additional stats for supp

AllenInstitute · Sep 1, 2023 · 7854471 · 7854471
1 parent f45eb84
commit 7854471
Showing 1 changed file with 104 additions and 8 deletions.
diff --git a/notebooks/l1_morph_metrics.ipynb b/notebooks/l1_morph_metrics.ipynb
@@ -51,7 +51,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -61,7 +61,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -76,7 +76,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -128,7 +128,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -144,7 +144,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -155,7 +155,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -165,7 +165,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -183,7 +183,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -194,6 +194,102 @@
     "combined = pd.concat([mouse_l12, human_l12], sort=False)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/local1/storage/envs/ipfx3/lib/python3.7/site-packages/statsmodels/base/model.py:1873: ValueWarning: covariance of constraints does not have full rank. The number of constraints is 9, but rank is 8\n",
+      "  'rank is %d' % (J, J_), ValueWarning)\n",
+      "/local1/storage/envs/ipfx3/lib/python3.7/site-packages/statsmodels/base/model.py:1873: ValueWarning: covariance of constraints does not have full rank. The number of constraints is 9, but rank is 8\n",
+      "  'rank is %d' % (J, J_), ValueWarning)\n"
+     ]
+    },
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>eta_p_species</th>\n",
+       "      <th>pval_species</th>\n",
+       "      <th>pval_species:homology_type</th>\n",
+       "      <th>rsquared</th>\n",
+       "      <th>interaction</th>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>feature</th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "      <th></th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>dendrite_cross_section_peak</th>\n",
+       "      <td>0.148563</td>\n",
+       "      <td>0.000098</td>\n",
+       "      <td>0.447207</td>\n",
+       "      <td>0.228495</td>\n",
+       "      <td>False</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>dendrite_volume</th>\n",
+       "      <td>0.020263</td>\n",
+       "      <td>0.147459</td>\n",
+       "      <td>0.447207</td>\n",
+       "      <td>0.157628</td>\n",
+       "      <td>False</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                             eta_p_species  pval_species  \\\n",
+       "feature                                                    \n",
+       "dendrite_cross_section_peak       0.148563      0.000098   \n",
+       "dendrite_volume                   0.020263      0.147459   \n",
+       "\n",
+       "                             pval_species:homology_type  rsquared  interaction  \n",
+       "feature                                                                         \n",
+       "dendrite_cross_section_peak                    0.447207  0.228495        False  \n",
+       "dendrite_volume                                0.447207  0.157628        False  "
+      ]
+     },
+     "execution_count": 13,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "groups = ['PAX6', 'LAMP5', 'MC4R', 'L1 VIP']\n",
+    "features = ['dendrite_volume', 'dendrite_cross_section_peak']\n",
+    "res = utils.run_species_subclass_stats(combined, features, groups=groups)\n",
+    "res"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 13,