Jul 2025 11:56:47 -0700
Subject: [PATCH] clean plot styling

---
 ..._Generation_for_Antibody_Engineering.ipynb |   9 ++----
 ...sic_Scoring_for_Antibody_Engineering.ipynb |   9 ++----
 ...ral_Scoring_for_Antibody_Engineering.ipynb |   9 ++----
 ..._Downstream_for_Antibody_Engineering.ipynb |   7 ++---
 {font => content/helpers}/Geist-Regular.ttf   | Bin
 content/helpers/styling.py                    |  27 ++++++++++++++++++
 6 files changed, 38 insertions(+), 23 deletions(-)
 rename {font => content/helpers}/Geist-Regular.ttf (100%)
 create mode 100644 content/helpers/styling.py

diff --git a/content/9.0_Generation_for_Antibody_Engineering.ipynb b/content/9.0_Generation_for_Antibody_Engineering.ipynb
index 5a78656..aa27221 100644
--- a/content/9.0_Generation_for_Antibody_Engineering.ipynb
+++ b/content/9.0_Generation_for_Antibody_Engineering.ipynb
@@ -47,7 +47,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 57,
+   "execution_count": 2,
    "id": "b8ed5dc9",
    "metadata": {
     "scrolled": true
@@ -70,11 +70,8 @@
     "from Bio.PDB import *\n",
     "\n",
     "from biolmai import BioLM\n",
-    "from matplotlib.font_manager import fontManager, FontProperties\n",
-    "font_path = \"../font/Geist-Regular.ttf\"\n",
-    "fontManager.addfont(font_path)\n",
-    "prop = FontProperties(fname=font_path)\n",
-    "sns.set_theme(font=prop.get_name(), style=\"white\", context='notebook', palette='pastel')"
+    "from helpers.styling import apply_plot_styling\n",
+    "apply_plot_styling()"
    ]
   },
   {
diff --git a/content/9.1_Intrinsic_Scoring_for_Antibody_Engineering.ipynb b/content/9.1_Intrinsic_Scoring_for_Antibody_Engineering.ipynb
index c4bef6b..f7e151d 100644
--- a/content/9.1_Intrinsic_Scoring_for_Antibody_Engineering.ipynb
+++ b/content/9.1_Intrinsic_Scoring_for_Antibody_Engineering.ipynb
@@ -53,7 +53,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 1,
    "id": "b8ed5dc9",
    "metadata": {},
    "outputs": [],
@@ -73,11 +73,8 @@
     "from Bio.PDB import *\n",
     "\n",
     "from biolmai import BioLM\n",
-    "from matplotlib.font_manager import fontManager, FontProperties\n",
-    "font_path = \"../font/Geist-Regular.ttf\"\n",
-    "fontManager.addfont(font_path)\n",
-    "prop = FontProperties(fname=font_path)\n",
-    "sns.set_theme(font=prop.get_name(), style=\"white\", context='notebook', palette='pastel')"
+    "from helpers.styling import apply_plot_styling\n",
+    "apply_plot_styling()"
    ]
   },
   {
diff --git a/content/9.2_Structural_Scoring_for_Antibody_Engineering.ipynb b/content/9.2_Structural_Scoring_for_Antibody_Engineering.ipynb
index a25877b..17fcf02 100644
--- a/content/9.2_Structural_Scoring_for_Antibody_Engineering.ipynb
+++ b/content/9.2_Structural_Scoring_for_Antibody_Engineering.ipynb
@@ -46,7 +46,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 36,
+   "execution_count": 1,
    "id": "b8ed5dc9",
    "metadata": {},
    "outputs": [],
@@ -66,11 +66,8 @@
     "from Bio.PDB import *\n",
     "import os\n",
     "from biolmai import BioLM\n",
-    "from matplotlib.font_manager import fontManager, FontProperties\n",
-    "font_path = \"../font/Geist-Regular.ttf\"\n",
-    "fontManager.addfont(font_path)\n",
-    "prop = FontProperties(fname=font_path)\n",
-    "sns.set_theme(font=prop.get_name(), style=\"white\", context='notebook', palette='pastel')"
+    "from helpers.styling import apply_plot_styling\n",
+    "apply_plot_styling()"
    ]
   },
   {
diff --git a/content/9.3_Downstream_for_Antibody_Engineering.ipynb b/content/9.3_Downstream_for_Antibody_Engineering.ipynb
index 0b0ce33..037a8cd 100644
--- a/content/9.3_Downstream_for_Antibody_Engineering.ipynb
+++ b/content/9.3_Downstream_for_Antibody_Engineering.ipynb
@@ -68,11 +68,8 @@
     "from Bio.PDB import *\n",
     "\n",
     "from biolmai import BioLM\n",
-    "from matplotlib.font_manager import fontManager, FontProperties\n",
-    "font_path = \"../font/Geist-Regular.ttf\"\n",
-    "fontManager.addfont(font_path)\n",
-    "prop = FontProperties(fname=font_path)\n",
-    "sns.set_theme(font=prop.get_name(), style=\"white\", context='notebook', palette='pastel')"
+    "from helpers.styling import apply_plot_styling\n",
+    "apply_plot_styling()"
    ]
   },
   {
diff --git a/font/Geist-Regular.ttf b/content/helpers/Geist-Regular.ttf
similarity index 100%
rename from font/Geist-Regular.ttf
rename to content/helpers/Geist-Regular.ttf
diff --git a/content/helpers/styling.py b/content/helpers/styling.py
new file mode 100644
index 0000000..27c9f43
--- /dev/null
+++ b/content/helpers/styling.py
@@ -0,0 +1,27 @@
+import seaborn as sns
+import os
+from matplotlib import rcParams
+from matplotlib.font_manager import fontManager, FontProperties
+
+def apply_plot_styling(font_filename="Geist-Regular.ttf"):
+    """
+    Applies custom font and Seaborn theme styling for consistent plot visuals.
+    
+    Parameters:
+        font_filename (str): Name of the .ttf font file located in the same directory as this script.
+    """
+    current_dir = os.path.dirname(os.path.abspath(__file__))
+    font_path = os.path.join(current_dir, font_filename)
+
+    fontManager.addfont(font_path)
+    prop = FontProperties(fname=font_path)
+    font_name = prop.get_name()
+
+    sns.set_theme(
+        font=font_name,
+        style="white",
+        context="notebook",
+        palette="pastel"
+    )
+
+    rcParams['font.family'] = font_name
\ No newline at end of file