{
 "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": "markdown",
   "metadata": {},
   "source": [
    "看文件名就能大致推断这些是 L1000（基因表达）实验数据的不同处理版本。拆一下：\n",
    "\n",
    "replicate_level_l1k.csv.gz\n",
    "\n",
    "replicate level 表示这是原始的重复水平（每个实验重复、每个孔的独立测量）。\n",
    "\n",
    "没有额外后缀，通常代表的是比较“基础”的数值（可能是直接从测序/芯片信号经过标准化后的结果）。\n",
    "\n",
    "replicate_level_l1k_pclfc.csv.gz\n",
    "\n",
    "pclfc 应该是 plate-centered log fold change 的缩写。\n",
    "\n",
    "意味着：对同一板（plate）的数据做了中心化（plate centering），再计算 log fold change，相当于消除板间差异的影响。\n",
    "\n",
    "replicate_level_l1k_pczscore.csv.gz\n",
    "\n",
    "pczscore = plate-centered z-score。\n",
    "\n",
    "在每个板内，先做中心化，再按标准差缩放，得到标准正态分布的 z-score 值。常用于跨板比较，因为板效应（batch effect）被部分去掉。\n",
    "\n",
    "replicate_level_l1k_vczscore.csv.gz\n",
    "\n",
    "vczscore = vehicle-centered z-score。\n",
    "\n",
    "是以 对照组（vehicle control） 为基准，做 z-score 标准化。这样更直接衡量药物相对对照的扰动幅度。\n",
    "\n",
    "treatment_level_l1k.csv.gz\n",
    "\n",
    "treatment level 表示已经把 replicate-level 聚合到 处理水平（treatment level）。\n",
    "\n",
    "一个药物 × 剂量 × 时间点的所有重复实验已经合并成一个代表性 profile（比如均值或中位数）。\n",
    "\n",
    "通常用于下游分析（聚类、表型比较），因为它去掉了重复的噪声。"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "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": "markdown",
   "metadata": {},
   "source": [
    "如果你要做 模型训练，通常会优先用 replicate_level，因为保留了最大的信息量；如果要做 统计比较或可视化聚类，则 treatment_level 更合适。"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(6929, 988) (21122, 627)\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/tmp/ipykernel_677882/2722565432.py:7: DtypeWarning: Columns (981,982,983) have mixed types. Specify dtype option on import or set low_memory=False.\n",
      "  GE_CSV = pd.read_csv(GE_path)\n"
     ]
    }
   ],
   "source": [
    "# root = '/home/bob/boom/VCBench/data/MVC/CDRP-BBBC047-Bray/'\n",
    "\n",
    "CP_path = 'CellPainting/replicate_level_cp_normalized_variable_selected.csv.gz'\n",
    "GE_path = '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(GE_CSV.shape, CP_CSV.shape)\n",
    "# GE_CSV.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "        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": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GE_CSV.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "\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_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_Mito_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_10_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>-0.329832</td>\n",
       "      <td>0.066800</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>-0.116072</td>\n",
       "      <td>0.174417</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>-0.028661</td>\n",
       "      <td>0.115051</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>-0.009591</td>\n",
       "      <td>0.322316</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>-0.057382</td>\n",
       "      <td>0.437593</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 × 627 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_Mito_10_0  \\\n",
       "0    BRD-K18250272  ...                         -0.329832   \n",
       "1    BRD-K18316707  ...                         -0.116072   \n",
       "2    BRD-K18438502  ...                         -0.028661   \n",
       "3    BRD-K18550767  ...                         -0.009591   \n",
       "4    BRD-K18574842  ...                         -0.057382   \n",
       "\n",
       "  Nuclei_Texture_Variance_RNA_10_0  Metadata_pert_iname Metadata_pert_iname2  \\\n",
       "0                         0.066800         propoxycaine         propoxycaine   \n",
       "1                         0.174417               O-1918        BRD-K18316707   \n",
       "2                         0.115051                  NaN                  NaN   \n",
       "3                         0.322316             bergenin             bergenin   \n",
       "4                         0.437593            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 627 columns]"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "1917 386\n"
     ]
    }
   ],
   "source": [
    "print(len(GE_CSV['CPD_SMILES'].unique()), len(GE_CSV['det_plate'].unique()))  # 这里错了"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "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>17594</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>control</td>\n",
       "      <td>3528</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     index  pert_type\n",
       "0      trt      17594\n",
       "1  control       3528"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV['pert_type'].value_counts().reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2239"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(CP_CSV['Metadata_pert_id'].unique())"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "映射字典大小: 1917\n",
      "匹配成功: 15012/21122 (71.07%)\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": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(18540, 628)"
      ]
     },
     "execution_count": 11,
     "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": 12,
   "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_10_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>0.066800</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>0.174417</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>0.115051</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>0.322316</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>0.437593</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 × 628 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_10_0 Metadata_pert_iname  \\\n",
       "0    BRD-K18250272  ...                         0.066800        propoxycaine   \n",
       "1    BRD-K18316707  ...                         0.174417              O-1918   \n",
       "2    BRD-K18438502  ...                         0.115051                 NaN   \n",
       "3    BRD-K18550767  ...                         0.322316            bergenin   \n",
       "4    BRD-K18574842  ...                         0.437593           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 628 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</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>15012</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>control</td>\n",
       "      <td>3528</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     index  pert_type\n",
       "0      trt      15012\n",
       "1  control       3528"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched['pert_type'].value_counts().reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "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": 25,
     "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": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
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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_Center_X</th>\n",
       "      <th>Cells_AreaShape_Compactness</th>\n",
       "      <th>...</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_10_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>-0.070346</td>\n",
       "      <td>0.256710</td>\n",
       "      <td>...</td>\n",
       "      <td>0.066800</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>0.041380</td>\n",
       "      <td>0.050962</td>\n",
       "      <td>...</td>\n",
       "      <td>0.174417</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>-0.130346</td>\n",
       "      <td>-0.098185</td>\n",
       "      <td>...</td>\n",
       "      <td>0.115051</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>-0.316555</td>\n",
       "      <td>0.410722</td>\n",
       "      <td>...</td>\n",
       "      <td>0.322316</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>-0.047587</td>\n",
       "      <td>0.248559</td>\n",
       "      <td>...</td>\n",
       "      <td>0.437593</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 × 619 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_Center_X  \\\n",
       "0                  DMSO                trt                 -0.070346   \n",
       "1                  DMSO                trt                  0.041380   \n",
       "2                  DMSO                trt                 -0.130346   \n",
       "3                  DMSO                trt                 -0.316555   \n",
       "4                  DMSO                trt                 -0.047587   \n",
       "\n",
       "   Cells_AreaShape_Compactness  ...  Nuclei_Texture_Variance_RNA_10_0  \\\n",
       "0                     0.256710  ...                          0.066800   \n",
       "1                     0.050962  ...                          0.174417   \n",
       "2                    -0.098185  ...                          0.115051   \n",
       "3                     0.410722  ...                          0.322316   \n",
       "4                     0.248559  ...                          0.437593   \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 619 columns]"
      ]
     },
     "execution_count": 14,
     "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": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\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_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_Center_X</th>\n",
       "      <th>Cells_AreaShape_Compactness</th>\n",
       "      <th>...</th>\n",
       "      <th>Nuclei_Texture_SumVariance_ER_10_0</th>\n",
       "      <th>Nuclei_Texture_SumVariance_RNA_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_AGP_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_ER_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_Mito_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_10_0</th>\n",
       "      <th>Metadata_moa</th>\n",
       "      <th>Metadata_mmoles_per_liter2</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>-0.070346</td>\n",
       "      <td>0.256710</td>\n",
       "      <td>...</td>\n",
       "      <td>0.006318</td>\n",
       "      <td>-0.024573</td>\n",
       "      <td>-0.362861</td>\n",
       "      <td>-0.199743</td>\n",
       "      <td>-0.329832</td>\n",
       "      <td>0.066800</td>\n",
       "      <td>local anesthetic</td>\n",
       "      <td>6.05</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>0.041380</td>\n",
       "      <td>0.050962</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.089380</td>\n",
       "      <td>-0.041392</td>\n",
       "      <td>-0.220610</td>\n",
       "      <td>-0.154711</td>\n",
       "      <td>-0.116072</td>\n",
       "      <td>0.174417</td>\n",
       "      <td>cannabinoid receptor antagonist</td>\n",
       "      <td>10.00</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>-0.130346</td>\n",
       "      <td>-0.098185</td>\n",
       "      <td>...</td>\n",
       "      <td>0.020954</td>\n",
       "      <td>-0.089633</td>\n",
       "      <td>0.075818</td>\n",
       "      <td>-0.021001</td>\n",
       "      <td>-0.028661</td>\n",
       "      <td>0.115051</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10.00</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>-0.316555</td>\n",
       "      <td>0.410722</td>\n",
       "      <td>...</td>\n",
       "      <td>0.031178</td>\n",
       "      <td>0.103611</td>\n",
       "      <td>-0.070876</td>\n",
       "      <td>-0.044751</td>\n",
       "      <td>-0.009591</td>\n",
       "      <td>0.322316</td>\n",
       "      <td>interleukin inhibitor</td>\n",
       "      <td>10.00</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>-0.047587</td>\n",
       "      <td>0.248559</td>\n",
       "      <td>...</td>\n",
       "      <td>0.339794</td>\n",
       "      <td>0.238471</td>\n",
       "      <td>-0.157253</td>\n",
       "      <td>-0.002357</td>\n",
       "      <td>-0.057382</td>\n",
       "      <td>0.437593</td>\n",
       "      <td>bacterial cell wall synthesis inhibitor</td>\n",
       "      <td>4.39</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 × 614 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_Center_X  \\\n",
       "0                  DMSO                trt                 -0.070346   \n",
       "1                  DMSO                trt                  0.041380   \n",
       "2                  DMSO                trt                 -0.130346   \n",
       "3                  DMSO                trt                 -0.316555   \n",
       "4                  DMSO                trt                 -0.047587   \n",
       "\n",
       "   Cells_AreaShape_Compactness  ...  Nuclei_Texture_SumVariance_ER_10_0  \\\n",
       "0                     0.256710  ...                            0.006318   \n",
       "1                     0.050962  ...                           -0.089380   \n",
       "2                    -0.098185  ...                            0.020954   \n",
       "3                     0.410722  ...                            0.031178   \n",
       "4                     0.248559  ...                            0.339794   \n",
       "\n",
       "   Nuclei_Texture_SumVariance_RNA_10_0  Nuclei_Texture_Variance_AGP_10_0  \\\n",
       "0                            -0.024573                         -0.362861   \n",
       "1                            -0.041392                         -0.220610   \n",
       "2                            -0.089633                          0.075818   \n",
       "3                             0.103611                         -0.070876   \n",
       "4                             0.238471                         -0.157253   \n",
       "\n",
       "   Nuclei_Texture_Variance_ER_10_0  Nuclei_Texture_Variance_Mito_10_0  \\\n",
       "0                        -0.199743                          -0.329832   \n",
       "1                        -0.154711                          -0.116072   \n",
       "2                        -0.021001                          -0.028661   \n",
       "3                        -0.044751                          -0.009591   \n",
       "4                        -0.002357                          -0.057382   \n",
       "\n",
       "   Nuclei_Texture_Variance_RNA_10_0                             Metadata_moa  \\\n",
       "0                          0.066800                         local anesthetic   \n",
       "1                          0.174417          cannabinoid receptor antagonist   \n",
       "2                          0.115051                                      NaN   \n",
       "3                          0.322316                    interleukin inhibitor   \n",
       "4                          0.437593  bacterial cell wall synthesis inhibitor   \n",
       "\n",
       "   Metadata_mmoles_per_liter2  control_type  \\\n",
       "0                        6.05           NaN   \n",
       "1                       10.00           NaN   \n",
       "2                       10.00           NaN   \n",
       "3                       10.00           NaN   \n",
       "4                        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 614 columns]"
      ]
     },
     "execution_count": 15,
     "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_target', 'pert_type'])\n",
    "CP_CSV_matched_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    .dataframe thead th {\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>Cells_AreaShape_Center_X</th>\n",
       "      <th>Cells_AreaShape_Compactness</th>\n",
       "      <th>Cells_AreaShape_Extent</th>\n",
       "      <th>Cells_AreaShape_FormFactor</th>\n",
       "      <th>Cells_AreaShape_Orientation</th>\n",
       "      <th>Cells_AreaShape_Perimeter</th>\n",
       "      <th>Cells_AreaShape_Solidity</th>\n",
       "      <th>Cells_AreaShape_Zernike_1_1</th>\n",
       "      <th>Cells_AreaShape_Zernike_2_0</th>\n",
       "      <th>...</th>\n",
       "      <th>Nuclei_Texture_SumEntropy_RNA_5_0</th>\n",
       "      <th>Nuclei_Texture_SumVariance_ER_10_0</th>\n",
       "      <th>Nuclei_Texture_SumVariance_RNA_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_AGP_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_ER_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_Mito_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_10_0</th>\n",
       "      <th>Metadata_moa</th>\n",
       "      <th>Metadata_mmoles_per_liter2</th>\n",
       "      <th>SMILES</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>24277</td>\n",
       "      <td>-0.070346</td>\n",
       "      <td>0.256710</td>\n",
       "      <td>-0.114990</td>\n",
       "      <td>-0.237090</td>\n",
       "      <td>-0.037928</td>\n",
       "      <td>0.525950</td>\n",
       "      <td>0.072795</td>\n",
       "      <td>0.008488</td>\n",
       "      <td>-0.228257</td>\n",
       "      <td>...</td>\n",
       "      <td>0.118997</td>\n",
       "      <td>0.006318</td>\n",
       "      <td>-0.024573</td>\n",
       "      <td>-0.362861</td>\n",
       "      <td>-0.199743</td>\n",
       "      <td>-0.329832</td>\n",
       "      <td>0.066800</td>\n",
       "      <td>local anesthetic</td>\n",
       "      <td>6.05</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>0.041380</td>\n",
       "      <td>0.050962</td>\n",
       "      <td>0.051053</td>\n",
       "      <td>-0.033733</td>\n",
       "      <td>0.064711</td>\n",
       "      <td>0.298818</td>\n",
       "      <td>0.145941</td>\n",
       "      <td>-0.070826</td>\n",
       "      <td>0.050313</td>\n",
       "      <td>...</td>\n",
       "      <td>0.065822</td>\n",
       "      <td>-0.089380</td>\n",
       "      <td>-0.041392</td>\n",
       "      <td>-0.220610</td>\n",
       "      <td>-0.154711</td>\n",
       "      <td>-0.116072</td>\n",
       "      <td>0.174417</td>\n",
       "      <td>cannabinoid receptor antagonist</td>\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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>24277</td>\n",
       "      <td>-0.130346</td>\n",
       "      <td>-0.098185</td>\n",
       "      <td>0.044212</td>\n",
       "      <td>0.164668</td>\n",
       "      <td>-0.130904</td>\n",
       "      <td>0.001828</td>\n",
       "      <td>0.094736</td>\n",
       "      <td>0.119333</td>\n",
       "      <td>-0.033444</td>\n",
       "      <td>...</td>\n",
       "      <td>0.079777</td>\n",
       "      <td>0.020954</td>\n",
       "      <td>-0.089633</td>\n",
       "      <td>0.075818</td>\n",
       "      <td>-0.021001</td>\n",
       "      <td>-0.028661</td>\n",
       "      <td>0.115051</td>\n",
       "      <td>NaN</td>\n",
       "      <td>10.00</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>-0.316555</td>\n",
       "      <td>0.410722</td>\n",
       "      <td>-0.236208</td>\n",
       "      <td>-0.055084</td>\n",
       "      <td>-0.099876</td>\n",
       "      <td>0.503035</td>\n",
       "      <td>0.154239</td>\n",
       "      <td>-0.172400</td>\n",
       "      <td>-0.215598</td>\n",
       "      <td>...</td>\n",
       "      <td>0.339100</td>\n",
       "      <td>0.031178</td>\n",
       "      <td>0.103611</td>\n",
       "      <td>-0.070876</td>\n",
       "      <td>-0.044751</td>\n",
       "      <td>-0.009591</td>\n",
       "      <td>0.322316</td>\n",
       "      <td>interleukin inhibitor</td>\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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>24277</td>\n",
       "      <td>-0.047587</td>\n",
       "      <td>0.248559</td>\n",
       "      <td>-0.020058</td>\n",
       "      <td>0.085772</td>\n",
       "      <td>0.096394</td>\n",
       "      <td>0.545575</td>\n",
       "      <td>0.214587</td>\n",
       "      <td>-0.086168</td>\n",
       "      <td>-0.090049</td>\n",
       "      <td>...</td>\n",
       "      <td>0.415623</td>\n",
       "      <td>0.339794</td>\n",
       "      <td>0.238471</td>\n",
       "      <td>-0.157253</td>\n",
       "      <td>-0.002357</td>\n",
       "      <td>-0.057382</td>\n",
       "      <td>0.437593</td>\n",
       "      <td>bacterial cell wall synthesis inhibitor</td>\n",
       "      <td>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 × 606 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   Metadata_Plate  Cells_AreaShape_Center_X  Cells_AreaShape_Compactness  \\\n",
       "0           24277                 -0.070346                     0.256710   \n",
       "1           24277                  0.041380                     0.050962   \n",
       "2           24277                 -0.130346                    -0.098185   \n",
       "3           24277                 -0.316555                     0.410722   \n",
       "4           24277                 -0.047587                     0.248559   \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_Orientation  Cells_AreaShape_Perimeter  \\\n",
       "0                    -0.037928                   0.525950   \n",
       "1                     0.064711                   0.298818   \n",
       "2                    -0.130904                   0.001828   \n",
       "3                    -0.099876                   0.503035   \n",
       "4                     0.096394                   0.545575   \n",
       "\n",
       "   Cells_AreaShape_Solidity  Cells_AreaShape_Zernike_1_1  \\\n",
       "0                  0.072795                     0.008488   \n",
       "1                  0.145941                    -0.070826   \n",
       "2                  0.094736                     0.119333   \n",
       "3                  0.154239                    -0.172400   \n",
       "4                  0.214587                    -0.086168   \n",
       "\n",
       "   Cells_AreaShape_Zernike_2_0  ...  Nuclei_Texture_SumEntropy_RNA_5_0  \\\n",
       "0                    -0.228257  ...                           0.118997   \n",
       "1                     0.050313  ...                           0.065822   \n",
       "2                    -0.033444  ...                           0.079777   \n",
       "3                    -0.215598  ...                           0.339100   \n",
       "4                    -0.090049  ...                           0.415623   \n",
       "\n",
       "   Nuclei_Texture_SumVariance_ER_10_0  Nuclei_Texture_SumVariance_RNA_10_0  \\\n",
       "0                            0.006318                            -0.024573   \n",
       "1                           -0.089380                            -0.041392   \n",
       "2                            0.020954                            -0.089633   \n",
       "3                            0.031178                             0.103611   \n",
       "4                            0.339794                             0.238471   \n",
       "\n",
       "   Nuclei_Texture_Variance_AGP_10_0  Nuclei_Texture_Variance_ER_10_0  \\\n",
       "0                         -0.362861                        -0.199743   \n",
       "1                         -0.220610                        -0.154711   \n",
       "2                          0.075818                        -0.021001   \n",
       "3                         -0.070876                        -0.044751   \n",
       "4                         -0.157253                        -0.002357   \n",
       "\n",
       "   Nuclei_Texture_Variance_Mito_10_0  Nuclei_Texture_Variance_RNA_10_0  \\\n",
       "0                          -0.329832                          0.066800   \n",
       "1                          -0.116072                          0.174417   \n",
       "2                          -0.028661                          0.115051   \n",
       "3                          -0.009591                          0.322316   \n",
       "4                          -0.057382                          0.437593   \n",
       "\n",
       "                              Metadata_moa  Metadata_mmoles_per_liter2  \\\n",
       "0                         local anesthetic                        6.05   \n",
       "1          cannabinoid receptor antagonist                       10.00   \n",
       "2                                      NaN                       10.00   \n",
       "3                    interleukin inhibitor                       10.00   \n",
       "4  bacterial cell wall synthesis inhibitor                        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 606 columns]"
      ]
     },
     "execution_count": 16,
     "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": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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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>Metadata_moa</th>\n",
       "      <th>Metadata_mmoles_per_liter2</th>\n",
       "      <th>SMILES</th>\n",
       "      <th>Metadata_Plate</th>\n",
       "      <th>Cells_AreaShape_Center_X</th>\n",
       "      <th>Cells_AreaShape_Compactness</th>\n",
       "      <th>Cells_AreaShape_Extent</th>\n",
       "      <th>Cells_AreaShape_FormFactor</th>\n",
       "      <th>Cells_AreaShape_Orientation</th>\n",
       "      <th>Cells_AreaShape_Perimeter</th>\n",
       "      <th>...</th>\n",
       "      <th>Nuclei_Texture_SumEntropy_DNA_10_0</th>\n",
       "      <th>Nuclei_Texture_SumEntropy_ER_10_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_10_0</th>\n",
       "      <th>Nuclei_Texture_SumVariance_RNA_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_AGP_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_ER_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_Mito_10_0</th>\n",
       "      <th>Nuclei_Texture_Variance_RNA_10_0</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>local anesthetic</td>\n",
       "      <td>6.05</td>\n",
       "      <td>CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC</td>\n",
       "      <td>24277</td>\n",
       "      <td>-0.070346</td>\n",
       "      <td>0.256710</td>\n",
       "      <td>-0.114990</td>\n",
       "      <td>-0.237090</td>\n",
       "      <td>-0.037928</td>\n",
       "      <td>0.525950</td>\n",
       "      <td>...</td>\n",
       "      <td>0.099029</td>\n",
       "      <td>0.271039</td>\n",
       "      <td>-0.010427</td>\n",
       "      <td>0.118997</td>\n",
       "      <td>0.006318</td>\n",
       "      <td>-0.024573</td>\n",
       "      <td>-0.362861</td>\n",
       "      <td>-0.199743</td>\n",
       "      <td>-0.329832</td>\n",
       "      <td>0.066800</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>cannabinoid receptor antagonist</td>\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>0.041380</td>\n",
       "      <td>0.050962</td>\n",
       "      <td>0.051053</td>\n",
       "      <td>-0.033733</td>\n",
       "      <td>0.064711</td>\n",
       "      <td>0.298818</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.042474</td>\n",
       "      <td>0.254293</td>\n",
       "      <td>-0.058560</td>\n",
       "      <td>0.065822</td>\n",
       "      <td>-0.089380</td>\n",
       "      <td>-0.041392</td>\n",
       "      <td>-0.220610</td>\n",
       "      <td>-0.154711</td>\n",
       "      <td>-0.116072</td>\n",
       "      <td>0.174417</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>NaN</td>\n",
       "      <td>10.00</td>\n",
       "      <td>COc1cc(O)cc(\\C=C\\c2ccccc2)c1</td>\n",
       "      <td>24277</td>\n",
       "      <td>-0.130346</td>\n",
       "      <td>-0.098185</td>\n",
       "      <td>0.044212</td>\n",
       "      <td>0.164668</td>\n",
       "      <td>-0.130904</td>\n",
       "      <td>0.001828</td>\n",
       "      <td>...</td>\n",
       "      <td>0.097992</td>\n",
       "      <td>0.230331</td>\n",
       "      <td>0.029891</td>\n",
       "      <td>0.079777</td>\n",
       "      <td>0.020954</td>\n",
       "      <td>-0.089633</td>\n",
       "      <td>0.075818</td>\n",
       "      <td>-0.021001</td>\n",
       "      <td>-0.028661</td>\n",
       "      <td>0.115051</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>interleukin inhibitor</td>\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>-0.316555</td>\n",
       "      <td>0.410722</td>\n",
       "      <td>-0.236208</td>\n",
       "      <td>-0.055084</td>\n",
       "      <td>-0.099876</td>\n",
       "      <td>0.503035</td>\n",
       "      <td>...</td>\n",
       "      <td>0.389063</td>\n",
       "      <td>0.208347</td>\n",
       "      <td>0.015408</td>\n",
       "      <td>0.339100</td>\n",
       "      <td>0.031178</td>\n",
       "      <td>0.103611</td>\n",
       "      <td>-0.070876</td>\n",
       "      <td>-0.044751</td>\n",
       "      <td>-0.009591</td>\n",
       "      <td>0.322316</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>bacterial cell wall synthesis inhibitor</td>\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>-0.047587</td>\n",
       "      <td>0.248559</td>\n",
       "      <td>-0.020058</td>\n",
       "      <td>0.085772</td>\n",
       "      <td>0.096394</td>\n",
       "      <td>0.545575</td>\n",
       "      <td>...</td>\n",
       "      <td>0.610344</td>\n",
       "      <td>0.426826</td>\n",
       "      <td>0.118873</td>\n",
       "      <td>0.415623</td>\n",
       "      <td>0.339794</td>\n",
       "      <td>0.238471</td>\n",
       "      <td>-0.157253</td>\n",
       "      <td>-0.002357</td>\n",
       "      <td>-0.057382</td>\n",
       "      <td>0.437593</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 606 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                              Metadata_moa  Metadata_mmoles_per_liter2  \\\n",
       "0                         local anesthetic                        6.05   \n",
       "1          cannabinoid receptor antagonist                       10.00   \n",
       "2                                      NaN                       10.00   \n",
       "3                    interleukin inhibitor                       10.00   \n",
       "4  bacterial cell wall synthesis inhibitor                        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_Center_X  Cells_AreaShape_Compactness  \\\n",
       "0                 -0.070346                     0.256710   \n",
       "1                  0.041380                     0.050962   \n",
       "2                 -0.130346                    -0.098185   \n",
       "3                 -0.316555                     0.410722   \n",
       "4                 -0.047587                     0.248559   \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_Orientation  Cells_AreaShape_Perimeter  ...  \\\n",
       "0                    -0.037928                   0.525950  ...   \n",
       "1                     0.064711                   0.298818  ...   \n",
       "2                    -0.130904                   0.001828  ...   \n",
       "3                    -0.099876                   0.503035  ...   \n",
       "4                     0.096394                   0.545575  ...   \n",
       "\n",
       "   Nuclei_Texture_SumEntropy_DNA_10_0  Nuclei_Texture_SumEntropy_ER_10_0  \\\n",
       "0                            0.099029                           0.271039   \n",
       "1                           -0.042474                           0.254293   \n",
       "2                            0.097992                           0.230331   \n",
       "3                            0.389063                           0.208347   \n",
       "4                            0.610344                           0.426826   \n",
       "\n",
       "   Nuclei_Texture_SumEntropy_Mito_3_0  Nuclei_Texture_SumEntropy_RNA_5_0  \\\n",
       "0                           -0.010427                           0.118997   \n",
       "1                           -0.058560                           0.065822   \n",
       "2                            0.029891                           0.079777   \n",
       "3                            0.015408                           0.339100   \n",
       "4                            0.118873                           0.415623   \n",
       "\n",
       "   Nuclei_Texture_SumVariance_ER_10_0  Nuclei_Texture_SumVariance_RNA_10_0  \\\n",
       "0                            0.006318                            -0.024573   \n",
       "1                           -0.089380                            -0.041392   \n",
       "2                            0.020954                            -0.089633   \n",
       "3                            0.031178                             0.103611   \n",
       "4                            0.339794                             0.238471   \n",
       "\n",
       "   Nuclei_Texture_Variance_AGP_10_0  Nuclei_Texture_Variance_ER_10_0  \\\n",
       "0                         -0.362861                        -0.199743   \n",
       "1                         -0.220610                        -0.154711   \n",
       "2                          0.075818                        -0.021001   \n",
       "3                         -0.070876                        -0.044751   \n",
       "4                         -0.157253                        -0.002357   \n",
       "\n",
       "   Nuclei_Texture_Variance_Mito_10_0  Nuclei_Texture_Variance_RNA_10_0  \n",
       "0                          -0.329832                          0.066800  \n",
       "1                          -0.116072                          0.174417  \n",
       "2                          -0.028661                          0.115051  \n",
       "3                          -0.009591                          0.322316  \n",
       "4                          -0.057382                          0.437593  \n",
       "\n",
       "[5 rows x 606 columns]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# 把最后3列移动到前面\n",
    "cols = CP_CSV_matched_filter.columns.tolist()\n",
    "cols = cols[-3:] + cols[:-3]   # 取最后3列 + 前面所有列\n",
    "CP_CSV_matched_filter = CP_CSV_matched_filter[cols]\n",
    "CP_CSV_matched_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "NaN count in SMILES: 3528\n",
      "NaN ratio in SMILES: 19.03%\n"
     ]
    }
   ],
   "source": [
    "# 统计 NaN 数量\n",
    "nan_count = CP_CSV_matched_filter['SMILES'].isna().sum()\n",
    "print(f\"NaN count in SMILES: {nan_count}\")\n",
    "\n",
    "# 也可以看比例\n",
    "nan_ratio = nan_count / len(CP_CSV_matched_filter)\n",
    "print(f\"NaN ratio in SMILES: {nan_ratio:.2%}\")\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>index</th>\n",
       "      <th>SMILES</th>\n",
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       "      <td>DMSO</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CC(C)NCC(O)COc1cccc2[nH]ccc12</td>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>CC(C)(C)NC[C@@H](O)COc1cccc2C(=O)CCCc12</td>\n",
       "      <td>16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>COc1ccc(CCN(C)CCc2ccc(OC)c(OC)c2)cc1OC</td>\n",
       "      <td>8</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>C\\C=C(\\C)C(=O)O[C@@H]1Cc2c(OC1(C)C)ccc1ccc(=O)...</td>\n",
       "      <td>8</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>1912</th>\n",
       "      <td>CCCC1CC2=CC(=O)CCC2(C)C2CCC3(C)C(CCC3(O)CCC(O)...</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1913</th>\n",
       "      <td>COC(=O)C1=C(C)NC(C)=C([C@@H]1c1cccc(c1)[N+]([O...</td>\n",
       "      <td>6</td>\n",
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       "    <tr>\n",
       "      <th>1914</th>\n",
       "      <td>CC(C)(Cc1c[nH]c2ccc(Cl)cc12)NCCOc1ccccc1OCC1CC1</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1915</th>\n",
       "      <td>OCCSC1=C(SCCO)C(=O)c2ccccc2C1=O</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1916</th>\n",
       "      <td>CCc1ccc(OCc2ccccc2C(=O)Nc2ccc3nc(C)cc(N)c3c2)cc1</td>\n",
       "      <td>4</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1917 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                  index  SMILES\n",
       "0                                                  DMSO    3528\n",
       "1                         CC(C)NCC(O)COc1cccc2[nH]ccc12      16\n",
       "2               CC(C)(C)NC[C@@H](O)COc1cccc2C(=O)CCCc12      16\n",
       "3                COc1ccc(CCN(C)CCc2ccc(OC)c(OC)c2)cc1OC       8\n",
       "4     C\\C=C(\\C)C(=O)O[C@@H]1Cc2c(OC1(C)C)ccc1ccc(=O)...       8\n",
       "...                                                 ...     ...\n",
       "1912  CCCC1CC2=CC(=O)CCC2(C)C2CCC3(C)C(CCC3(O)CCC(O)...       7\n",
       "1913  COC(=O)C1=C(C)NC(C)=C([C@@H]1c1cccc(c1)[N+]([O...       6\n",
       "1914    CC(C)(Cc1c[nH]c2ccc(Cl)cc12)NCCOc1ccccc1OCC1CC1       6\n",
       "1915                    OCCSC1=C(SCCO)C(=O)c2ccccc2C1=O       6\n",
       "1916   CCc1ccc(OCc2ccccc2C(=O)Nc2ccc3nc(C)cc(N)c3c2)cc1       4\n",
       "\n",
       "[1917 rows x 2 columns]"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched_filter['SMILES'] = CP_CSV_matched_filter['SMILES'].fillna(\"DMSO\")\n",
    "\n",
    "CP_CSV_matched_filter['SMILES'].value_counts().reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "CP_CSV_matched_filter.to_parquet('./CP_data.parquet', index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 处理基因表达"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "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>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": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GE_CSV.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
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       "\n",
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       "\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>BROAD_CPD_ID</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>DMSO</td>\n",
       "      <td>3478</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>BRD-K09635134</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>BRD-K13994703</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>BRD-K13959223</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>BRD-K13819402</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1912</th>\n",
       "      <td>BRD-K47278471</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1913</th>\n",
       "      <td>BRD-K50388907</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1914</th>\n",
       "      <td>BRD-K59163477</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1915</th>\n",
       "      <td>BRD-K60230970</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1916</th>\n",
       "      <td>BRD-K18550767</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1917 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "              index  BROAD_CPD_ID\n",
       "0              DMSO          3478\n",
       "1     BRD-K09635134             2\n",
       "2     BRD-K13994703             2\n",
       "3     BRD-K13959223             2\n",
       "4     BRD-K13819402             2\n",
       "...             ...           ...\n",
       "1912  BRD-K47278471             1\n",
       "1913  BRD-K50388907             1\n",
       "1914  BRD-K59163477             1\n",
       "1915  BRD-K60230970             1\n",
       "1916  BRD-K18550767             1\n",
       "\n",
       "[1917 rows x 2 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GE_CSV['BROAD_CPD_ID'].value_counts().reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "        vertical-align: top;\n",
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       "\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>control</td>\n",
       "      <td>3478</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>trt</td>\n",
       "      <td>3451</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     index  pert_type\n",
       "0  control       3478\n",
       "1      trt       3451"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GE_CSV['pert_type'].value_counts().reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\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>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>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>pert_dose</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>-0.97559</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>50.0</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>0.25051</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>12.7</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>0.05681</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>50.0</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>-0.16129</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>16.2</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>0.00784</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>12.5</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 × 980 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  ...  211071_s_at  203341_at  \\\n",
       "0   0.247915    -0.159028  -1.249049   0.357185  ...     -0.97559  -1.740605   \n",
       "1   0.214315     0.144271   0.106551  -0.051834  ...      0.25051  -0.025625   \n",
       "2  -0.053195     0.167971  -0.215449  -0.273714  ...      0.05681   0.130695   \n",
       "3  -0.323985     0.294872  -0.371449  -0.099914  ...     -0.16129   0.365195   \n",
       "4   0.031425     0.044482   0.223351   0.163186  ...      0.00784   0.093595   \n",
       "\n",
       "   202801_at  206414_s_at  204978_at  205379_at  203897_at  pert_dose  \\\n",
       "0   0.340382     0.498778   0.352152    0.53591    0.52484       50.0   \n",
       "1  -0.024428    -0.225122   0.533052   -0.19329   -0.25436       12.7   \n",
       "2   0.005919    -0.408722  -0.057177   -0.25699    0.31004       50.0   \n",
       "3  -0.040848    -0.251122   0.040732    0.17091   -0.05144       16.2   \n",
       "4  -0.303418     0.474878  -0.022947   -0.28589    0.06423       12.5   \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 980 columns]"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GE_CSV_filter = GE_CSV.drop(columns=['CPD_TYPE', 'pert_id', 'BROAD_CPD_ID', 'CPD_NAME', 'pert_type', 'control_type', 'pert_sample_dose', 'pert_id_dose'])\n",
    "GE_CSV_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "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>pert_dose</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>...</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>50.0</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",
       "      <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>...</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>12.7</td>\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>...</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>50.0</td>\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>...</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>16.2</td>\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>...</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>12.5</td>\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>...</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 × 980 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   pert_dose                      det_plate  \\\n",
       "0       50.0  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "1       12.7  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "2       50.0  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "3       16.2  PAC001_U2OS_6H_X1_B1_UNI4445L   \n",
       "4       12.5  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",
       "   ...  218397_at  202996_at  204608_at  211071_s_at  203341_at  202801_at  \\\n",
       "0  ...  -0.529905   0.804992   0.430269     -0.97559  -1.740605   0.340382   \n",
       "1  ...   0.228895  -0.381308   0.556969      0.25051  -0.025625  -0.024428   \n",
       "2  ...  -0.031795  -0.051728  -0.017741      0.05681   0.130695   0.005919   \n",
       "3  ...  -0.013787  -0.177608   0.219869     -0.16129   0.365195  -0.040848   \n",
       "4  ...  -0.052585  -0.196108   0.245469      0.00784   0.093595  -0.303418   \n",
       "\n",
       "   206414_s_at  204978_at  205379_at  203897_at  \n",
       "0     0.498778   0.352152    0.53591    0.52484  \n",
       "1    -0.225122   0.533052   -0.19329   -0.25436  \n",
       "2    -0.408722  -0.057177   -0.25699    0.31004  \n",
       "3    -0.251122   0.040732    0.17091   -0.05144  \n",
       "4     0.474878  -0.022947   -0.28589    0.06423  \n",
       "\n",
       "[5 rows x 980 columns]"
      ]
     },
     "execution_count": 24,
     "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[-3:] + cols[:-3]\n",
    "GE_CSV_filter = GE_CSV_filter[cols]\n",
    "GE_CSV_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "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"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "boom",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
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