update drug response notebook

colleenXu · Mar 23, 2022 · 860c20c · 860c20c
1 parent 2c1a970
commit 860c20c
Showing 1 changed file with 98 additions and 30 deletions.
diff --git a/ExploringDrugResponseData.ipynb b/ExploringDrugResponseData.ipynb
@@ -16,11 +16,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {
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-     "end_time": "2022-03-23T06:07:20.597680Z",
-     "start_time": "2022-03-23T06:07:20.311775Z"
+     "end_time": "2022-03-23T06:23:06.680479Z",
+     "start_time": "2022-03-23T06:23:06.320579Z"
     }
    },
    "outputs": [],
@@ -40,11 +40,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 3,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2022-03-23T06:07:44.110657Z",
-     "start_time": "2022-03-23T06:07:21.604415Z"
+     "end_time": "2022-03-23T06:23:30.352564Z",
+     "start_time": "2022-03-23T06:23:07.123019Z"
     }
    },
    "outputs": [
@@ -63,7 +63,7 @@
        "      dtype='object')"
       ]
      },
-     "execution_count": 2,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     },
@@ -73,7 +73,7 @@
        "(5667705, 22)"
       ]
      },
-     "execution_count": 2,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -88,11 +88,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2022-03-23T06:08:28.760954Z",
-     "start_time": "2022-03-23T06:08:20.850820Z"
+     "end_time": "2022-03-23T06:23:44.392619Z",
+     "start_time": "2022-03-23T06:23:36.346842Z"
     }
    },
    "outputs": [
@@ -102,29 +102,30 @@
        "(5667705, 22)"
       ]
      },
-     "execution_count": 3,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "## are there lines where everything is duplicated? no\n",
+    "## are there lines where every value is duplicated? no\n",
     "\n",
     "drug_response.drop_duplicates().shape"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2022-03-23T06:09:01.990867Z",
-     "start_time": "2022-03-23T06:08:59.426279Z"
+     "end_time": "2022-03-23T06:23:48.558269Z",
+     "start_time": "2022-03-23T06:23:45.982333Z"
     }
    },
    "outputs": [],
    "source": [
-    "## there are lines where everything we focus on is duplicated\n",
+    "## there are lines where everything we focus on is duplicated: subject, object, predicate, disease context\n",
+    "## yes\n",
     "duplicates = drug_response[drug_response.duplicated(subset=[\"Subject_Ensembl_gene_ID\",\n",
     "                                      \"Subject_NCBI_Gene_ID\",\n",
     "                                      \"Object_id\",\n",
@@ -134,11 +135,36 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2022-03-23T06:23:54.880837Z",
+     "start_time": "2022-03-23T06:23:54.876704Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(10768, 22)"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "duplicates.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2022-03-23T06:09:04.608770Z",
-     "start_time": "2022-03-23T06:09:04.591452Z"
+     "end_time": "2022-03-23T06:23:56.694550Z",
+     "start_time": "2022-03-23T06:23:56.675307Z"
     }
    },
    "outputs": [],
@@ -153,11 +179,11 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 8,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2022-03-23T06:09:05.429827Z",
-     "start_time": "2022-03-23T06:09:05.410093Z"
+     "end_time": "2022-03-23T06:23:57.499037Z",
+     "start_time": "2022-03-23T06:23:57.479394Z"
     }
    },
    "outputs": [
@@ -398,7 +424,7 @@
        "[5 rows x 22 columns]"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -415,27 +441,69 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 12,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2022-03-23T06:26:13.234740Z",
+     "start_time": "2022-03-23T06:26:13.214329Z"
+    }
+   },
+   "outputs": [],
+   "source": [
+    "## sets of duplicates: 5384 \n",
+    "\n",
+    "sets_of_dups = duplicates.value_counts(subset = [\"Subject_Ensembl_gene_ID\",\"Subject_NCBI_Gene_ID\",\n",
+    "                          \"Object_id\",\"Predicate\", \"Edge_attribute_MONDO_ID\"])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 13,
    "metadata": {
     "ExecuteTime": {
-     "end_time": "2022-03-23T06:09:37.986230Z",
-     "start_time": "2022-03-23T06:09:37.982258Z"
+     "end_time": "2022-03-23T06:26:16.342056Z",
+     "start_time": "2022-03-23T06:26:16.338543Z"
     }
    },
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "(10768, 22)"
+       "(5384,)"
       ]
      },
-     "execution_count": 8,
+     "execution_count": 13,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
-    "duplicates.shape"
+    "sets_of_dups.shape"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "metadata": {
+    "ExecuteTime": {
+     "end_time": "2022-03-23T06:26:39.157796Z",
+     "start_time": "2022-03-23T06:26:39.154206Z"
+    }
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "10768"
+      ]
+     },
+     "execution_count": 14,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "5384 *2  ## so these are likely 5384 pairs (2 duplicates for each set)"
    ]
   },
   {