Extract shared palette module — remove 4x duplication across scripts

Author: Ekin-Kahraman

scripts/08_publication_figures.py

@@ -6,21 +6,11 @@
 import pandas as pd
 from pathlib import Path
 
+from palette import PALETTE
+
 RESULTS_DIR = Path("results")
 FIG_DIR = RESULTS_DIR / "figures"
 
-# Colour palette (colourblind-friendly)
-PALETTE = {
-    "CD4+ T cells": "#E69F00",
-    "CD8+ T cells": "#56B4E9",
-    "NK cells": "#009E73",
-    "B cells": "#F0E442",
-    "CD14+ Monocytes": "#0072B2",
-    "FCGR3A+ Monocytes": "#D55E00",
-    "Dendritic cells": "#CC79A7",
-    "Megakaryocytes": "#999999",
-}
-
 # Key marker genes for heatmap
 KEY_MARKERS = [
     "CD3D", "IL7R", "CD8A", "NKG7", "GNLY",

scripts/make_3d_umap_gif.py

@@ -5,20 +5,11 @@
 import imageio.v3 as iio
 from pathlib import Path
 from io import BytesIO
+from palette import PALETTE
 
 RESULTS_DIR = Path("results")
 DOCS_DIR = Path("docs")
 
-PALETTE = {
-    "CD4+ T cells": "#E69F00",
-    "CD8+ T cells": "#56B4E9",
-    "NK cells": "#009E73",
-    "B cells": "#F0E442",
-    "CD14+ Monocytes": "#0072B2",
-    "FCGR3A+ Monocytes": "#D55E00",
-    "Dendritic cells": "#CC79A7",
-    "Megakaryocytes": "#999999",
-}
 
 N_FRAMES = 120
 FPS = 24

scripts/make_profile_banner.py

@@ -6,19 +6,10 @@
 import imageio.v3 as iio
 from pathlib import Path
 from io import BytesIO
+from palette import PALETTE
 
 RESULTS_DIR = Path("results")
 
-PALETTE = {
-    "CD4+ T cells": "#E69F00",
-    "CD8+ T cells": "#56B4E9",
-    "NK cells": "#009E73",
-    "B cells": "#F0E442",
-    "CD14+ Monocytes": "#0072B2",
-    "FCGR3A+ Monocytes": "#D55E00",
-    "Dendritic cells": "#CC79A7",
-    "Megakaryocytes": "#999999",
-}
 
 BG = "#0d1117"  # GitHub dark mode background
 TEXT = "#e6edf3"

scripts/make_slow_rotation.py

@@ -5,19 +5,10 @@
 import imageio.v3 as iio
 from pathlib import Path
 from io import BytesIO
+from palette import PALETTE
 
 RESULTS_DIR = Path("results")
 
-PALETTE = {
-    "CD4+ T cells": "#E69F00",
-    "CD8+ T cells": "#56B4E9",
-    "NK cells": "#009E73",
-    "B cells": "#F0E442",
-    "CD14+ Monocytes": "#0072B2",
-    "FCGR3A+ Monocytes": "#D55E00",
-    "Dendritic cells": "#CC79A7",
-    "Megakaryocytes": "#999999",
-}
 
 BG = "#0d1117"
 N_FRAMES = 120

scripts/palette.py

@@ -0,0 +1,12 @@
+"""Shared Okabe-Ito colourblind-friendly palette for PBMC cell types."""
+
+PALETTE = {
+    "CD4+ T cells": "#E69F00",
+    "CD8+ T cells": "#56B4E9",
+    "NK cells": "#009E73",
+    "B cells": "#F0E442",
+    "CD14+ Monocytes": "#0072B2",
+    "FCGR3A+ Monocytes": "#D55E00",
+    "Dendritic cells": "#CC79A7",
+    "Megakaryocytes": "#999999",
+}