Generating plots for XGB model

JulianKlug · Mar 28, 2023 · d1c8b92 · d1c8b92
1 parent 2ad82f9
commit d1c8b92
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Showing 4 changed files with 739 additions and 14 deletions.
diff --git a/prediction/figures/roc_and_pr_curve_figure/roc_and_pr_curve.ipynb b/prediction/figures/roc_and_pr_curve_figure/roc_and_pr_curve.ipynb
@@ -15,6 +15,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import os\n",
     "import pickle\n",
     "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
@@ -32,10 +33,19 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "lstm_bs_predictions_path = '/Users/jk1/temp/opsum_prediction_output/LSTM_72h_testing/3M_mRS01/2023_01_06_1847/test_LSTM_sigmoid_all_unchanged_0.0_2_True_RMSprop_3M mRS 0-1_128_3/bootstrapped_gt_and_pred.pkl'\n",
+    "lstm_bs_predictions_path = '/Users/jk1/temp/opsum_prediction_output/LSTM_72h_testing/3M_mRS02/2023_01_02_1057/test_LSTM_sigmoid_all_balanced_0.2_2_True_RMSprop_3M mRS 0-2_16_3/bootstrapped_gt_and_pred.pkl'\n",
     "thrive_c_bs_predictions_path = '/Users/jk1/temp/opsum_prediction_output/THRIVE_C/THRIVE_C_predictions/bootstrapped_gt_and_pred.pkl'\n",
     "xgb_bs_predictions_path = '/Users/jk1/temp/opsum_prediction_output/linear_72h_xgb/with_feature_aggregration/testing/bootstrapped_gt_and_pred.pkl'\n",
-    "# outcome = '3M mRS 0-1'"
+    "outcome = '3M mRS 0-2'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "output_dir = '/Users/jk1/Downloads'"
    ]
   },
   {
@@ -148,8 +158,8 @@
     "ax = sns.lineplot(data=thrivec_resampled_roc_df, x='fpr', y='tpr', color=all_colors_palette[1], label='THRIVE-C (area = %0.2f)' % np.median(thrivec_bs_roc_aucs),\n",
     "                   ax=ax, errorbar='sd')\n",
     "\n",
-    "ax = sns.lineplot(data=xgb_resampled_roc_df, x='fpr', y='tpr', color=all_colors_palette[2], label='XGBoost (area = %0.2f)' % np.median(xgb_bs_roc_aucs),\n",
-    "                   ax=ax, errorbar='sd')\n",
+    "# ax = sns.lineplot(data=xgb_resampled_roc_df, x='fpr', y='tpr', color=all_colors_palette[2], label='XGBoost (area = %0.2f)' % np.median(xgb_bs_roc_aucs),\n",
+    "#                    ax=ax, errorbar='sd')\n",
     "\n",
     "ax.plot([0, 1], [0, 1], color='grey', lw=1, linestyle='--', alpha=0.5)\n",
     "\n",
@@ -162,8 +172,9 @@
     "    legend_markers, legend_labels = ax.get_legend_handles_labels()\n",
     "    sd1_patch = mpatches.Patch(color=all_colors_palette[0], alpha=0.3)\n",
     "    sd2_patch = mpatches.Patch(color=all_colors_palette[1], alpha=0.3)\n",
-    "    sd3_patch = mpatches.Patch(color=all_colors_palette[2], alpha=0.3)\n",
-    "    sd_marker = (sd1_patch, sd2_patch, sd3_patch)\n",
+    "    # sd3_patch = mpatches.Patch(color=all_colors_palette[2], alpha=0.3)\n",
+    "    sd_marker = (sd1_patch, sd2_patch)\n",
+    "    # sd_marker = (sd1_patch, sd2_patch, sd3_patch)\n",
     "    sd_labels = '± s.d.'\n",
     "    legend_markers.append(sd_marker)\n",
     "    legend_labels.append(sd_labels)\n",
@@ -177,6 +188,17 @@
     "plt.show()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# # save fig\n",
+    "# fig = ax.get_figure()\n",
+    "# fig.savefig(os.path.join(output_dir, 'roc_curve.svg'), bbox_inches='tight')"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {
@@ -208,8 +230,8 @@
     "ax1 = sns.lineplot(data=thrivec_resampled_pr_df, x='recall', y='precision', color=all_colors_palette[1], label='THRIVE-C (area = %0.2f)' % np.median(thrivec_bs_pr_aucs),\n",
     "                   ax=ax1, errorbar='sd')\n",
     "\n",
-    "ax1 = sns.lineplot(data=xgb_resampled_pr_df, x='recall', y='precision', color=all_colors_palette[2], label='XGBoost (area = %0.2f)' % np.median(xgb_bs_pr_aucs),\n",
-    "                   ax=ax1, errorbar='sd')\n",
+    "# ax1 = sns.lineplot(data=xgb_resampled_pr_df, x='recall', y='precision', color=all_colors_palette[2], label='XGBoost (area = %0.2f)' % np.median(xgb_bs_pr_aucs),\n",
+    "#                    ax=ax1, errorbar='sd')\n",
     "\n",
     "\n",
     "ax1.set_xlabel('Recall', fontsize=label_font_size)\n",
@@ -221,8 +243,9 @@
     "    legend_markers, legend_labels = ax1.get_legend_handles_labels()\n",
     "    sd1_patch = mpatches.Patch(color=all_colors_palette[0], alpha=0.3)\n",
     "    sd2_patch = mpatches.Patch(color=all_colors_palette[1], alpha=0.3)\n",
-    "    sd3_patch = mpatches.Patch(color=all_colors_palette[2], alpha=0.3)\n",
-    "    sd_marker = (sd1_patch, sd2_patch, sd3_patch)\n",
+    "    # sd3_patch = mpatches.Patch(color=all_colors_palette[2], alpha=0.3)\n",
+    "    sd_marker = (sd1_patch, sd2_patch)\n",
+    "    # sd_marker = (sd1_patch, sd2_patch, sd3_patch)\n",
     "    sd_labels = '± s.d.'\n",
     "    legend_markers.append(sd_marker)\n",
     "    legend_labels.append(sd_labels)\n",
@@ -236,6 +259,17 @@
     "plt.show()"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# # save fig\n",
+    "# fig = ax1.get_figure()\n",
+    "# fig.savefig(os.path.join(output_dir, 'pr_curve.svg'), bbox_inches='tight')"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,