{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 数据处理：SMILES信息在Gene里，CP里面没有，所以首先在这里实现映射和对齐"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "import seaborn as sns\n",
    "import os\n",
    "import h5py\n",
    "\n",
    "def load_from_HDF(fname):\n",
    "    \"\"\"Load data from a HDF5 file to a dictionary.\"\"\"\n",
    "    data = dict()\n",
    "    with h5py.File(fname, 'r') as f:\n",
    "        for key in f:\n",
    "            data[key] = np.asarray(f[key])\n",
    "            if isinstance(data[key][0], np.bytes_):\n",
    "                data[key] = data[key].astype(str)\n",
    "    return data\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/tmp/ipykernel_274271/1834547549.py:6: DtypeWarning: Columns (911,912,913,914) have mixed types. Specify dtype option on import or set low_memory=False.\n",
      "  CP_CSV = pd.read_csv(CP_path)\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(153386, 919) (68120, 988)\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/tmp/ipykernel_274271/1834547549.py:7: DtypeWarning: Columns (987) have mixed types. Specify dtype option on import or set low_memory=False.\n",
      "  GE_CSV = pd.read_csv(GE_path)\n"
     ]
    },
    {
     "data": {
      "text/html": [
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       "        vertical-align: middle;\n",
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       "\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>221227_x_at</th>\n",
       "      <th>212345_s_at</th>\n",
       "      <th>218597_s_at</th>\n",
       "      <th>217140_s_at</th>\n",
       "      <th>209253_at</th>\n",
       "      <th>214404_x_at</th>\n",
       "      <th>219888_at</th>\n",
       "      <th>201225_s_at</th>\n",
       "      <th>202535_at</th>\n",
       "      <th>219499_at</th>\n",
       "      <th>...</th>\n",
       "      <th>pert_dose</th>\n",
       "      <th>det_plate</th>\n",
       "      <th>BROAD_CPD_ID</th>\n",
       "      <th>CPD_NAME</th>\n",
       "      <th>CPD_TYPE</th>\n",
       "      <th>CPD_SMILES</th>\n",
       "      <th>pert_id_dose</th>\n",
       "      <th>pert_sample_dose</th>\n",
       "      <th>pert_type</th>\n",
       "      <th>control_type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>-0.118505</td>\n",
       "      <td>-0.293445</td>\n",
       "      <td>-0.294088</td>\n",
       "      <td>0.292745</td>\n",
       "      <td>-0.145896</td>\n",
       "      <td>0.97358</td>\n",
       "      <td>0.247915</td>\n",
       "      <td>-0.159028</td>\n",
       "      <td>-1.249049</td>\n",
       "      <td>0.357185</td>\n",
       "      <td>...</td>\n",
       "      <td>50.0</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>BRD-K07762753</td>\n",
       "      <td>aminopurvalanol A</td>\n",
       "      <td>BIO</td>\n",
       "      <td>CC(C)[C@H](CO)Nc1nc(Nc2cc(N)cc(Cl)c2)c2ncn(C(C...</td>\n",
       "      <td>BRD-K07762753_50.0</td>\n",
       "      <td>BRD-K07762753-001-03-6_50.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.043264</td>\n",
       "      <td>-0.264945</td>\n",
       "      <td>-0.000633</td>\n",
       "      <td>0.000935</td>\n",
       "      <td>0.177604</td>\n",
       "      <td>-0.50472</td>\n",
       "      <td>0.214315</td>\n",
       "      <td>0.144271</td>\n",
       "      <td>0.106551</td>\n",
       "      <td>-0.051834</td>\n",
       "      <td>...</td>\n",
       "      <td>12.7</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>BRD-K09991945</td>\n",
       "      <td>GSK-3 inhibitor II</td>\n",
       "      <td>BIO</td>\n",
       "      <td>Ic1cccc(CSc2nnc(o2)-c2ccncc2)c1</td>\n",
       "      <td>BRD-K09991945_12.7</td>\n",
       "      <td>BRD-K09991945-001-02-0_12.7</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>-0.070805</td>\n",
       "      <td>0.195755</td>\n",
       "      <td>0.004606</td>\n",
       "      <td>-0.040855</td>\n",
       "      <td>-0.067346</td>\n",
       "      <td>-0.19872</td>\n",
       "      <td>-0.053195</td>\n",
       "      <td>0.167971</td>\n",
       "      <td>-0.215449</td>\n",
       "      <td>-0.273714</td>\n",
       "      <td>...</td>\n",
       "      <td>50.0</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>BRD-K46678324</td>\n",
       "      <td>RHO-kinase inhibitor II</td>\n",
       "      <td>BIO</td>\n",
       "      <td>Clc1cc(Cl)c(NC(=O)Nc2ccncc2)c(Cl)c1</td>\n",
       "      <td>BRD-K46678324_50.0</td>\n",
       "      <td>BRD-K46678324-001-03-7_50.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.027165</td>\n",
       "      <td>-0.149545</td>\n",
       "      <td>0.173113</td>\n",
       "      <td>-0.100695</td>\n",
       "      <td>-0.309296</td>\n",
       "      <td>-0.20782</td>\n",
       "      <td>-0.323985</td>\n",
       "      <td>0.294872</td>\n",
       "      <td>-0.371449</td>\n",
       "      <td>-0.099914</td>\n",
       "      <td>...</td>\n",
       "      <td>16.2</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>BRD-K67860401</td>\n",
       "      <td>GSK-3beta inhibitor VIII</td>\n",
       "      <td>BIO</td>\n",
       "      <td>COc1ccc(CNC(=O)Nc2ncc(s2)[N+]([O-])=O)cc1</td>\n",
       "      <td>BRD-K67860401_16.2</td>\n",
       "      <td>BRD-K67860401-001-02-3_16.2</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0.303294</td>\n",
       "      <td>0.254455</td>\n",
       "      <td>-0.055418</td>\n",
       "      <td>-0.053635</td>\n",
       "      <td>0.000455</td>\n",
       "      <td>-0.10908</td>\n",
       "      <td>0.031425</td>\n",
       "      <td>0.044482</td>\n",
       "      <td>0.223351</td>\n",
       "      <td>0.163186</td>\n",
       "      <td>...</td>\n",
       "      <td>12.5</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>BRD-K52620403</td>\n",
       "      <td>STO 609</td>\n",
       "      <td>BIO</td>\n",
       "      <td>OC(=O)c1ccc2c3nc4ccccc4n3c(=O)c3cccc1c23</td>\n",
       "      <td>BRD-K52620403_12.5</td>\n",
       "      <td>BRD-K52620403-001-01-8_12.5</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 988 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   221227_x_at  212345_s_at  218597_s_at  217140_s_at  209253_at  214404_x_at  \\\n",
       "0    -0.118505    -0.293445    -0.294088     0.292745  -0.145896      0.97358   \n",
       "1     0.043264    -0.264945    -0.000633     0.000935   0.177604     -0.50472   \n",
       "2    -0.070805     0.195755     0.004606    -0.040855  -0.067346     -0.19872   \n",
       "3     0.027165    -0.149545     0.173113    -0.100695  -0.309296     -0.20782   \n",
       "4     0.303294     0.254455    -0.055418    -0.053635   0.000455     -0.10908   \n",
       "\n",
       "   219888_at  201225_s_at  202535_at  219499_at  ...  pert_dose  \\\n",
       "0   0.247915    -0.159028  -1.249049   0.357185  ...       50.0   \n",
       "1   0.214315     0.144271   0.106551  -0.051834  ...       12.7   \n",
       "2  -0.053195     0.167971  -0.215449  -0.273714  ...       50.0   \n",
       "3  -0.323985     0.294872  -0.371449  -0.099914  ...       16.2   \n",
       "4   0.031425     0.044482   0.223351   0.163186  ...       12.5   \n",
       "\n",
       "                       det_plate   BROAD_CPD_ID                  CPD_NAME  \\\n",
       "0  PAC001_U2OS_6H_X1_B1_UNI4445L  BRD-K07762753         aminopurvalanol A   \n",
       "1  PAC001_U2OS_6H_X1_B1_UNI4445L  BRD-K09991945        GSK-3 inhibitor II   \n",
       "2  PAC001_U2OS_6H_X1_B1_UNI4445L  BRD-K46678324   RHO-kinase inhibitor II   \n",
       "3  PAC001_U2OS_6H_X1_B1_UNI4445L  BRD-K67860401  GSK-3beta inhibitor VIII   \n",
       "4  PAC001_U2OS_6H_X1_B1_UNI4445L  BRD-K52620403                   STO 609   \n",
       "\n",
       "   CPD_TYPE                                         CPD_SMILES  \\\n",
       "0       BIO  CC(C)[C@H](CO)Nc1nc(Nc2cc(N)cc(Cl)c2)c2ncn(C(C...   \n",
       "1       BIO                    Ic1cccc(CSc2nnc(o2)-c2ccncc2)c1   \n",
       "2       BIO                Clc1cc(Cl)c(NC(=O)Nc2ccncc2)c(Cl)c1   \n",
       "3       BIO          COc1ccc(CNC(=O)Nc2ncc(s2)[N+]([O-])=O)cc1   \n",
       "4       BIO           OC(=O)c1ccc2c3nc4ccccc4n3c(=O)c3cccc1c23   \n",
       "\n",
       "         pert_id_dose             pert_sample_dose  pert_type  control_type  \n",
       "0  BRD-K07762753_50.0  BRD-K07762753-001-03-6_50.0        trt           NaN  \n",
       "1  BRD-K09991945_12.7  BRD-K09991945-001-02-0_12.7        trt           NaN  \n",
       "2  BRD-K46678324_50.0  BRD-K46678324-001-03-7_50.0        trt           NaN  \n",
       "3  BRD-K67860401_16.2  BRD-K67860401-001-02-3_16.2        trt           NaN  \n",
       "4  BRD-K52620403_12.5  BRD-K52620403-001-01-8_12.5        trt           NaN  \n",
       "\n",
       "[5 rows x 988 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "root = '/home/bob/boom/VCBench/data/MVC/CDRP-BBBC047-Bray/'\n",
    "\n",
    "CP_path = root + 'CellPainting/replicate_level_cp_normalized_variable_selected.csv.gz'\n",
    "GE_path = root + 'L1000/replicate_level_l1k.csv.gz'\n",
    "\n",
    "CP_CSV = pd.read_csv(CP_path)\n",
    "GE_CSV = pd.read_csv(GE_path)\n",
    "print(CP_CSV.shape, GE_CSV.shape)\n",
    "GE_CSV.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "988"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GE_CSV_columns = GE_CSV.columns.to_list()\n",
    "len(GE_CSV_columns)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "932 False\n",
      "未匹配到的 probe 数量: 56\n",
      "['209691_s_at', '212770_at', '210695_s_at', '213152_s_at', '57703_at', '218948_at', '213531_s_at', '210241_s_at', '212830_at', '203596_s_at', '203646_at', '204755_x_at', '214221_at', '205741_s_at', '210811_s_at', '204925_at', '208741_at', '213918_s_at', '221560_at', '202331_at']\n"
     ]
    }
   ],
   "source": [
    "# 2. 读gene信息\n",
    "Gene_info = pd.read_csv('/home/bob/boom/VCBench/data/LINCS2020/geneinfo_processed.csv')\n",
    "\n",
    "# 3. 按 pr_id 匹配，提取对应的基因symbol\n",
    "matched_info = Gene_info[Gene_info['pr_id'].isin(GE_CSV_columns)]\n",
    "GE_genes = matched_info['pr_gene_symbol'].tolist()\n",
    "print(len(GE_genes), len(GE_genes) == len(GE_CSV_columns))\n",
    "\n",
    "# 4. 打印未匹配到的 probe ID\n",
    "not_found_genes = [pid for pid in GE_CSV_columns if pid not in matched_info['pr_id'].values]\n",
    "print(\"未匹配到的 probe 数量:\", len(not_found_genes))\n",
    "print(not_found_genes[:20])  # 只看前20个\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(932, 56)"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(GE_genes), len(not_found_genes)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(153386, 919)\n"
     ]
    },
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Metadata_Plate</th>\n",
       "      <th>Metadata_Well</th>\n",
       "      <th>Metadata_Assay_Plate_Barcode</th>\n",
       "      <th>Metadata_Plate_Map_Name</th>\n",
       "      <th>Metadata_well_position</th>\n",
       "      <th>Metadata_ASSAY_WELL_ROLE</th>\n",
       "      <th>Metadata_broad_sample</th>\n",
       "      <th>Metadata_mmoles_per_liter</th>\n",
       "      <th>Metadata_solvent</th>\n",
       "      <th>Metadata_pert_id</th>\n",
       "      <th>...</th>\n",
       "      <th>Nuclei_Texture_Variance_ER_5_0</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_5_0</th>\n",
       "      <th>Metadata_pert_iname</th>\n",
       "      <th>Metadata_pert_iname2</th>\n",
       "      <th>Metadata_moa</th>\n",
       "      <th>Metadata_target</th>\n",
       "      <th>Metadata_mmoles_per_liter2</th>\n",
       "      <th>Metadata_Sample_Dose</th>\n",
       "      <th>pert_type</th>\n",
       "      <th>control_type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>24277</td>\n",
       "      <td>a01</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a01</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18250272-003-03-7</td>\n",
       "      <td>3.022516</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18250272</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.199967</td>\n",
       "      <td>-0.075658</td>\n",
       "      <td>propoxycaine</td>\n",
       "      <td>propoxycaine</td>\n",
       "      <td>local anesthetic</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6.05</td>\n",
       "      <td>BRD-K18250272-003-03-7_6.05</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>24277</td>\n",
       "      <td>a02</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a02</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18316707-001-01-9</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18316707</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.126183</td>\n",
       "      <td>0.018563</td>\n",
       "      <td>O-1918</td>\n",
       "      <td>BRD-K18316707</td>\n",
       "      <td>cannabinoid receptor antagonist</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10.00</td>\n",
       "      <td>BRD-K18316707-001-01-9_10.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>24277</td>\n",
       "      <td>a03</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a03</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18438502-001-02-6</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18438502</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.034355</td>\n",
       "      <td>0.052914</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10.00</td>\n",
       "      <td>BRD-K18438502-001-02-6_10.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>24277</td>\n",
       "      <td>a04</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a04</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18550767-001-02-8</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18550767</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.042241</td>\n",
       "      <td>0.249977</td>\n",
       "      <td>bergenin</td>\n",
       "      <td>bergenin</td>\n",
       "      <td>interleukin inhibitor</td>\n",
       "      <td>IL1B, TNF</td>\n",
       "      <td>10.00</td>\n",
       "      <td>BRD-K18550767-001-02-8_10.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>24277</td>\n",
       "      <td>a05</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a05</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18574842-323-03-3</td>\n",
       "      <td>2.195487</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18574842</td>\n",
       "      <td>...</td>\n",
       "      <td>0.080018</td>\n",
       "      <td>0.335890</td>\n",
       "      <td>nafcillin</td>\n",
       "      <td>nafcillin</td>\n",
       "      <td>bacterial cell wall synthesis inhibitor</td>\n",
       "      <td>CYP1A2, CYP3A4, SLC22A6</td>\n",
       "      <td>4.39</td>\n",
       "      <td>BRD-K18574842-323-03-3_4.39</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 919 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   Metadata_Plate Metadata_Well  Metadata_Assay_Plate_Barcode  \\\n",
       "0           24277           a01                         24277   \n",
       "1           24277           a02                         24277   \n",
       "2           24277           a03                         24277   \n",
       "3           24277           a04                         24277   \n",
       "4           24277           a05                         24277   \n",
       "\n",
       "  Metadata_Plate_Map_Name Metadata_well_position Metadata_ASSAY_WELL_ROLE  \\\n",
       "0            H-BIOA-004-3                    a01                  treated   \n",
       "1            H-BIOA-004-3                    a02                  treated   \n",
       "2            H-BIOA-004-3                    a03                  treated   \n",
       "3            H-BIOA-004-3                    a04                  treated   \n",
       "4            H-BIOA-004-3                    a05                  treated   \n",
       "\n",
       "    Metadata_broad_sample  Metadata_mmoles_per_liter Metadata_solvent  \\\n",
       "0  BRD-K18250272-003-03-7                   3.022516             DMSO   \n",
       "1  BRD-K18316707-001-01-9                   5.000000             DMSO   \n",
       "2  BRD-K18438502-001-02-6                   5.000000             DMSO   \n",
       "3  BRD-K18550767-001-02-8                   5.000000             DMSO   \n",
       "4  BRD-K18574842-323-03-3                   2.195487             DMSO   \n",
       "\n",
       "  Metadata_pert_id  ... Nuclei_Texture_Variance_ER_5_0  \\\n",
       "0    BRD-K18250272  ...                      -0.199967   \n",
       "1    BRD-K18316707  ...                      -0.126183   \n",
       "2    BRD-K18438502  ...                      -0.034355   \n",
       "3    BRD-K18550767  ...                      -0.042241   \n",
       "4    BRD-K18574842  ...                       0.080018   \n",
       "\n",
       "  Nuclei_Texture_Variance_RNA_5_0  Metadata_pert_iname Metadata_pert_iname2  \\\n",
       "0                       -0.075658         propoxycaine         propoxycaine   \n",
       "1                        0.018563               O-1918        BRD-K18316707   \n",
       "2                        0.052914                  NaN                  NaN   \n",
       "3                        0.249977             bergenin             bergenin   \n",
       "4                        0.335890            nafcillin            nafcillin   \n",
       "\n",
       "                              Metadata_moa          Metadata_target  \\\n",
       "0                         local anesthetic                      NaN   \n",
       "1          cannabinoid receptor antagonist                      NaN   \n",
       "2                                      NaN                      NaN   \n",
       "3                    interleukin inhibitor                IL1B, TNF   \n",
       "4  bacterial cell wall synthesis inhibitor  CYP1A2, CYP3A4, SLC22A6   \n",
       "\n",
       "  Metadata_mmoles_per_liter2         Metadata_Sample_Dose  pert_type  \\\n",
       "0                       6.05  BRD-K18250272-003-03-7_6.05        trt   \n",
       "1                      10.00  BRD-K18316707-001-01-9_10.0        trt   \n",
       "2                      10.00  BRD-K18438502-001-02-6_10.0        trt   \n",
       "3                      10.00  BRD-K18550767-001-02-8_10.0        trt   \n",
       "4                       4.39  BRD-K18574842-323-03-3_4.39        trt   \n",
       "\n",
       "   control_type  \n",
       "0           NaN  \n",
       "1           NaN  \n",
       "2           NaN  \n",
       "3           NaN  \n",
       "4           NaN  \n",
       "\n",
       "[5 rows x 919 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "print(CP_CSV.shape)\n",
    "CP_CSV.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "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>index</th>\n",
       "      <th>pert_type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>trt</td>\n",
       "      <td>126814</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>control</td>\n",
       "      <td>26572</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     index  pert_type\n",
       "0      trt     126814\n",
       "1  control      26572"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV['pert_type'].value_counts().reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "30413"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(CP_CSV['Metadata_pert_id'].unique())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "映射字典大小: 21782\n",
      "匹配成功: 86844/153386 (56.62%)\n"
     ]
    }
   ],
   "source": [
    "# 创建BROAD_CPD_ID到CPD_SMILES的映射字典\n",
    "smiles_mapping = dict(zip(GE_CSV['BROAD_CPD_ID'], GE_CSV['CPD_SMILES']))\n",
    "\n",
    "# 检查映射是否唯一（键值对数量应等于唯一ID数量）\n",
    "print(f\"映射字典大小: {len(smiles_mapping)}\")\n",
    "\n",
    "# 使用映射为CP_CSV添加SMILES列\n",
    "CP_CSV['SMILES'] = CP_CSV['Metadata_pert_id'].map(smiles_mapping)\n",
    "\n",
    "# 检查匹配情况\n",
    "matched = CP_CSV['SMILES'].notna().sum()\n",
    "total = len(CP_CSV)\n",
    "print(f\"匹配成功: {matched}/{total} ({matched/total:.2%})\")\n",
    "\n",
    "# 保存结果\n",
    "# CP_CSV.to_csv('path/to/updated_cp_data.csv', index=False)   "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(113416, 920)"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# 提取匹配成功或者pert_type为'control'的记录（或关系）\n",
    "\n",
    "CP_CSV_matched = CP_CSV[\n",
    "    (CP_CSV['SMILES'].notna()) |  # 匹配成功的记录\n",
    "    (CP_CSV['pert_type'] == 'control')  # 或pert_type为control的记录\n",
    "].copy()\n",
    "CP_CSV_matched.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "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>Metadata_Plate</th>\n",
       "      <th>Metadata_Well</th>\n",
       "      <th>Metadata_Assay_Plate_Barcode</th>\n",
       "      <th>Metadata_Plate_Map_Name</th>\n",
       "      <th>Metadata_well_position</th>\n",
       "      <th>Metadata_ASSAY_WELL_ROLE</th>\n",
       "      <th>Metadata_broad_sample</th>\n",
       "      <th>Metadata_mmoles_per_liter</th>\n",
       "      <th>Metadata_solvent</th>\n",
       "      <th>Metadata_pert_id</th>\n",
       "      <th>...</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_5_0</th>\n",
       "      <th>Metadata_pert_iname</th>\n",
       "      <th>Metadata_pert_iname2</th>\n",
       "      <th>Metadata_moa</th>\n",
       "      <th>Metadata_target</th>\n",
       "      <th>Metadata_mmoles_per_liter2</th>\n",
       "      <th>Metadata_Sample_Dose</th>\n",
       "      <th>pert_type</th>\n",
       "      <th>control_type</th>\n",
       "      <th>SMILES</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>24277</td>\n",
       "      <td>a01</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a01</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18250272-003-03-7</td>\n",
       "      <td>3.022516</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18250272</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.075658</td>\n",
       "      <td>propoxycaine</td>\n",
       "      <td>propoxycaine</td>\n",
       "      <td>local anesthetic</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6.05</td>\n",
       "      <td>BRD-K18250272-003-03-7_6.05</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>24277</td>\n",
       "      <td>a02</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a02</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18316707-001-01-9</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18316707</td>\n",
       "      <td>...</td>\n",
       "      <td>0.018563</td>\n",
       "      <td>O-1918</td>\n",
       "      <td>BRD-K18316707</td>\n",
       "      <td>cannabinoid receptor antagonist</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10.00</td>\n",
       "      <td>BRD-K18316707-001-01-9_10.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>24277</td>\n",
       "      <td>a03</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a03</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18438502-001-02-6</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18438502</td>\n",
       "      <td>...</td>\n",
       "      <td>0.052914</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10.00</td>\n",
       "      <td>BRD-K18438502-001-02-6_10.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>COc1cc(O)cc(\\C=C\\c2ccccc2)c1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>24277</td>\n",
       "      <td>a04</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a04</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18550767-001-02-8</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18550767</td>\n",
       "      <td>...</td>\n",
       "      <td>0.249977</td>\n",
       "      <td>bergenin</td>\n",
       "      <td>bergenin</td>\n",
       "      <td>interleukin inhibitor</td>\n",
       "      <td>IL1B, TNF</td>\n",
       "      <td>10.00</td>\n",
       "      <td>BRD-K18550767-001-02-8_10.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>24277</td>\n",
       "      <td>a05</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a05</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18574842-323-03-3</td>\n",
       "      <td>2.195487</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18574842</td>\n",
       "      <td>...</td>\n",
       "      <td>0.335890</td>\n",
       "      <td>nafcillin</td>\n",
       "      <td>nafcillin</td>\n",
       "      <td>bacterial cell wall synthesis inhibitor</td>\n",
       "      <td>CYP1A2, CYP3A4, SLC22A6</td>\n",
       "      <td>4.39</td>\n",
       "      <td>BRD-K18574842-323-03-3_4.39</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 920 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   Metadata_Plate Metadata_Well  Metadata_Assay_Plate_Barcode  \\\n",
       "0           24277           a01                         24277   \n",
       "1           24277           a02                         24277   \n",
       "2           24277           a03                         24277   \n",
       "3           24277           a04                         24277   \n",
       "4           24277           a05                         24277   \n",
       "\n",
       "  Metadata_Plate_Map_Name Metadata_well_position Metadata_ASSAY_WELL_ROLE  \\\n",
       "0            H-BIOA-004-3                    a01                  treated   \n",
       "1            H-BIOA-004-3                    a02                  treated   \n",
       "2            H-BIOA-004-3                    a03                  treated   \n",
       "3            H-BIOA-004-3                    a04                  treated   \n",
       "4            H-BIOA-004-3                    a05                  treated   \n",
       "\n",
       "    Metadata_broad_sample  Metadata_mmoles_per_liter Metadata_solvent  \\\n",
       "0  BRD-K18250272-003-03-7                   3.022516             DMSO   \n",
       "1  BRD-K18316707-001-01-9                   5.000000             DMSO   \n",
       "2  BRD-K18438502-001-02-6                   5.000000             DMSO   \n",
       "3  BRD-K18550767-001-02-8                   5.000000             DMSO   \n",
       "4  BRD-K18574842-323-03-3                   2.195487             DMSO   \n",
       "\n",
       "  Metadata_pert_id  ... Nuclei_Texture_Variance_RNA_5_0 Metadata_pert_iname  \\\n",
       "0    BRD-K18250272  ...                       -0.075658        propoxycaine   \n",
       "1    BRD-K18316707  ...                        0.018563              O-1918   \n",
       "2    BRD-K18438502  ...                        0.052914                 NaN   \n",
       "3    BRD-K18550767  ...                        0.249977            bergenin   \n",
       "4    BRD-K18574842  ...                        0.335890           nafcillin   \n",
       "\n",
       "   Metadata_pert_iname2                             Metadata_moa  \\\n",
       "0          propoxycaine                         local anesthetic   \n",
       "1         BRD-K18316707          cannabinoid receptor antagonist   \n",
       "2                   NaN                                      NaN   \n",
       "3              bergenin                    interleukin inhibitor   \n",
       "4             nafcillin  bacterial cell wall synthesis inhibitor   \n",
       "\n",
       "           Metadata_target Metadata_mmoles_per_liter2  \\\n",
       "0                      NaN                       6.05   \n",
       "1                      NaN                      10.00   \n",
       "2                      NaN                      10.00   \n",
       "3                IL1B, TNF                      10.00   \n",
       "4  CYP1A2, CYP3A4, SLC22A6                       4.39   \n",
       "\n",
       "          Metadata_Sample_Dose  pert_type  control_type  \\\n",
       "0  BRD-K18250272-003-03-7_6.05        trt           NaN   \n",
       "1  BRD-K18316707-001-01-9_10.0        trt           NaN   \n",
       "2  BRD-K18438502-001-02-6_10.0        trt           NaN   \n",
       "3  BRD-K18550767-001-02-8_10.0        trt           NaN   \n",
       "4  BRD-K18574842-323-03-3_4.39        trt           NaN   \n",
       "\n",
       "                                              SMILES  \n",
       "0                     CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC  \n",
       "1       COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C  \n",
       "2                       COc1cc(O)cc(\\C=C\\c2ccccc2)c1  \n",
       "3  COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...  \n",
       "4  CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...  \n",
       "\n",
       "[5 rows x 920 columns]"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>index</th>\n",
       "      <th>pert_type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>trt</td>\n",
       "      <td>86844</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>control</td>\n",
       "      <td>26572</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     index  pert_type\n",
       "0      trt      86844\n",
       "1  control      26572"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched['pert_type'].value_counts().reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\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>Metadata_Plate</th>\n",
       "      <th>Metadata_Well</th>\n",
       "      <th>Metadata_Assay_Plate_Barcode</th>\n",
       "      <th>Metadata_Plate_Map_Name</th>\n",
       "      <th>Metadata_well_position</th>\n",
       "      <th>Metadata_ASSAY_WELL_ROLE</th>\n",
       "      <th>Metadata_broad_sample</th>\n",
       "      <th>Metadata_mmoles_per_liter</th>\n",
       "      <th>Metadata_solvent</th>\n",
       "      <th>Metadata_pert_id</th>\n",
       "      <th>...</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_5_0</th>\n",
       "      <th>Metadata_pert_iname</th>\n",
       "      <th>Metadata_pert_iname2</th>\n",
       "      <th>Metadata_moa</th>\n",
       "      <th>Metadata_target</th>\n",
       "      <th>Metadata_mmoles_per_liter2</th>\n",
       "      <th>Metadata_Sample_Dose</th>\n",
       "      <th>pert_type</th>\n",
       "      <th>control_type</th>\n",
       "      <th>SMILES</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>24277</td>\n",
       "      <td>a01</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a01</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18250272-003-03-7</td>\n",
       "      <td>3.022516</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18250272</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.075658</td>\n",
       "      <td>propoxycaine</td>\n",
       "      <td>propoxycaine</td>\n",
       "      <td>local anesthetic</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6.05</td>\n",
       "      <td>BRD-K18250272-003-03-7_6.05</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>24277</td>\n",
       "      <td>a02</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a02</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18316707-001-01-9</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18316707</td>\n",
       "      <td>...</td>\n",
       "      <td>0.018563</td>\n",
       "      <td>O-1918</td>\n",
       "      <td>BRD-K18316707</td>\n",
       "      <td>cannabinoid receptor antagonist</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10.00</td>\n",
       "      <td>BRD-K18316707-001-01-9_10.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>24277</td>\n",
       "      <td>a03</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a03</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18438502-001-02-6</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18438502</td>\n",
       "      <td>...</td>\n",
       "      <td>0.052914</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10.00</td>\n",
       "      <td>BRD-K18438502-001-02-6_10.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>COc1cc(O)cc(\\C=C\\c2ccccc2)c1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>24277</td>\n",
       "      <td>a04</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a04</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18550767-001-02-8</td>\n",
       "      <td>5.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18550767</td>\n",
       "      <td>...</td>\n",
       "      <td>0.249977</td>\n",
       "      <td>bergenin</td>\n",
       "      <td>bergenin</td>\n",
       "      <td>interleukin inhibitor</td>\n",
       "      <td>IL1B, TNF</td>\n",
       "      <td>10.00</td>\n",
       "      <td>BRD-K18550767-001-02-8_10.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>24277</td>\n",
       "      <td>a05</td>\n",
       "      <td>24277</td>\n",
       "      <td>H-BIOA-004-3</td>\n",
       "      <td>a05</td>\n",
       "      <td>treated</td>\n",
       "      <td>BRD-K18574842-323-03-3</td>\n",
       "      <td>2.195487</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>BRD-K18574842</td>\n",
       "      <td>...</td>\n",
       "      <td>0.335890</td>\n",
       "      <td>nafcillin</td>\n",
       "      <td>nafcillin</td>\n",
       "      <td>bacterial cell wall synthesis inhibitor</td>\n",
       "      <td>CYP1A2, CYP3A4, SLC22A6</td>\n",
       "      <td>4.39</td>\n",
       "      <td>BRD-K18574842-323-03-3_4.39</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 920 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   Metadata_Plate Metadata_Well  Metadata_Assay_Plate_Barcode  \\\n",
       "0           24277           a01                         24277   \n",
       "1           24277           a02                         24277   \n",
       "2           24277           a03                         24277   \n",
       "3           24277           a04                         24277   \n",
       "4           24277           a05                         24277   \n",
       "\n",
       "  Metadata_Plate_Map_Name Metadata_well_position Metadata_ASSAY_WELL_ROLE  \\\n",
       "0            H-BIOA-004-3                    a01                  treated   \n",
       "1            H-BIOA-004-3                    a02                  treated   \n",
       "2            H-BIOA-004-3                    a03                  treated   \n",
       "3            H-BIOA-004-3                    a04                  treated   \n",
       "4            H-BIOA-004-3                    a05                  treated   \n",
       "\n",
       "    Metadata_broad_sample  Metadata_mmoles_per_liter Metadata_solvent  \\\n",
       "0  BRD-K18250272-003-03-7                   3.022516             DMSO   \n",
       "1  BRD-K18316707-001-01-9                   5.000000             DMSO   \n",
       "2  BRD-K18438502-001-02-6                   5.000000             DMSO   \n",
       "3  BRD-K18550767-001-02-8                   5.000000             DMSO   \n",
       "4  BRD-K18574842-323-03-3                   2.195487             DMSO   \n",
       "\n",
       "  Metadata_pert_id  ... Nuclei_Texture_Variance_RNA_5_0 Metadata_pert_iname  \\\n",
       "0    BRD-K18250272  ...                       -0.075658        propoxycaine   \n",
       "1    BRD-K18316707  ...                        0.018563              O-1918   \n",
       "2    BRD-K18438502  ...                        0.052914                 NaN   \n",
       "3    BRD-K18550767  ...                        0.249977            bergenin   \n",
       "4    BRD-K18574842  ...                        0.335890           nafcillin   \n",
       "\n",
       "   Metadata_pert_iname2                             Metadata_moa  \\\n",
       "0          propoxycaine                         local anesthetic   \n",
       "1         BRD-K18316707          cannabinoid receptor antagonist   \n",
       "2                   NaN                                      NaN   \n",
       "3              bergenin                    interleukin inhibitor   \n",
       "4             nafcillin  bacterial cell wall synthesis inhibitor   \n",
       "\n",
       "           Metadata_target Metadata_mmoles_per_liter2  \\\n",
       "0                      NaN                       6.05   \n",
       "1                      NaN                      10.00   \n",
       "2                      NaN                      10.00   \n",
       "3                IL1B, TNF                      10.00   \n",
       "4  CYP1A2, CYP3A4, SLC22A6                       4.39   \n",
       "\n",
       "          Metadata_Sample_Dose  pert_type  control_type  \\\n",
       "0  BRD-K18250272-003-03-7_6.05        trt           NaN   \n",
       "1  BRD-K18316707-001-01-9_10.0        trt           NaN   \n",
       "2  BRD-K18438502-001-02-6_10.0        trt           NaN   \n",
       "3  BRD-K18550767-001-02-8_10.0        trt           NaN   \n",
       "4  BRD-K18574842-323-03-3_4.39        trt           NaN   \n",
       "\n",
       "                                              SMILES  \n",
       "0                     CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC  \n",
       "1       COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C  \n",
       "2                       COc1cc(O)cc(\\C=C\\c2ccccc2)c1  \n",
       "3  COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...  \n",
       "4  CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...  \n",
       "\n",
       "[5 rows x 920 columns]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 删除无关元素，保留核心"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Metadata_Plate</th>\n",
       "      <th>Metadata_pert_mfc_id</th>\n",
       "      <th>Metadata_pert_well</th>\n",
       "      <th>Metadata_pert_id_vendor</th>\n",
       "      <th>Metadata_cell_id</th>\n",
       "      <th>Metadata_broad_sample_type</th>\n",
       "      <th>Metadata_pert_vehicle</th>\n",
       "      <th>Metadata_pert_type</th>\n",
       "      <th>Cells_AreaShape_Compactness</th>\n",
       "      <th>Cells_AreaShape_EulerNumber</th>\n",
       "      <th>...</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_5_0</th>\n",
       "      <th>Metadata_pert_iname</th>\n",
       "      <th>Metadata_pert_iname2</th>\n",
       "      <th>Metadata_moa</th>\n",
       "      <th>Metadata_target</th>\n",
       "      <th>Metadata_mmoles_per_liter2</th>\n",
       "      <th>Metadata_Sample_Dose</th>\n",
       "      <th>pert_type</th>\n",
       "      <th>control_type</th>\n",
       "      <th>SMILES</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>24277</td>\n",
       "      <td>BRD-K18250272-003-03-7</td>\n",
       "      <td>a01</td>\n",
       "      <td>NaN</td>\n",
       "      <td>U2OS</td>\n",
       "      <td>trt</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>trt</td>\n",
       "      <td>0.256710</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.075658</td>\n",
       "      <td>propoxycaine</td>\n",
       "      <td>propoxycaine</td>\n",
       "      <td>local anesthetic</td>\n",
       "      <td>NaN</td>\n",
       "      <td>6.05</td>\n",
       "      <td>BRD-K18250272-003-03-7_6.05</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>24277</td>\n",
       "      <td>BRD-K18316707-001-01-9</td>\n",
       "      <td>a02</td>\n",
       "      <td>NaN</td>\n",
       "      <td>U2OS</td>\n",
       "      <td>trt</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>trt</td>\n",
       "      <td>0.050962</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>0.018563</td>\n",
       "      <td>O-1918</td>\n",
       "      <td>BRD-K18316707</td>\n",
       "      <td>cannabinoid receptor antagonist</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10.00</td>\n",
       "      <td>BRD-K18316707-001-01-9_10.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>24277</td>\n",
       "      <td>BRD-K18438502-001-02-6</td>\n",
       "      <td>a03</td>\n",
       "      <td>NaN</td>\n",
       "      <td>U2OS</td>\n",
       "      <td>trt</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>trt</td>\n",
       "      <td>-0.098185</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>0.052914</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10.00</td>\n",
       "      <td>BRD-K18438502-001-02-6_10.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>COc1cc(O)cc(\\C=C\\c2ccccc2)c1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>24277</td>\n",
       "      <td>BRD-K18550767-001-02-8</td>\n",
       "      <td>a04</td>\n",
       "      <td>NaN</td>\n",
       "      <td>U2OS</td>\n",
       "      <td>trt</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>trt</td>\n",
       "      <td>0.410722</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>0.249977</td>\n",
       "      <td>bergenin</td>\n",
       "      <td>bergenin</td>\n",
       "      <td>interleukin inhibitor</td>\n",
       "      <td>IL1B, TNF</td>\n",
       "      <td>10.00</td>\n",
       "      <td>BRD-K18550767-001-02-8_10.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>24277</td>\n",
       "      <td>BRD-K18574842-323-03-3</td>\n",
       "      <td>a05</td>\n",
       "      <td>NaN</td>\n",
       "      <td>U2OS</td>\n",
       "      <td>trt</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>trt</td>\n",
       "      <td>0.248559</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>0.335890</td>\n",
       "      <td>nafcillin</td>\n",
       "      <td>nafcillin</td>\n",
       "      <td>bacterial cell wall synthesis inhibitor</td>\n",
       "      <td>CYP1A2, CYP3A4, SLC22A6</td>\n",
       "      <td>4.39</td>\n",
       "      <td>BRD-K18574842-323-03-3_4.39</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 911 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   Metadata_Plate    Metadata_pert_mfc_id Metadata_pert_well  \\\n",
       "0           24277  BRD-K18250272-003-03-7                a01   \n",
       "1           24277  BRD-K18316707-001-01-9                a02   \n",
       "2           24277  BRD-K18438502-001-02-6                a03   \n",
       "3           24277  BRD-K18550767-001-02-8                a04   \n",
       "4           24277  BRD-K18574842-323-03-3                a05   \n",
       "\n",
       "   Metadata_pert_id_vendor Metadata_cell_id Metadata_broad_sample_type  \\\n",
       "0                      NaN             U2OS                        trt   \n",
       "1                      NaN             U2OS                        trt   \n",
       "2                      NaN             U2OS                        trt   \n",
       "3                      NaN             U2OS                        trt   \n",
       "4                      NaN             U2OS                        trt   \n",
       "\n",
       "  Metadata_pert_vehicle Metadata_pert_type  Cells_AreaShape_Compactness  \\\n",
       "0                  DMSO                trt                     0.256710   \n",
       "1                  DMSO                trt                     0.050962   \n",
       "2                  DMSO                trt                    -0.098185   \n",
       "3                  DMSO                trt                     0.410722   \n",
       "4                  DMSO                trt                     0.248559   \n",
       "\n",
       "   Cells_AreaShape_EulerNumber  ...  Nuclei_Texture_Variance_RNA_5_0  \\\n",
       "0                          NaN  ...                        -0.075658   \n",
       "1                          NaN  ...                         0.018563   \n",
       "2                          NaN  ...                         0.052914   \n",
       "3                          NaN  ...                         0.249977   \n",
       "4                          NaN  ...                         0.335890   \n",
       "\n",
       "   Metadata_pert_iname  Metadata_pert_iname2  \\\n",
       "0         propoxycaine          propoxycaine   \n",
       "1               O-1918         BRD-K18316707   \n",
       "2                  NaN                   NaN   \n",
       "3             bergenin              bergenin   \n",
       "4            nafcillin             nafcillin   \n",
       "\n",
       "                              Metadata_moa          Metadata_target  \\\n",
       "0                         local anesthetic                      NaN   \n",
       "1          cannabinoid receptor antagonist                      NaN   \n",
       "2                                      NaN                      NaN   \n",
       "3                    interleukin inhibitor                IL1B, TNF   \n",
       "4  bacterial cell wall synthesis inhibitor  CYP1A2, CYP3A4, SLC22A6   \n",
       "\n",
       "   Metadata_mmoles_per_liter2         Metadata_Sample_Dose  pert_type  \\\n",
       "0                        6.05  BRD-K18250272-003-03-7_6.05        trt   \n",
       "1                       10.00  BRD-K18316707-001-01-9_10.0        trt   \n",
       "2                       10.00  BRD-K18438502-001-02-6_10.0        trt   \n",
       "3                       10.00  BRD-K18550767-001-02-8_10.0        trt   \n",
       "4                        4.39  BRD-K18574842-323-03-3_4.39        trt   \n",
       "\n",
       "   control_type                                             SMILES  \n",
       "0           NaN                     CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC  \n",
       "1           NaN       COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C  \n",
       "2           NaN                       COc1cc(O)cc(\\C=C\\c2ccccc2)c1  \n",
       "3           NaN  COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...  \n",
       "4           NaN  CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...  \n",
       "\n",
       "[5 rows x 911 columns]"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched_filter = CP_CSV_matched.drop(columns=['Metadata_Well', 'Metadata_Assay_Plate_Barcode', 'Metadata_Plate_Map_Name', 'Metadata_well_position',\\\n",
    "    'Metadata_ASSAY_WELL_ROLE', 'Metadata_broad_sample', 'Metadata_mmoles_per_liter', 'Metadata_solvent', 'Metadata_pert_id'])\n",
    "CP_CSV_matched_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>Metadata_Plate</th>\n",
       "      <th>Metadata_pert_mfc_id</th>\n",
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       "      <th>Metadata_pert_id_vendor</th>\n",
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       "      <th>Cells_AreaShape_EulerNumber</th>\n",
       "      <th>...</th>\n",
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       "      <th>Nuclei_Texture_SumVariance_RNA_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_AGP_5_0</th>\n",
       "      <th>Nuclei_Texture_Variance_ER_5_0</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_5_0</th>\n",
       "      <th>Metadata_mmoles_per_liter2</th>\n",
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       "      <th>control_type</th>\n",
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       "      <td>DMSO</td>\n",
       "      <td>trt</td>\n",
       "      <td>-0.098185</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.007979</td>\n",
       "      <td>0.081155</td>\n",
       "      <td>-0.089633</td>\n",
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       "      <td>10.00</td>\n",
       "      <td>BRD-K18438502-001-02-6_10.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>COc1cc(O)cc(\\C=C\\c2ccccc2)c1</td>\n",
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       "      <td>a04</td>\n",
       "      <td>NaN</td>\n",
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       "      <td>trt</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>trt</td>\n",
       "      <td>0.410722</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.034251</td>\n",
       "      <td>-0.047597</td>\n",
       "      <td>0.103611</td>\n",
       "      <td>-0.139579</td>\n",
       "      <td>-0.042241</td>\n",
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       "      <td>NaN</td>\n",
       "      <td>COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...</td>\n",
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       "      <td>-0.033797</td>\n",
       "      <td>0.080018</td>\n",
       "      <td>0.335890</td>\n",
       "      <td>4.39</td>\n",
       "      <td>BRD-K18574842-323-03-3_4.39</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...</td>\n",
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       "</table>\n",
       "<p>5 rows × 906 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   Metadata_Plate    Metadata_pert_mfc_id Metadata_pert_well  \\\n",
       "0           24277  BRD-K18250272-003-03-7                a01   \n",
       "1           24277  BRD-K18316707-001-01-9                a02   \n",
       "2           24277  BRD-K18438502-001-02-6                a03   \n",
       "3           24277  BRD-K18550767-001-02-8                a04   \n",
       "4           24277  BRD-K18574842-323-03-3                a05   \n",
       "\n",
       "   Metadata_pert_id_vendor Metadata_cell_id Metadata_broad_sample_type  \\\n",
       "0                      NaN             U2OS                        trt   \n",
       "1                      NaN             U2OS                        trt   \n",
       "2                      NaN             U2OS                        trt   \n",
       "3                      NaN             U2OS                        trt   \n",
       "4                      NaN             U2OS                        trt   \n",
       "\n",
       "  Metadata_pert_vehicle Metadata_pert_type  Cells_AreaShape_Compactness  \\\n",
       "0                  DMSO                trt                     0.256710   \n",
       "1                  DMSO                trt                     0.050962   \n",
       "2                  DMSO                trt                    -0.098185   \n",
       "3                  DMSO                trt                     0.410722   \n",
       "4                  DMSO                trt                     0.248559   \n",
       "\n",
       "   Cells_AreaShape_EulerNumber  ...  Nuclei_Texture_SumVariance_ER_3_0  \\\n",
       "0                          NaN  ...                          -0.156442   \n",
       "1                          NaN  ...                          -0.113721   \n",
       "2                          NaN  ...                          -0.007979   \n",
       "3                          NaN  ...                          -0.034251   \n",
       "4                          NaN  ...                           0.257598   \n",
       "\n",
       "   Nuclei_Texture_SumVariance_Mito_5_0  Nuclei_Texture_SumVariance_RNA_10_0  \\\n",
       "0                            -0.018014                            -0.024573   \n",
       "1                            -0.089807                            -0.041392   \n",
       "2                             0.081155                            -0.089633   \n",
       "3                            -0.047597                             0.103611   \n",
       "4                             0.193370                             0.238471   \n",
       "\n",
       "   Nuclei_Texture_Variance_AGP_5_0  Nuclei_Texture_Variance_ER_5_0  \\\n",
       "0                        -0.383890                       -0.199967   \n",
       "1                        -0.248967                       -0.126183   \n",
       "2                         0.043140                       -0.034355   \n",
       "3                        -0.139579                       -0.042241   \n",
       "4                        -0.033797                        0.080018   \n",
       "\n",
       "   Nuclei_Texture_Variance_RNA_5_0  Metadata_mmoles_per_liter2  \\\n",
       "0                        -0.075658                        6.05   \n",
       "1                         0.018563                       10.00   \n",
       "2                         0.052914                       10.00   \n",
       "3                         0.249977                       10.00   \n",
       "4                         0.335890                        4.39   \n",
       "\n",
       "          Metadata_Sample_Dose  control_type  \\\n",
       "0  BRD-K18250272-003-03-7_6.05           NaN   \n",
       "1  BRD-K18316707-001-01-9_10.0           NaN   \n",
       "2  BRD-K18438502-001-02-6_10.0           NaN   \n",
       "3  BRD-K18550767-001-02-8_10.0           NaN   \n",
       "4  BRD-K18574842-323-03-3_4.39           NaN   \n",
       "\n",
       "                                              SMILES  \n",
       "0                     CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC  \n",
       "1       COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C  \n",
       "2                       COc1cc(O)cc(\\C=C\\c2ccccc2)c1  \n",
       "3  COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...  \n",
       "4  CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...  \n",
       "\n",
       "[5 rows x 906 columns]"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched_filter = CP_CSV_matched_filter.drop(columns=['Metadata_pert_iname', 'Metadata_Sample_Dose', \\\n",
    "    'Metadata_pert_iname2', 'Metadata_moa', 'Metadata_target', 'pert_type'])\n",
    "CP_CSV_matched_filter.head()\n",
    "## Metadata_mmoles_per_liter2 Metadata_Sample_Dose"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
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       "      <th>2</th>\n",
       "      <td>24277</td>\n",
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       "      <td>0.044212</td>\n",
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       "      <td>0.011985</td>\n",
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       "      <td>0.094736</td>\n",
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       "      <td>-0.089633</td>\n",
       "      <td>0.043140</td>\n",
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       "      <td>0.052914</td>\n",
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       "      <td>COc1cc(O)cc(\\C=C\\c2ccccc2)c1</td>\n",
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       "      <th>3</th>\n",
       "      <td>24277</td>\n",
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       "      <td>-0.221396</td>\n",
       "      <td>-0.086168</td>\n",
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       "      <td>0.257598</td>\n",
       "      <td>0.193370</td>\n",
       "      <td>0.238471</td>\n",
       "      <td>-0.033797</td>\n",
       "      <td>0.080018</td>\n",
       "      <td>0.335890</td>\n",
       "      <td>4.39</td>\n",
       "      <td>BRD-K18574842-323-03-3_4.39</td>\n",
       "      <td>CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 898 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   Metadata_Plate  Cells_AreaShape_Compactness  Cells_AreaShape_EulerNumber  \\\n",
       "0           24277                     0.256710                          NaN   \n",
       "1           24277                     0.050962                          NaN   \n",
       "2           24277                    -0.098185                          NaN   \n",
       "3           24277                     0.410722                          NaN   \n",
       "4           24277                     0.248559                          NaN   \n",
       "\n",
       "   Cells_AreaShape_Extent  Cells_AreaShape_FormFactor  \\\n",
       "0               -0.114990                   -0.237090   \n",
       "1                0.051053                   -0.033733   \n",
       "2                0.044212                    0.164668   \n",
       "3               -0.236208                   -0.055084   \n",
       "4               -0.020058                    0.085772   \n",
       "\n",
       "   Cells_AreaShape_MaxFeretDiameter  Cells_AreaShape_MaximumRadius  \\\n",
       "0                          0.615594                       0.550434   \n",
       "1                          0.271953                       0.172714   \n",
       "2                          0.011985                       0.127098   \n",
       "3                          0.694648                       0.516785   \n",
       "4                          0.678742                       0.671897   \n",
       "\n",
       "   Cells_AreaShape_Solidity  Cells_AreaShape_Zernike_0_0  \\\n",
       "0                  0.072795                    -0.210908   \n",
       "1                  0.145941                    -0.039057   \n",
       "2                  0.094736                     0.078257   \n",
       "3                  0.154239                    -0.347572   \n",
       "4                  0.214587                    -0.221396   \n",
       "\n",
       "   Cells_AreaShape_Zernike_1_1  ...  Nuclei_Texture_SumEntropy_RNA_5_0  \\\n",
       "0                     0.008488  ...                           0.118997   \n",
       "1                    -0.070826  ...                           0.065822   \n",
       "2                     0.119333  ...                           0.079777   \n",
       "3                    -0.172400  ...                           0.339100   \n",
       "4                    -0.086168  ...                           0.415623   \n",
       "\n",
       "   Nuclei_Texture_SumVariance_ER_3_0  Nuclei_Texture_SumVariance_Mito_5_0  \\\n",
       "0                          -0.156442                            -0.018014   \n",
       "1                          -0.113721                            -0.089807   \n",
       "2                          -0.007979                             0.081155   \n",
       "3                          -0.034251                            -0.047597   \n",
       "4                           0.257598                             0.193370   \n",
       "\n",
       "   Nuclei_Texture_SumVariance_RNA_10_0  Nuclei_Texture_Variance_AGP_5_0  \\\n",
       "0                            -0.024573                        -0.383890   \n",
       "1                            -0.041392                        -0.248967   \n",
       "2                            -0.089633                         0.043140   \n",
       "3                             0.103611                        -0.139579   \n",
       "4                             0.238471                        -0.033797   \n",
       "\n",
       "   Nuclei_Texture_Variance_ER_5_0  Nuclei_Texture_Variance_RNA_5_0  \\\n",
       "0                       -0.199967                        -0.075658   \n",
       "1                       -0.126183                         0.018563   \n",
       "2                       -0.034355                         0.052914   \n",
       "3                       -0.042241                         0.249977   \n",
       "4                        0.080018                         0.335890   \n",
       "\n",
       "   Metadata_mmoles_per_liter2         Metadata_Sample_Dose  \\\n",
       "0                        6.05  BRD-K18250272-003-03-7_6.05   \n",
       "1                       10.00  BRD-K18316707-001-01-9_10.0   \n",
       "2                       10.00  BRD-K18438502-001-02-6_10.0   \n",
       "3                       10.00  BRD-K18550767-001-02-8_10.0   \n",
       "4                        4.39  BRD-K18574842-323-03-3_4.39   \n",
       "\n",
       "                                              SMILES  \n",
       "0                     CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC  \n",
       "1       COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C  \n",
       "2                       COc1cc(O)cc(\\C=C\\c2ccccc2)c1  \n",
       "3  COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...  \n",
       "4  CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...  \n",
       "\n",
       "[5 rows x 898 columns]"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched_filter = CP_CSV_matched_filter.drop(columns=['Metadata_pert_mfc_id', 'Metadata_pert_type', 'control_type', \\\n",
    "    'Metadata_pert_well', 'Metadata_pert_id_vendor', 'Metadata_cell_id', 'Metadata_broad_sample_type', 'Metadata_pert_vehicle'])\n",
    "CP_CSV_matched_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Metadata_mmoles_per_liter2</th>\n",
       "      <th>SMILES</th>\n",
       "      <th>Metadata_Plate</th>\n",
       "      <th>Cells_AreaShape_Compactness</th>\n",
       "      <th>Cells_AreaShape_EulerNumber</th>\n",
       "      <th>Cells_AreaShape_Extent</th>\n",
       "      <th>Cells_AreaShape_FormFactor</th>\n",
       "      <th>Cells_AreaShape_MaxFeretDiameter</th>\n",
       "      <th>Cells_AreaShape_MaximumRadius</th>\n",
       "      <th>Cells_AreaShape_Solidity</th>\n",
       "      <th>...</th>\n",
       "      <th>Nuclei_Texture_SumEntropy_DNA_5_0</th>\n",
       "      <th>Nuclei_Texture_SumEntropy_ER_3_0</th>\n",
       "      <th>Nuclei_Texture_SumEntropy_Mito_3_0</th>\n",
       "      <th>Nuclei_Texture_SumEntropy_RNA_5_0</th>\n",
       "      <th>Nuclei_Texture_SumVariance_ER_3_0</th>\n",
       "      <th>Nuclei_Texture_SumVariance_Mito_5_0</th>\n",
       "      <th>Nuclei_Texture_SumVariance_RNA_10_0</th>\n",
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>6.05</td>\n",
       "      <td>CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC</td>\n",
       "      <td>24277</td>\n",
       "      <td>0.256710</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.114990</td>\n",
       "      <td>-0.237090</td>\n",
       "      <td>0.615594</td>\n",
       "      <td>0.550434</td>\n",
       "      <td>0.072795</td>\n",
       "      <td>...</td>\n",
       "      <td>0.090021</td>\n",
       "      <td>0.375747</td>\n",
       "      <td>-0.010427</td>\n",
       "      <td>0.118997</td>\n",
       "      <td>-0.156442</td>\n",
       "      <td>-0.018014</td>\n",
       "      <td>-0.024573</td>\n",
       "      <td>-0.383890</td>\n",
       "      <td>-0.199967</td>\n",
       "      <td>-0.075658</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>10.00</td>\n",
       "      <td>COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C</td>\n",
       "      <td>24277</td>\n",
       "      <td>0.050962</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.051053</td>\n",
       "      <td>-0.033733</td>\n",
       "      <td>0.271953</td>\n",
       "      <td>0.172714</td>\n",
       "      <td>0.145941</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.030338</td>\n",
       "      <td>0.390687</td>\n",
       "      <td>-0.058560</td>\n",
       "      <td>0.065822</td>\n",
       "      <td>-0.113721</td>\n",
       "      <td>-0.089807</td>\n",
       "      <td>-0.041392</td>\n",
       "      <td>-0.248967</td>\n",
       "      <td>-0.126183</td>\n",
       "      <td>0.018563</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>10.00</td>\n",
       "      <td>COc1cc(O)cc(\\C=C\\c2ccccc2)c1</td>\n",
       "      <td>24277</td>\n",
       "      <td>-0.098185</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.044212</td>\n",
       "      <td>0.164668</td>\n",
       "      <td>0.011985</td>\n",
       "      <td>0.127098</td>\n",
       "      <td>0.094736</td>\n",
       "      <td>...</td>\n",
       "      <td>0.102946</td>\n",
       "      <td>0.279148</td>\n",
       "      <td>0.029891</td>\n",
       "      <td>0.079777</td>\n",
       "      <td>-0.007979</td>\n",
       "      <td>0.081155</td>\n",
       "      <td>-0.089633</td>\n",
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       "      <td>-0.034355</td>\n",
       "      <td>0.052914</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>10.00</td>\n",
       "      <td>COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...</td>\n",
       "      <td>24277</td>\n",
       "      <td>0.410722</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.236208</td>\n",
       "      <td>-0.055084</td>\n",
       "      <td>0.694648</td>\n",
       "      <td>0.516785</td>\n",
       "      <td>0.154239</td>\n",
       "      <td>...</td>\n",
       "      <td>0.470516</td>\n",
       "      <td>0.214792</td>\n",
       "      <td>0.015408</td>\n",
       "      <td>0.339100</td>\n",
       "      <td>-0.034251</td>\n",
       "      <td>-0.047597</td>\n",
       "      <td>0.103611</td>\n",
       "      <td>-0.139579</td>\n",
       "      <td>-0.042241</td>\n",
       "      <td>0.249977</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4.39</td>\n",
       "      <td>CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...</td>\n",
       "      <td>24277</td>\n",
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       "      <td>0.085772</td>\n",
       "      <td>0.678742</td>\n",
       "      <td>0.671897</td>\n",
       "      <td>0.214587</td>\n",
       "      <td>...</td>\n",
       "      <td>0.671790</td>\n",
       "      <td>0.424186</td>\n",
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       "      <td>0.193370</td>\n",
       "      <td>0.238471</td>\n",
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       "      <td>0.080018</td>\n",
       "      <td>0.335890</td>\n",
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       "</table>\n",
       "<p>5 rows × 897 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   Metadata_mmoles_per_liter2  \\\n",
       "0                        6.05   \n",
       "1                       10.00   \n",
       "2                       10.00   \n",
       "3                       10.00   \n",
       "4                        4.39   \n",
       "\n",
       "                                              SMILES  Metadata_Plate  \\\n",
       "0                     CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC           24277   \n",
       "1       COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C           24277   \n",
       "2                       COc1cc(O)cc(\\C=C\\c2ccccc2)c1           24277   \n",
       "3  COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...           24277   \n",
       "4  CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...           24277   \n",
       "\n",
       "   Cells_AreaShape_Compactness  Cells_AreaShape_EulerNumber  \\\n",
       "0                     0.256710                          NaN   \n",
       "1                     0.050962                          NaN   \n",
       "2                    -0.098185                          NaN   \n",
       "3                     0.410722                          NaN   \n",
       "4                     0.248559                          NaN   \n",
       "\n",
       "   Cells_AreaShape_Extent  Cells_AreaShape_FormFactor  \\\n",
       "0               -0.114990                   -0.237090   \n",
       "1                0.051053                   -0.033733   \n",
       "2                0.044212                    0.164668   \n",
       "3               -0.236208                   -0.055084   \n",
       "4               -0.020058                    0.085772   \n",
       "\n",
       "   Cells_AreaShape_MaxFeretDiameter  Cells_AreaShape_MaximumRadius  \\\n",
       "0                          0.615594                       0.550434   \n",
       "1                          0.271953                       0.172714   \n",
       "2                          0.011985                       0.127098   \n",
       "3                          0.694648                       0.516785   \n",
       "4                          0.678742                       0.671897   \n",
       "\n",
       "   Cells_AreaShape_Solidity  ...  Nuclei_Texture_SumEntropy_DNA_5_0  \\\n",
       "0                  0.072795  ...                           0.090021   \n",
       "1                  0.145941  ...                          -0.030338   \n",
       "2                  0.094736  ...                           0.102946   \n",
       "3                  0.154239  ...                           0.470516   \n",
       "4                  0.214587  ...                           0.671790   \n",
       "\n",
       "   Nuclei_Texture_SumEntropy_ER_3_0  Nuclei_Texture_SumEntropy_Mito_3_0  \\\n",
       "0                          0.375747                           -0.010427   \n",
       "1                          0.390687                           -0.058560   \n",
       "2                          0.279148                            0.029891   \n",
       "3                          0.214792                            0.015408   \n",
       "4                          0.424186                            0.118873   \n",
       "\n",
       "   Nuclei_Texture_SumEntropy_RNA_5_0  Nuclei_Texture_SumVariance_ER_3_0  \\\n",
       "0                           0.118997                          -0.156442   \n",
       "1                           0.065822                          -0.113721   \n",
       "2                           0.079777                          -0.007979   \n",
       "3                           0.339100                          -0.034251   \n",
       "4                           0.415623                           0.257598   \n",
       "\n",
       "   Nuclei_Texture_SumVariance_Mito_5_0  Nuclei_Texture_SumVariance_RNA_10_0  \\\n",
       "0                            -0.018014                            -0.024573   \n",
       "1                            -0.089807                            -0.041392   \n",
       "2                             0.081155                            -0.089633   \n",
       "3                            -0.047597                             0.103611   \n",
       "4                             0.193370                             0.238471   \n",
       "\n",
       "   Nuclei_Texture_Variance_AGP_5_0  Nuclei_Texture_Variance_ER_5_0  \\\n",
       "0                        -0.383890                       -0.199967   \n",
       "1                        -0.248967                       -0.126183   \n",
       "2                         0.043140                       -0.034355   \n",
       "3                        -0.139579                       -0.042241   \n",
       "4                        -0.033797                        0.080018   \n",
       "\n",
       "   Nuclei_Texture_Variance_RNA_5_0  \n",
       "0                        -0.075658  \n",
       "1                         0.018563  \n",
       "2                         0.052914  \n",
       "3                         0.249977  \n",
       "4                         0.335890  \n",
       "\n",
       "[5 rows x 897 columns]"
      ]
     },
     "execution_count": 29,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# 把最后一列移动到第一列\n",
    "cols = CP_CSV_matched_filter.columns.tolist()\n",
    "cols = [cols[-1]] + cols[:-1]\n",
    "CP_CSV_matched_filter = CP_CSV_matched_filter[cols]\n",
    "CP_CSV_matched_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>0</th>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>10.00</td>\n",
       "      <td>COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C</td>\n",
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       "      <td>0.051053</td>\n",
       "      <td>-0.033733</td>\n",
       "      <td>0.271953</td>\n",
       "      <td>0.172714</td>\n",
       "      <td>0.145941</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.030338</td>\n",
       "      <td>0.390687</td>\n",
       "      <td>-0.058560</td>\n",
       "      <td>0.065822</td>\n",
       "      <td>-0.113721</td>\n",
       "      <td>-0.089807</td>\n",
       "      <td>-0.041392</td>\n",
       "      <td>-0.248967</td>\n",
       "      <td>-0.126183</td>\n",
       "      <td>0.018563</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>10.00</td>\n",
       "      <td>COc1cc(O)cc(\\C=C\\c2ccccc2)c1</td>\n",
       "      <td>24277</td>\n",
       "      <td>-0.098185</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.044212</td>\n",
       "      <td>0.164668</td>\n",
       "      <td>0.011985</td>\n",
       "      <td>0.127098</td>\n",
       "      <td>0.094736</td>\n",
       "      <td>...</td>\n",
       "      <td>0.102946</td>\n",
       "      <td>0.279148</td>\n",
       "      <td>0.029891</td>\n",
       "      <td>0.079777</td>\n",
       "      <td>-0.007979</td>\n",
       "      <td>0.081155</td>\n",
       "      <td>-0.089633</td>\n",
       "      <td>0.043140</td>\n",
       "      <td>-0.034355</td>\n",
       "      <td>0.052914</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>10.00</td>\n",
       "      <td>COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...</td>\n",
       "      <td>24277</td>\n",
       "      <td>0.410722</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.236208</td>\n",
       "      <td>-0.055084</td>\n",
       "      <td>0.694648</td>\n",
       "      <td>0.516785</td>\n",
       "      <td>0.154239</td>\n",
       "      <td>...</td>\n",
       "      <td>0.470516</td>\n",
       "      <td>0.214792</td>\n",
       "      <td>0.015408</td>\n",
       "      <td>0.339100</td>\n",
       "      <td>-0.034251</td>\n",
       "      <td>-0.047597</td>\n",
       "      <td>0.103611</td>\n",
       "      <td>-0.139579</td>\n",
       "      <td>-0.042241</td>\n",
       "      <td>0.249977</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4.39</td>\n",
       "      <td>CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...</td>\n",
       "      <td>24277</td>\n",
       "      <td>0.248559</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.020058</td>\n",
       "      <td>0.085772</td>\n",
       "      <td>0.678742</td>\n",
       "      <td>0.671897</td>\n",
       "      <td>0.214587</td>\n",
       "      <td>...</td>\n",
       "      <td>0.671790</td>\n",
       "      <td>0.424186</td>\n",
       "      <td>0.118873</td>\n",
       "      <td>0.415623</td>\n",
       "      <td>0.257598</td>\n",
       "      <td>0.193370</td>\n",
       "      <td>0.238471</td>\n",
       "      <td>-0.033797</td>\n",
       "      <td>0.080018</td>\n",
       "      <td>0.335890</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 897 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    does                                             SMILES  Metadata_Plate  \\\n",
       "0   6.05                     CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC           24277   \n",
       "1  10.00       COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C           24277   \n",
       "2  10.00                       COc1cc(O)cc(\\C=C\\c2ccccc2)c1           24277   \n",
       "3  10.00  COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...           24277   \n",
       "4   4.39  CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...           24277   \n",
       "\n",
       "   Cells_AreaShape_Compactness  Cells_AreaShape_EulerNumber  \\\n",
       "0                     0.256710                          NaN   \n",
       "1                     0.050962                          NaN   \n",
       "2                    -0.098185                          NaN   \n",
       "3                     0.410722                          NaN   \n",
       "4                     0.248559                          NaN   \n",
       "\n",
       "   Cells_AreaShape_Extent  Cells_AreaShape_FormFactor  \\\n",
       "0               -0.114990                   -0.237090   \n",
       "1                0.051053                   -0.033733   \n",
       "2                0.044212                    0.164668   \n",
       "3               -0.236208                   -0.055084   \n",
       "4               -0.020058                    0.085772   \n",
       "\n",
       "   Cells_AreaShape_MaxFeretDiameter  Cells_AreaShape_MaximumRadius  \\\n",
       "0                          0.615594                       0.550434   \n",
       "1                          0.271953                       0.172714   \n",
       "2                          0.011985                       0.127098   \n",
       "3                          0.694648                       0.516785   \n",
       "4                          0.678742                       0.671897   \n",
       "\n",
       "   Cells_AreaShape_Solidity  ...  Nuclei_Texture_SumEntropy_DNA_5_0  \\\n",
       "0                  0.072795  ...                           0.090021   \n",
       "1                  0.145941  ...                          -0.030338   \n",
       "2                  0.094736  ...                           0.102946   \n",
       "3                  0.154239  ...                           0.470516   \n",
       "4                  0.214587  ...                           0.671790   \n",
       "\n",
       "   Nuclei_Texture_SumEntropy_ER_3_0  Nuclei_Texture_SumEntropy_Mito_3_0  \\\n",
       "0                          0.375747                           -0.010427   \n",
       "1                          0.390687                           -0.058560   \n",
       "2                          0.279148                            0.029891   \n",
       "3                          0.214792                            0.015408   \n",
       "4                          0.424186                            0.118873   \n",
       "\n",
       "   Nuclei_Texture_SumEntropy_RNA_5_0  Nuclei_Texture_SumVariance_ER_3_0  \\\n",
       "0                           0.118997                          -0.156442   \n",
       "1                           0.065822                          -0.113721   \n",
       "2                           0.079777                          -0.007979   \n",
       "3                           0.339100                          -0.034251   \n",
       "4                           0.415623                           0.257598   \n",
       "\n",
       "   Nuclei_Texture_SumVariance_Mito_5_0  Nuclei_Texture_SumVariance_RNA_10_0  \\\n",
       "0                            -0.018014                            -0.024573   \n",
       "1                            -0.089807                            -0.041392   \n",
       "2                             0.081155                            -0.089633   \n",
       "3                            -0.047597                             0.103611   \n",
       "4                             0.193370                             0.238471   \n",
       "\n",
       "   Nuclei_Texture_Variance_AGP_5_0  Nuclei_Texture_Variance_ER_5_0  \\\n",
       "0                        -0.383890                       -0.199967   \n",
       "1                        -0.248967                       -0.126183   \n",
       "2                         0.043140                       -0.034355   \n",
       "3                        -0.139579                       -0.042241   \n",
       "4                        -0.033797                        0.080018   \n",
       "\n",
       "   Nuclei_Texture_Variance_RNA_5_0  \n",
       "0                        -0.075658  \n",
       "1                         0.018563  \n",
       "2                         0.052914  \n",
       "3                         0.249977  \n",
       "4                         0.335890  \n",
       "\n",
       "[5 rows x 897 columns]"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# 把CP_CSV_matched_filter第一列的列名改为does \n",
    "\n",
    "CP_CSV_matched_filter.rename(columns={CP_CSV_matched_filter.columns[0]: 'does'}, inplace=True)\n",
    "CP_CSV_matched_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "CP_CSV_matched_filter.to_csv('./BBBC047_CP_data.csv', index=False)    \n",
    "\n",
    "# CP_CSV_matched_filter.to_parquet('./CP_data.parquet', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "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>does</th>\n",
       "      <th>SMILES</th>\n",
       "      <th>Metadata_Plate</th>\n",
       "      <th>Cells_AreaShape_Compactness</th>\n",
       "      <th>Cells_AreaShape_EulerNumber</th>\n",
       "      <th>Cells_AreaShape_Extent</th>\n",
       "      <th>Cells_AreaShape_FormFactor</th>\n",
       "      <th>Cells_AreaShape_MaxFeretDiameter</th>\n",
       "      <th>Cells_AreaShape_MaximumRadius</th>\n",
       "      <th>Cells_AreaShape_Solidity</th>\n",
       "      <th>...</th>\n",
       "      <th>Nuclei_Texture_SumEntropy_DNA_5_0</th>\n",
       "      <th>Nuclei_Texture_SumEntropy_ER_3_0</th>\n",
       "      <th>Nuclei_Texture_SumEntropy_Mito_3_0</th>\n",
       "      <th>Nuclei_Texture_SumEntropy_RNA_5_0</th>\n",
       "      <th>Nuclei_Texture_SumVariance_ER_3_0</th>\n",
       "      <th>Nuclei_Texture_SumVariance_Mito_5_0</th>\n",
       "      <th>Nuclei_Texture_SumVariance_RNA_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_AGP_5_0</th>\n",
       "      <th>Nuclei_Texture_Variance_ER_5_0</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_5_0</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>6.05</td>\n",
       "      <td>CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC</td>\n",
       "      <td>24277</td>\n",
       "      <td>0.256710</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.114990</td>\n",
       "      <td>-0.237090</td>\n",
       "      <td>0.615594</td>\n",
       "      <td>0.550434</td>\n",
       "      <td>0.072795</td>\n",
       "      <td>...</td>\n",
       "      <td>0.090021</td>\n",
       "      <td>0.375747</td>\n",
       "      <td>-0.010427</td>\n",
       "      <td>0.118997</td>\n",
       "      <td>-0.156442</td>\n",
       "      <td>-0.018014</td>\n",
       "      <td>-0.024573</td>\n",
       "      <td>-0.383890</td>\n",
       "      <td>-0.199967</td>\n",
       "      <td>-0.075658</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>10.00</td>\n",
       "      <td>COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C</td>\n",
       "      <td>24277</td>\n",
       "      <td>0.050962</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.051053</td>\n",
       "      <td>-0.033733</td>\n",
       "      <td>0.271953</td>\n",
       "      <td>0.172714</td>\n",
       "      <td>0.145941</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.030338</td>\n",
       "      <td>0.390687</td>\n",
       "      <td>-0.058560</td>\n",
       "      <td>0.065822</td>\n",
       "      <td>-0.113721</td>\n",
       "      <td>-0.089807</td>\n",
       "      <td>-0.041392</td>\n",
       "      <td>-0.248967</td>\n",
       "      <td>-0.126183</td>\n",
       "      <td>0.018563</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>10.00</td>\n",
       "      <td>COc1cc(O)cc(\\C=C\\c2ccccc2)c1</td>\n",
       "      <td>24277</td>\n",
       "      <td>-0.098185</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.044212</td>\n",
       "      <td>0.164668</td>\n",
       "      <td>0.011985</td>\n",
       "      <td>0.127098</td>\n",
       "      <td>0.094736</td>\n",
       "      <td>...</td>\n",
       "      <td>0.102946</td>\n",
       "      <td>0.279148</td>\n",
       "      <td>0.029891</td>\n",
       "      <td>0.079777</td>\n",
       "      <td>-0.007979</td>\n",
       "      <td>0.081155</td>\n",
       "      <td>-0.089633</td>\n",
       "      <td>0.043140</td>\n",
       "      <td>-0.034355</td>\n",
       "      <td>0.052914</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>10.00</td>\n",
       "      <td>COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...</td>\n",
       "      <td>24277</td>\n",
       "      <td>0.410722</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.236208</td>\n",
       "      <td>-0.055084</td>\n",
       "      <td>0.694648</td>\n",
       "      <td>0.516785</td>\n",
       "      <td>0.154239</td>\n",
       "      <td>...</td>\n",
       "      <td>0.470516</td>\n",
       "      <td>0.214792</td>\n",
       "      <td>0.015408</td>\n",
       "      <td>0.339100</td>\n",
       "      <td>-0.034251</td>\n",
       "      <td>-0.047597</td>\n",
       "      <td>0.103611</td>\n",
       "      <td>-0.139579</td>\n",
       "      <td>-0.042241</td>\n",
       "      <td>0.249977</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4.39</td>\n",
       "      <td>CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...</td>\n",
       "      <td>24277</td>\n",
       "      <td>0.248559</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.020058</td>\n",
       "      <td>0.085772</td>\n",
       "      <td>0.678742</td>\n",
       "      <td>0.671897</td>\n",
       "      <td>0.214587</td>\n",
       "      <td>...</td>\n",
       "      <td>0.671790</td>\n",
       "      <td>0.424186</td>\n",
       "      <td>0.118873</td>\n",
       "      <td>0.415623</td>\n",
       "      <td>0.257598</td>\n",
       "      <td>0.193370</td>\n",
       "      <td>0.238471</td>\n",
       "      <td>-0.033797</td>\n",
       "      <td>0.080018</td>\n",
       "      <td>0.335890</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 897 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    does                                             SMILES  Metadata_Plate  \\\n",
       "0   6.05                     CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC           24277   \n",
       "1  10.00       COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C           24277   \n",
       "2  10.00                       COc1cc(O)cc(\\C=C\\c2ccccc2)c1           24277   \n",
       "3  10.00  COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...           24277   \n",
       "4   4.39  CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...           24277   \n",
       "\n",
       "   Cells_AreaShape_Compactness  Cells_AreaShape_EulerNumber  \\\n",
       "0                     0.256710                          NaN   \n",
       "1                     0.050962                          NaN   \n",
       "2                    -0.098185                          NaN   \n",
       "3                     0.410722                          NaN   \n",
       "4                     0.248559                          NaN   \n",
       "\n",
       "   Cells_AreaShape_Extent  Cells_AreaShape_FormFactor  \\\n",
       "0               -0.114990                   -0.237090   \n",
       "1                0.051053                   -0.033733   \n",
       "2                0.044212                    0.164668   \n",
       "3               -0.236208                   -0.055084   \n",
       "4               -0.020058                    0.085772   \n",
       "\n",
       "   Cells_AreaShape_MaxFeretDiameter  Cells_AreaShape_MaximumRadius  \\\n",
       "0                          0.615594                       0.550434   \n",
       "1                          0.271953                       0.172714   \n",
       "2                          0.011985                       0.127098   \n",
       "3                          0.694648                       0.516785   \n",
       "4                          0.678742                       0.671897   \n",
       "\n",
       "   Cells_AreaShape_Solidity  ...  Nuclei_Texture_SumEntropy_DNA_5_0  \\\n",
       "0                  0.072795  ...                           0.090021   \n",
       "1                  0.145941  ...                          -0.030338   \n",
       "2                  0.094736  ...                           0.102946   \n",
       "3                  0.154239  ...                           0.470516   \n",
       "4                  0.214587  ...                           0.671790   \n",
       "\n",
       "   Nuclei_Texture_SumEntropy_ER_3_0  Nuclei_Texture_SumEntropy_Mito_3_0  \\\n",
       "0                          0.375747                           -0.010427   \n",
       "1                          0.390687                           -0.058560   \n",
       "2                          0.279148                            0.029891   \n",
       "3                          0.214792                            0.015408   \n",
       "4                          0.424186                            0.118873   \n",
       "\n",
       "   Nuclei_Texture_SumEntropy_RNA_5_0  Nuclei_Texture_SumVariance_ER_3_0  \\\n",
       "0                           0.118997                          -0.156442   \n",
       "1                           0.065822                          -0.113721   \n",
       "2                           0.079777                          -0.007979   \n",
       "3                           0.339100                          -0.034251   \n",
       "4                           0.415623                           0.257598   \n",
       "\n",
       "   Nuclei_Texture_SumVariance_Mito_5_0  Nuclei_Texture_SumVariance_RNA_10_0  \\\n",
       "0                            -0.018014                            -0.024573   \n",
       "1                            -0.089807                            -0.041392   \n",
       "2                             0.081155                            -0.089633   \n",
       "3                            -0.047597                             0.103611   \n",
       "4                             0.193370                             0.238471   \n",
       "\n",
       "   Nuclei_Texture_Variance_AGP_5_0  Nuclei_Texture_Variance_ER_5_0  \\\n",
       "0                        -0.383890                       -0.199967   \n",
       "1                        -0.248967                       -0.126183   \n",
       "2                         0.043140                       -0.034355   \n",
       "3                        -0.139579                       -0.042241   \n",
       "4                        -0.033797                        0.080018   \n",
       "\n",
       "   Nuclei_Texture_Variance_RNA_5_0  \n",
       "0                        -0.075658  \n",
       "1                         0.018563  \n",
       "2                         0.052914  \n",
       "3                         0.249977  \n",
       "4                         0.335890  \n",
       "\n",
       "[5 rows x 897 columns]"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# read './BBBC047_CP_data.csv'\n",
    "df = pd.read_csv('BBBC047_CP_data.csv')\n",
    "\n",
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 处理基因表达"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>221227_x_at</th>\n",
       "      <th>212345_s_at</th>\n",
       "      <th>218597_s_at</th>\n",
       "      <th>217140_s_at</th>\n",
       "      <th>209253_at</th>\n",
       "      <th>214404_x_at</th>\n",
       "      <th>219888_at</th>\n",
       "      <th>201225_s_at</th>\n",
       "      <th>202535_at</th>\n",
       "      <th>219499_at</th>\n",
       "      <th>...</th>\n",
       "      <th>pert_dose</th>\n",
       "      <th>det_plate</th>\n",
       "      <th>BROAD_CPD_ID</th>\n",
       "      <th>CPD_NAME</th>\n",
       "      <th>CPD_TYPE</th>\n",
       "      <th>CPD_SMILES</th>\n",
       "      <th>pert_id_dose</th>\n",
       "      <th>pert_sample_dose</th>\n",
       "      <th>pert_type</th>\n",
       "      <th>control_type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>-0.118505</td>\n",
       "      <td>-0.293445</td>\n",
       "      <td>-0.294088</td>\n",
       "      <td>0.292745</td>\n",
       "      <td>-0.145896</td>\n",
       "      <td>0.97358</td>\n",
       "      <td>0.247915</td>\n",
       "      <td>-0.159028</td>\n",
       "      <td>-1.249049</td>\n",
       "      <td>0.357185</td>\n",
       "      <td>...</td>\n",
       "      <td>50.0</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>BRD-K07762753</td>\n",
       "      <td>aminopurvalanol A</td>\n",
       "      <td>BIO</td>\n",
       "      <td>CC(C)[C@H](CO)Nc1nc(Nc2cc(N)cc(Cl)c2)c2ncn(C(C...</td>\n",
       "      <td>BRD-K07762753_50.0</td>\n",
       "      <td>BRD-K07762753-001-03-6_50.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.043264</td>\n",
       "      <td>-0.264945</td>\n",
       "      <td>-0.000633</td>\n",
       "      <td>0.000935</td>\n",
       "      <td>0.177604</td>\n",
       "      <td>-0.50472</td>\n",
       "      <td>0.214315</td>\n",
       "      <td>0.144271</td>\n",
       "      <td>0.106551</td>\n",
       "      <td>-0.051834</td>\n",
       "      <td>...</td>\n",
       "      <td>12.7</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>BRD-K09991945</td>\n",
       "      <td>GSK-3 inhibitor II</td>\n",
       "      <td>BIO</td>\n",
       "      <td>Ic1cccc(CSc2nnc(o2)-c2ccncc2)c1</td>\n",
       "      <td>BRD-K09991945_12.7</td>\n",
       "      <td>BRD-K09991945-001-02-0_12.7</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>-0.070805</td>\n",
       "      <td>0.195755</td>\n",
       "      <td>0.004606</td>\n",
       "      <td>-0.040855</td>\n",
       "      <td>-0.067346</td>\n",
       "      <td>-0.19872</td>\n",
       "      <td>-0.053195</td>\n",
       "      <td>0.167971</td>\n",
       "      <td>-0.215449</td>\n",
       "      <td>-0.273714</td>\n",
       "      <td>...</td>\n",
       "      <td>50.0</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>BRD-K46678324</td>\n",
       "      <td>RHO-kinase inhibitor II</td>\n",
       "      <td>BIO</td>\n",
       "      <td>Clc1cc(Cl)c(NC(=O)Nc2ccncc2)c(Cl)c1</td>\n",
       "      <td>BRD-K46678324_50.0</td>\n",
       "      <td>BRD-K46678324-001-03-7_50.0</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.027165</td>\n",
       "      <td>-0.149545</td>\n",
       "      <td>0.173113</td>\n",
       "      <td>-0.100695</td>\n",
       "      <td>-0.309296</td>\n",
       "      <td>-0.20782</td>\n",
       "      <td>-0.323985</td>\n",
       "      <td>0.294872</td>\n",
       "      <td>-0.371449</td>\n",
       "      <td>-0.099914</td>\n",
       "      <td>...</td>\n",
       "      <td>16.2</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>BRD-K67860401</td>\n",
       "      <td>GSK-3beta inhibitor VIII</td>\n",
       "      <td>BIO</td>\n",
       "      <td>COc1ccc(CNC(=O)Nc2ncc(s2)[N+]([O-])=O)cc1</td>\n",
       "      <td>BRD-K67860401_16.2</td>\n",
       "      <td>BRD-K67860401-001-02-3_16.2</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0.303294</td>\n",
       "      <td>0.254455</td>\n",
       "      <td>-0.055418</td>\n",
       "      <td>-0.053635</td>\n",
       "      <td>0.000455</td>\n",
       "      <td>-0.10908</td>\n",
       "      <td>0.031425</td>\n",
       "      <td>0.044482</td>\n",
       "      <td>0.223351</td>\n",
       "      <td>0.163186</td>\n",
       "      <td>...</td>\n",
       "      <td>12.5</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>BRD-K52620403</td>\n",
       "      <td>STO 609</td>\n",
       "      <td>BIO</td>\n",
       "      <td>OC(=O)c1ccc2c3nc4ccccc4n3c(=O)c3cccc1c23</td>\n",
       "      <td>BRD-K52620403_12.5</td>\n",
       "      <td>BRD-K52620403-001-01-8_12.5</td>\n",
       "      <td>trt</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 988 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   221227_x_at  212345_s_at  218597_s_at  217140_s_at  209253_at  214404_x_at  \\\n",
       "0    -0.118505    -0.293445    -0.294088     0.292745  -0.145896      0.97358   \n",
       "1     0.043264    -0.264945    -0.000633     0.000935   0.177604     -0.50472   \n",
       "2    -0.070805     0.195755     0.004606    -0.040855  -0.067346     -0.19872   \n",
       "3     0.027165    -0.149545     0.173113    -0.100695  -0.309296     -0.20782   \n",
       "4     0.303294     0.254455    -0.055418    -0.053635   0.000455     -0.10908   \n",
       "\n",
       "   219888_at  201225_s_at  202535_at  219499_at  ...  pert_dose  \\\n",
       "0   0.247915    -0.159028  -1.249049   0.357185  ...       50.0   \n",
       "1   0.214315     0.144271   0.106551  -0.051834  ...       12.7   \n",
       "2  -0.053195     0.167971  -0.215449  -0.273714  ...       50.0   \n",
       "3  -0.323985     0.294872  -0.371449  -0.099914  ...       16.2   \n",
       "4   0.031425     0.044482   0.223351   0.163186  ...       12.5   \n",
       "\n",
       "                       det_plate   BROAD_CPD_ID                  CPD_NAME  \\\n",
       "0  PAC001_U2OS_6H_X1_B1_UNI4445L  BRD-K07762753         aminopurvalanol A   \n",
       "1  PAC001_U2OS_6H_X1_B1_UNI4445L  BRD-K09991945        GSK-3 inhibitor II   \n",
       "2  PAC001_U2OS_6H_X1_B1_UNI4445L  BRD-K46678324   RHO-kinase inhibitor II   \n",
       "3  PAC001_U2OS_6H_X1_B1_UNI4445L  BRD-K67860401  GSK-3beta inhibitor VIII   \n",
       "4  PAC001_U2OS_6H_X1_B1_UNI4445L  BRD-K52620403                   STO 609   \n",
       "\n",
       "   CPD_TYPE                                         CPD_SMILES  \\\n",
       "0       BIO  CC(C)[C@H](CO)Nc1nc(Nc2cc(N)cc(Cl)c2)c2ncn(C(C...   \n",
       "1       BIO                    Ic1cccc(CSc2nnc(o2)-c2ccncc2)c1   \n",
       "2       BIO                Clc1cc(Cl)c(NC(=O)Nc2ccncc2)c(Cl)c1   \n",
       "3       BIO          COc1ccc(CNC(=O)Nc2ncc(s2)[N+]([O-])=O)cc1   \n",
       "4       BIO           OC(=O)c1ccc2c3nc4ccccc4n3c(=O)c3cccc1c23   \n",
       "\n",
       "         pert_id_dose             pert_sample_dose  pert_type  control_type  \n",
       "0  BRD-K07762753_50.0  BRD-K07762753-001-03-6_50.0        trt           NaN  \n",
       "1  BRD-K09991945_12.7  BRD-K09991945-001-02-0_12.7        trt           NaN  \n",
       "2  BRD-K46678324_50.0  BRD-K46678324-001-03-7_50.0        trt           NaN  \n",
       "3  BRD-K67860401_16.2  BRD-K67860401-001-02-3_16.2        trt           NaN  \n",
       "4  BRD-K52620403_12.5  BRD-K52620403-001-01-8_12.5        trt           NaN  \n",
       "\n",
       "[5 rows x 988 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GE_CSV.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>221227_x_at</th>\n",
       "      <th>212345_s_at</th>\n",
       "      <th>218597_s_at</th>\n",
       "      <th>217140_s_at</th>\n",
       "      <th>209253_at</th>\n",
       "      <th>214404_x_at</th>\n",
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       "      <th>201225_s_at</th>\n",
       "      <th>202535_at</th>\n",
       "      <th>219499_at</th>\n",
       "      <th>...</th>\n",
       "      <th>204608_at</th>\n",
       "      <th>211071_s_at</th>\n",
       "      <th>203341_at</th>\n",
       "      <th>202801_at</th>\n",
       "      <th>206414_s_at</th>\n",
       "      <th>204978_at</th>\n",
       "      <th>205379_at</th>\n",
       "      <th>203897_at</th>\n",
       "      <th>det_plate</th>\n",
       "      <th>CPD_SMILES</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>-0.118505</td>\n",
       "      <td>-0.293445</td>\n",
       "      <td>-0.294088</td>\n",
       "      <td>0.292745</td>\n",
       "      <td>-0.145896</td>\n",
       "      <td>0.97358</td>\n",
       "      <td>0.247915</td>\n",
       "      <td>-0.159028</td>\n",
       "      <td>-1.249049</td>\n",
       "      <td>0.357185</td>\n",
       "      <td>...</td>\n",
       "      <td>0.430269</td>\n",
       "      <td>-0.97559</td>\n",
       "      <td>-1.740605</td>\n",
       "      <td>0.340382</td>\n",
       "      <td>0.498778</td>\n",
       "      <td>0.352152</td>\n",
       "      <td>0.53591</td>\n",
       "      <td>0.52484</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>CC(C)[C@H](CO)Nc1nc(Nc2cc(N)cc(Cl)c2)c2ncn(C(C...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>0.043264</td>\n",
       "      <td>-0.264945</td>\n",
       "      <td>-0.000633</td>\n",
       "      <td>0.000935</td>\n",
       "      <td>0.177604</td>\n",
       "      <td>-0.50472</td>\n",
       "      <td>0.214315</td>\n",
       "      <td>0.144271</td>\n",
       "      <td>0.106551</td>\n",
       "      <td>-0.051834</td>\n",
       "      <td>...</td>\n",
       "      <td>0.556969</td>\n",
       "      <td>0.25051</td>\n",
       "      <td>-0.025625</td>\n",
       "      <td>-0.024428</td>\n",
       "      <td>-0.225122</td>\n",
       "      <td>0.533052</td>\n",
       "      <td>-0.19329</td>\n",
       "      <td>-0.25436</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>Ic1cccc(CSc2nnc(o2)-c2ccncc2)c1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>-0.070805</td>\n",
       "      <td>0.195755</td>\n",
       "      <td>0.004606</td>\n",
       "      <td>-0.040855</td>\n",
       "      <td>-0.067346</td>\n",
       "      <td>-0.19872</td>\n",
       "      <td>-0.053195</td>\n",
       "      <td>0.167971</td>\n",
       "      <td>-0.215449</td>\n",
       "      <td>-0.273714</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.017741</td>\n",
       "      <td>0.05681</td>\n",
       "      <td>0.130695</td>\n",
       "      <td>0.005919</td>\n",
       "      <td>-0.408722</td>\n",
       "      <td>-0.057177</td>\n",
       "      <td>-0.25699</td>\n",
       "      <td>0.31004</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>Clc1cc(Cl)c(NC(=O)Nc2ccncc2)c(Cl)c1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.027165</td>\n",
       "      <td>-0.149545</td>\n",
       "      <td>0.173113</td>\n",
       "      <td>-0.100695</td>\n",
       "      <td>-0.309296</td>\n",
       "      <td>-0.20782</td>\n",
       "      <td>-0.323985</td>\n",
       "      <td>0.294872</td>\n",
       "      <td>-0.371449</td>\n",
       "      <td>-0.099914</td>\n",
       "      <td>...</td>\n",
       "      <td>0.219869</td>\n",
       "      <td>-0.16129</td>\n",
       "      <td>0.365195</td>\n",
       "      <td>-0.040848</td>\n",
       "      <td>-0.251122</td>\n",
       "      <td>0.040732</td>\n",
       "      <td>0.17091</td>\n",
       "      <td>-0.05144</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>COc1ccc(CNC(=O)Nc2ncc(s2)[N+]([O-])=O)cc1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>0.303294</td>\n",
       "      <td>0.254455</td>\n",
       "      <td>-0.055418</td>\n",
       "      <td>-0.053635</td>\n",
       "      <td>0.000455</td>\n",
       "      <td>-0.10908</td>\n",
       "      <td>0.031425</td>\n",
       "      <td>0.044482</td>\n",
       "      <td>0.223351</td>\n",
       "      <td>0.163186</td>\n",
       "      <td>...</td>\n",
       "      <td>0.245469</td>\n",
       "      <td>0.00784</td>\n",
       "      <td>0.093595</td>\n",
       "      <td>-0.303418</td>\n",
       "      <td>0.474878</td>\n",
       "      <td>-0.022947</td>\n",
       "      <td>-0.28589</td>\n",
       "      <td>0.06423</td>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>OC(=O)c1ccc2c3nc4ccccc4n3c(=O)c3cccc1c23</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 979 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   221227_x_at  212345_s_at  218597_s_at  217140_s_at  209253_at  214404_x_at  \\\n",
       "0    -0.118505    -0.293445    -0.294088     0.292745  -0.145896      0.97358   \n",
       "1     0.043264    -0.264945    -0.000633     0.000935   0.177604     -0.50472   \n",
       "2    -0.070805     0.195755     0.004606    -0.040855  -0.067346     -0.19872   \n",
       "3     0.027165    -0.149545     0.173113    -0.100695  -0.309296     -0.20782   \n",
       "4     0.303294     0.254455    -0.055418    -0.053635   0.000455     -0.10908   \n",
       "\n",
       "   219888_at  201225_s_at  202535_at  219499_at  ...  204608_at  211071_s_at  \\\n",
       "0   0.247915    -0.159028  -1.249049   0.357185  ...   0.430269     -0.97559   \n",
       "1   0.214315     0.144271   0.106551  -0.051834  ...   0.556969      0.25051   \n",
       "2  -0.053195     0.167971  -0.215449  -0.273714  ...  -0.017741      0.05681   \n",
       "3  -0.323985     0.294872  -0.371449  -0.099914  ...   0.219869     -0.16129   \n",
       "4   0.031425     0.044482   0.223351   0.163186  ...   0.245469      0.00784   \n",
       "\n",
       "   203341_at  202801_at  206414_s_at  204978_at  205379_at  203897_at  \\\n",
       "0  -1.740605   0.340382     0.498778   0.352152    0.53591    0.52484   \n",
       "1  -0.025625  -0.024428    -0.225122   0.533052   -0.19329   -0.25436   \n",
       "2   0.130695   0.005919    -0.408722  -0.057177   -0.25699    0.31004   \n",
       "3   0.365195  -0.040848    -0.251122   0.040732    0.17091   -0.05144   \n",
       "4   0.093595  -0.303418     0.474878  -0.022947   -0.28589    0.06423   \n",
       "\n",
       "                       det_plate  \\\n",
       "0  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "1  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "2  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "3  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "4  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "\n",
       "                                          CPD_SMILES  \n",
       "0  CC(C)[C@H](CO)Nc1nc(Nc2cc(N)cc(Cl)c2)c2ncn(C(C...  \n",
       "1                    Ic1cccc(CSc2nnc(o2)-c2ccncc2)c1  \n",
       "2                Clc1cc(Cl)c(NC(=O)Nc2ccncc2)c(Cl)c1  \n",
       "3          COc1ccc(CNC(=O)Nc2ncc(s2)[N+]([O-])=O)cc1  \n",
       "4           OC(=O)c1ccc2c3nc4ccccc4n3c(=O)c3cccc1c23  \n",
       "\n",
       "[5 rows x 979 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GE_CSV_filter = GE_CSV.drop(columns=['CPD_TYPE', 'pert_id', 'BROAD_CPD_ID', 'CPD_NAME', 'pert_dose', 'pert_type', 'control_type', 'pert_sample_dose', 'pert_id_dose'])\n",
    "GE_CSV_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "    }\n",
       "\n",
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       "        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>det_plate</th>\n",
       "      <th>CPD_SMILES</th>\n",
       "      <th>221227_x_at</th>\n",
       "      <th>212345_s_at</th>\n",
       "      <th>218597_s_at</th>\n",
       "      <th>217140_s_at</th>\n",
       "      <th>209253_at</th>\n",
       "      <th>214404_x_at</th>\n",
       "      <th>219888_at</th>\n",
       "      <th>201225_s_at</th>\n",
       "      <th>...</th>\n",
       "      <th>218397_at</th>\n",
       "      <th>202996_at</th>\n",
       "      <th>204608_at</th>\n",
       "      <th>211071_s_at</th>\n",
       "      <th>203341_at</th>\n",
       "      <th>202801_at</th>\n",
       "      <th>206414_s_at</th>\n",
       "      <th>204978_at</th>\n",
       "      <th>205379_at</th>\n",
       "      <th>203897_at</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>CC(C)[C@H](CO)Nc1nc(Nc2cc(N)cc(Cl)c2)c2ncn(C(C...</td>\n",
       "      <td>-0.118505</td>\n",
       "      <td>-0.293445</td>\n",
       "      <td>-0.294088</td>\n",
       "      <td>0.292745</td>\n",
       "      <td>-0.145896</td>\n",
       "      <td>0.97358</td>\n",
       "      <td>0.247915</td>\n",
       "      <td>-0.159028</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.529905</td>\n",
       "      <td>0.804992</td>\n",
       "      <td>0.430269</td>\n",
       "      <td>-0.97559</td>\n",
       "      <td>-1.740605</td>\n",
       "      <td>0.340382</td>\n",
       "      <td>0.498778</td>\n",
       "      <td>0.352152</td>\n",
       "      <td>0.53591</td>\n",
       "      <td>0.52484</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>Ic1cccc(CSc2nnc(o2)-c2ccncc2)c1</td>\n",
       "      <td>0.043264</td>\n",
       "      <td>-0.264945</td>\n",
       "      <td>-0.000633</td>\n",
       "      <td>0.000935</td>\n",
       "      <td>0.177604</td>\n",
       "      <td>-0.50472</td>\n",
       "      <td>0.214315</td>\n",
       "      <td>0.144271</td>\n",
       "      <td>...</td>\n",
       "      <td>0.228895</td>\n",
       "      <td>-0.381308</td>\n",
       "      <td>0.556969</td>\n",
       "      <td>0.25051</td>\n",
       "      <td>-0.025625</td>\n",
       "      <td>-0.024428</td>\n",
       "      <td>-0.225122</td>\n",
       "      <td>0.533052</td>\n",
       "      <td>-0.19329</td>\n",
       "      <td>-0.25436</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>Clc1cc(Cl)c(NC(=O)Nc2ccncc2)c(Cl)c1</td>\n",
       "      <td>-0.070805</td>\n",
       "      <td>0.195755</td>\n",
       "      <td>0.004606</td>\n",
       "      <td>-0.040855</td>\n",
       "      <td>-0.067346</td>\n",
       "      <td>-0.19872</td>\n",
       "      <td>-0.053195</td>\n",
       "      <td>0.167971</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.031795</td>\n",
       "      <td>-0.051728</td>\n",
       "      <td>-0.017741</td>\n",
       "      <td>0.05681</td>\n",
       "      <td>0.130695</td>\n",
       "      <td>0.005919</td>\n",
       "      <td>-0.408722</td>\n",
       "      <td>-0.057177</td>\n",
       "      <td>-0.25699</td>\n",
       "      <td>0.31004</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>COc1ccc(CNC(=O)Nc2ncc(s2)[N+]([O-])=O)cc1</td>\n",
       "      <td>0.027165</td>\n",
       "      <td>-0.149545</td>\n",
       "      <td>0.173113</td>\n",
       "      <td>-0.100695</td>\n",
       "      <td>-0.309296</td>\n",
       "      <td>-0.20782</td>\n",
       "      <td>-0.323985</td>\n",
       "      <td>0.294872</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.013787</td>\n",
       "      <td>-0.177608</td>\n",
       "      <td>0.219869</td>\n",
       "      <td>-0.16129</td>\n",
       "      <td>0.365195</td>\n",
       "      <td>-0.040848</td>\n",
       "      <td>-0.251122</td>\n",
       "      <td>0.040732</td>\n",
       "      <td>0.17091</td>\n",
       "      <td>-0.05144</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>PAC001_U2OS_6H_X1_B1_UNI4445L</td>\n",
       "      <td>OC(=O)c1ccc2c3nc4ccccc4n3c(=O)c3cccc1c23</td>\n",
       "      <td>0.303294</td>\n",
       "      <td>0.254455</td>\n",
       "      <td>-0.055418</td>\n",
       "      <td>-0.053635</td>\n",
       "      <td>0.000455</td>\n",
       "      <td>-0.10908</td>\n",
       "      <td>0.031425</td>\n",
       "      <td>0.044482</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.052585</td>\n",
       "      <td>-0.196108</td>\n",
       "      <td>0.245469</td>\n",
       "      <td>0.00784</td>\n",
       "      <td>0.093595</td>\n",
       "      <td>-0.303418</td>\n",
       "      <td>0.474878</td>\n",
       "      <td>-0.022947</td>\n",
       "      <td>-0.28589</td>\n",
       "      <td>0.06423</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 979 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                       det_plate  \\\n",
       "0  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "1  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "2  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "3  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "4  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "\n",
       "                                          CPD_SMILES  221227_x_at  \\\n",
       "0  CC(C)[C@H](CO)Nc1nc(Nc2cc(N)cc(Cl)c2)c2ncn(C(C...    -0.118505   \n",
       "1                    Ic1cccc(CSc2nnc(o2)-c2ccncc2)c1     0.043264   \n",
       "2                Clc1cc(Cl)c(NC(=O)Nc2ccncc2)c(Cl)c1    -0.070805   \n",
       "3          COc1ccc(CNC(=O)Nc2ncc(s2)[N+]([O-])=O)cc1     0.027165   \n",
       "4           OC(=O)c1ccc2c3nc4ccccc4n3c(=O)c3cccc1c23     0.303294   \n",
       "\n",
       "   212345_s_at  218597_s_at  217140_s_at  209253_at  214404_x_at  219888_at  \\\n",
       "0    -0.293445    -0.294088     0.292745  -0.145896      0.97358   0.247915   \n",
       "1    -0.264945    -0.000633     0.000935   0.177604     -0.50472   0.214315   \n",
       "2     0.195755     0.004606    -0.040855  -0.067346     -0.19872  -0.053195   \n",
       "3    -0.149545     0.173113    -0.100695  -0.309296     -0.20782  -0.323985   \n",
       "4     0.254455    -0.055418    -0.053635   0.000455     -0.10908   0.031425   \n",
       "\n",
       "   201225_s_at  ...  218397_at  202996_at  204608_at  211071_s_at  203341_at  \\\n",
       "0    -0.159028  ...  -0.529905   0.804992   0.430269     -0.97559  -1.740605   \n",
       "1     0.144271  ...   0.228895  -0.381308   0.556969      0.25051  -0.025625   \n",
       "2     0.167971  ...  -0.031795  -0.051728  -0.017741      0.05681   0.130695   \n",
       "3     0.294872  ...  -0.013787  -0.177608   0.219869     -0.16129   0.365195   \n",
       "4     0.044482  ...  -0.052585  -0.196108   0.245469      0.00784   0.093595   \n",
       "\n",
       "   202801_at  206414_s_at  204978_at  205379_at  203897_at  \n",
       "0   0.340382     0.498778   0.352152    0.53591    0.52484  \n",
       "1  -0.024428    -0.225122   0.533052   -0.19329   -0.25436  \n",
       "2   0.005919    -0.408722  -0.057177   -0.25699    0.31004  \n",
       "3  -0.040848    -0.251122   0.040732    0.17091   -0.05144  \n",
       "4  -0.303418     0.474878  -0.022947   -0.28589    0.06423  \n",
       "\n",
       "[5 rows x 979 columns]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# 把最后3列换成前面3列\n",
    "\n",
    "cols = GE_CSV_filter.columns.tolist()\n",
    "cols = cols[-2:] + cols[:-2]\n",
    "GE_CSV_filter = GE_CSV_filter[cols]\n",
    "GE_CSV_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [],
   "source": [
    "# save as GE_data.parquet\n",
    "\n",
    "GE_CSV_filter.to_parquet('./GE_data.parquet', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# GE_CSV_filter.to_csv('./GE_data.csv', index=False)    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(68120, 980)"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GE_CSV_filter.shape"
   ]
  }
 ],
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