run figshare plot generation script

greenelab · Jun 15, 2023 · df21929 · df21929
1 parent 9cdaed5
commit df21929
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Showing 3 changed files with 43 additions and 10 deletions.
diff --git a/01_stratified_classification/lasso_range_gene_optimizers.ipynb b/01_stratified_classification/lasso_range_gene_optimizers.ipynb
@@ -41,7 +41,7 @@
   {
    "cell_type": "code",
    "execution_count": 2,
-   "id": "8ecc9509-3356-45c8-ad0e-a8d605cfc6aa",
+   "id": "4e349b64-dc93-475d-b2e3-a277714f9510",
    "metadata": {
     "tags": [
      "parameters"
@@ -64,10 +64,30 @@
     "metric = 'aupr'\n",
     "\n",
     "output_plots = True\n",
-    "output_plots_dir = os.path.join(\n",
-    "    cfg.repo_root, '01_stratified_classification', 'optimizers_plots'\n",
-    "    # cfg.repo_root, '01_stratified_classification', 'optimizers_plots', 'figshare'\n",
-    ")"
+    "\n",
+    "# toggle this in papermill script to generate all results\n",
+    "figshare = False"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "7f5e3f07-fb50-4f86-a45d-7022b3d6984a",
+   "metadata": {
+    "tags": [
+     "parameters"
+    ]
+   },
+   "outputs": [],
+   "source": [
+    "if figshare:\n",
+    "    output_plots_dir = os.path.join(\n",
+    "        cfg.repo_root, '01_stratified_classification', 'optimizers_plots', 'figshare'\n",
+    "    )\n",
+    "else:\n",
+    "    output_plots_dir = os.path.join(\n",
+    "        cfg.repo_root, '01_stratified_classification', 'optimizers_plots'\n",
+    "    )"
    ]
   },
   {

diff --git a/01_stratified_classification/nbconverted/lasso_range_gene_optimizers.py b/01_stratified_classification/nbconverted/lasso_range_gene_optimizers.py
@@ -47,10 +47,22 @@
 metric = 'aupr'
 
 output_plots = True
-output_plots_dir = os.path.join(
-    cfg.repo_root, '01_stratified_classification', 'optimizers_plots'
-    # cfg.repo_root, '01_stratified_classification', 'optimizers_plots', 'figshare'
-)
+
+# toggle this in papermill script to generate all results
+figshare = False
+
+
+# In[2]:
+
+
+if figshare:
+    output_plots_dir = os.path.join(
+        cfg.repo_root, '01_stratified_classification', 'optimizers_plots', 'figshare'
+    )
+else:
+    output_plots_dir = os.path.join(
+        cfg.repo_root, '01_stratified_classification', 'optimizers_plots'
+    )
 
 
 # ### Get nonzero coefficient information for each lasso penalty

diff --git a/01_stratified_classification/scripts/plot_optimizers_for_genes.sh b/01_stratified_classification/scripts/plot_optimizers_for_genes.sh
@@ -23,7 +23,8 @@ for gene in "${genes[@]}"; do
     cmd="papermill lasso_range_gene_optimizers.ipynb "
     cmd+="${papermill_output_dir}/lasso_range_gene_optimizers.run.ipynb "
     cmd+="-k ${kernel_name} "
-    cmd+="-p plot_gene ${gene}"
+    cmd+="-p plot_gene ${gene} "
+    cmd+="-p figshare True"
     echo "Running: $cmd"
     eval $cmd