Jitter mean coverage boxplot

notebooks/tb_validation.ipynb

@@ -486,16 +486,26 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "paqc_mean_cov = km_tb_df[['Labnummer', 'mean_cov']]\n",
+    "paqc_mean_cov = km_tb_df[['Labnummer', 'mean_cov']].dropna()\n",
+    "counts = paqc_mean_cov[\"mean_cov\"].tolist()\n",
     "\n",
+    "# Create the plot\n",
     "plt.figure(figsize=(10, 8))\n",
-    "sns.boxplot(y='mean_cov', data=paqc_mean_cov)\n",
+    "\n",
+    "# Boxplot\n",
+    "plt.boxplot(counts)\n",
+    "\n",
+    "# Add jittered data points\n",
+    "jitter = 0.04  # Adjust the jitter as needed\n",
+    "x_jitter = np.random.normal(1, jitter, size=len(counts))\n",
+    "plt.scatter(x_jitter, counts, alpha=0.5, color=\"blue\")\n",
     "\n",
     "# Customize the plot\n",
     "plt.xlabel('Sample ID')\n",
     "plt.ylabel('Mean Coverage')\n",
-    "plt.title('Boxplot of mean coverage by sample name')\n",
+    "plt.title('Boxplot of Mean Coverage by Sample Name')\n",
     "\n",
+    "# Adjust layout and save the figure\n",
     "plt.tight_layout()\n",
     "plt.savefig(tb_validation_mean_cov_fig, dpi=600, bbox_inches='tight')\n",
     "plt.show()"