{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 数据处理：SMILES信息在Gene里，CP里面没有，所以首先在这里实现映射和对齐"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 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": [
    "# 先下载数据，按照 aws , 指令如下：这里面有多组数据，都是多模态的（同时包含基因和形态），但是好几组数据问题比较大，我们先用BBBC036\n",
    "\n",
    "aws s3 sync s3://cellpainting-gallery/cpg0003-rosetta/broad/workspace/preprocessed_data/ ./cpg0003 --exact-timestamps --no-sign-request"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "打开其中的BC036，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": 8,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(21122, 627) (6929, 988)\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/tmp/ipykernel_3471785/3133962603.py:8: 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/CDRPBIO-BBBC036-Bray/'\n",
    "\n",
    "# 只用里面的细胞形态数据\n",
    "CP_path = root + 'CellPainting/replicate_level_cp_normalized_variable_selected.csv.gz'\n",
    "GE_path = root + 'L1000/replicate_level_l1k.csv.gz'\n",
    "\n",
    "CP_CSV = pd.read_csv(CP_path)\n",
    "GE_CSV = pd.read_csv(GE_path)\n",
    "print(CP_CSV.shape, GE_CSV.shape)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>index</th>\n",
       "      <th>pert_type</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>trt</td>\n",
       "      <td>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": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV['pert_type'].value_counts().reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2239"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(CP_CSV['Metadata_pert_id'].unique())"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 读取基因是为了把里面的 SMIELS 迁移过来"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "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": 12,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(18540, 628)"
      ]
     },
     "execution_count": 12,
     "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": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "\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_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": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>pert_type</th>\n",
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       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>trt</td>\n",
       "      <td>15012</td>\n",
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       "      <th>1</th>\n",
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       "      <td>3528</td>\n",
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       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     index  pert_type\n",
       "0      trt      15012\n",
       "1  control       3528"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched['pert_type'].value_counts().reset_index()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "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",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21063</th>\n",
       "      <td>26247</td>\n",
       "      <td>n14</td>\n",
       "      <td>26247</td>\n",
       "      <td>H-BIOA-007-3</td>\n",
       "      <td>n14</td>\n",
       "      <td>mock</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>...</td>\n",
       "      <td>0.009180</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.00</td>\n",
       "      <td>negcon</td>\n",
       "      <td>control</td>\n",
       "      <td>negcon</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21084</th>\n",
       "      <td>26247</td>\n",
       "      <td>o11</td>\n",
       "      <td>26247</td>\n",
       "      <td>H-BIOA-007-3</td>\n",
       "      <td>o11</td>\n",
       "      <td>mock</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.203010</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.00</td>\n",
       "      <td>negcon</td>\n",
       "      <td>control</td>\n",
       "      <td>negcon</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21085</th>\n",
       "      <td>26247</td>\n",
       "      <td>o12</td>\n",
       "      <td>26247</td>\n",
       "      <td>H-BIOA-007-3</td>\n",
       "      <td>o12</td>\n",
       "      <td>mock</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.241133</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.00</td>\n",
       "      <td>negcon</td>\n",
       "      <td>control</td>\n",
       "      <td>negcon</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21108</th>\n",
       "      <td>26247</td>\n",
       "      <td>p11</td>\n",
       "      <td>26247</td>\n",
       "      <td>H-BIOA-007-3</td>\n",
       "      <td>p11</td>\n",
       "      <td>mock</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.109876</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.00</td>\n",
       "      <td>negcon</td>\n",
       "      <td>control</td>\n",
       "      <td>negcon</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>21109</th>\n",
       "      <td>26247</td>\n",
       "      <td>p12</td>\n",
       "      <td>26247</td>\n",
       "      <td>H-BIOA-007-3</td>\n",
       "      <td>p12</td>\n",
       "      <td>mock</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>DMSO</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.116873</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.00</td>\n",
       "      <td>negcon</td>\n",
       "      <td>control</td>\n",
       "      <td>negcon</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>18540 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",
       "21063           26247           n14                         26247   \n",
       "21084           26247           o11                         26247   \n",
       "21085           26247           o12                         26247   \n",
       "21108           26247           p11                         26247   \n",
       "21109           26247           p12                         26247   \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",
       "21063            H-BIOA-007-3                    n14                     mock   \n",
       "21084            H-BIOA-007-3                    o11                     mock   \n",
       "21085            H-BIOA-007-3                    o12                     mock   \n",
       "21108            H-BIOA-007-3                    p11                     mock   \n",
       "21109            H-BIOA-007-3                    p12                     mock   \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",
       "21063                    DMSO                   0.000000             DMSO   \n",
       "21084                    DMSO                   0.000000             DMSO   \n",
       "21085                    DMSO                   0.000000             DMSO   \n",
       "21108                    DMSO                   0.000000             DMSO   \n",
       "21109                    DMSO                   0.000000             DMSO   \n",
       "\n",
       "      Metadata_pert_id  ... Nuclei_Texture_Variance_RNA_10_0  \\\n",
       "0        BRD-K18250272  ...                         0.066800   \n",
       "1        BRD-K18316707  ...                         0.174417   \n",
       "2        BRD-K18438502  ...                         0.115051   \n",
       "3        BRD-K18550767  ...                         0.322316   \n",
       "4        BRD-K18574842  ...                         0.437593   \n",
       "...                ...  ...                              ...   \n",
       "21063             DMSO  ...                         0.009180   \n",
       "21084             DMSO  ...                        -0.203010   \n",
       "21085             DMSO  ...                        -0.241133   \n",
       "21108             DMSO  ...                        -0.109876   \n",
       "21109             DMSO  ...                        -0.116873   \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",
       "21063                 NaN                   NaN   \n",
       "21084                 NaN                   NaN   \n",
       "21085                 NaN                   NaN   \n",
       "21108                 NaN                   NaN   \n",
       "21109                 NaN                   NaN   \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",
       "21063                                      NaN                      NaN   \n",
       "21084                                      NaN                      NaN   \n",
       "21085                                      NaN                      NaN   \n",
       "21108                                      NaN                      NaN   \n",
       "21109                                      NaN                      NaN   \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",
       "21063                       0.00                       negcon    control   \n",
       "21084                       0.00                       negcon    control   \n",
       "21085                       0.00                       negcon    control   \n",
       "21108                       0.00                       negcon    control   \n",
       "21109                       0.00                       negcon    control   \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",
       "21063        negcon                                                NaN  \n",
       "21084        negcon                                                NaN  \n",
       "21085        negcon                                                NaN  \n",
       "21108        negcon                                                NaN  \n",
       "21109        negcon                                                NaN  \n",
       "\n",
       "[18540 rows x 628 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 删除无关元素，保留核心"
   ]
  },
  {
   "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>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": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched_filter = CP_CSV_matched.drop(columns=['Metadata_Well', 'Metadata_Assay_Plate_Barcode', 'Metadata_Plate_Map_Name', 'Metadata_well_position',\\\n",
    "    'Metadata_ASSAY_WELL_ROLE', 'Metadata_broad_sample', 'Metadata_mmoles_per_liter', 'Metadata_solvent', 'Metadata_pert_id'])\n",
    "CP_CSV_matched_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "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_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_mmoles_per_liter2</th>\n",
       "      <th>Metadata_Sample_Dose</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>6.05</td>\n",
       "      <td>BRD-K18250272-003-03-7_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>10.00</td>\n",
       "      <td>BRD-K18316707-001-01-9_10.0</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>10.00</td>\n",
       "      <td>BRD-K18438502-001-02-6_10.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>COc1cc(O)cc(\\C=C\\c2ccccc2)c1</td>\n",
       "    </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>10.00</td>\n",
       "      <td>BRD-K18550767-001-02-8_10.0</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>4.39</td>\n",
       "      <td>BRD-K18574842-323-03-3_4.39</td>\n",
       "      <td>NaN</td>\n",
       "      <td>CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...</td>\n",
       "    </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_mmoles_per_liter2  \\\n",
       "0                          0.066800                        6.05   \n",
       "1                          0.174417                       10.00   \n",
       "2                          0.115051                       10.00   \n",
       "3                          0.322316                       10.00   \n",
       "4                          0.437593                        4.39   \n",
       "\n",
       "          Metadata_Sample_Dose  control_type  \\\n",
       "0  BRD-K18250272-003-03-7_6.05           NaN   \n",
       "1  BRD-K18316707-001-01-9_10.0           NaN   \n",
       "2  BRD-K18438502-001-02-6_10.0           NaN   \n",
       "3  BRD-K18550767-001-02-8_10.0           NaN   \n",
       "4  BRD-K18574842-323-03-3_4.39           NaN   \n",
       "\n",
       "                                              SMILES  \n",
       "0                     CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC  \n",
       "1       COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C  \n",
       "2                       COc1cc(O)cc(\\C=C\\c2ccccc2)c1  \n",
       "3  COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...  \n",
       "4  CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...  \n",
       "\n",
       "[5 rows x 614 columns]"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched_filter = CP_CSV_matched_filter.drop(columns=['Metadata_pert_iname',\\\n",
    "    'Metadata_pert_iname2', 'Metadata_moa', 'Metadata_target', 'pert_type'])\n",
    "CP_CSV_matched_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
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       "      <th></th>\n",
       "      <th>Metadata_Plate</th>\n",
       "      <th>Cells_AreaShape_Center_X</th>\n",
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       "      <th>Cells_AreaShape_Zernike_2_0</th>\n",
       "      <th>...</th>\n",
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       "      <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",
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       "      <th>Metadata_mmoles_per_liter2</th>\n",
       "      <th>SMILES</th>\n",
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       "      <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>-0.010427</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",
       "      <td>6.05</td>\n",
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       "      <td>0.145941</td>\n",
       "      <td>-0.070826</td>\n",
       "      <td>0.050313</td>\n",
       "      <td>...</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",
       "      <td>10.00</td>\n",
       "      <td>COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C</td>\n",
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       "    <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>0.029891</td>\n",
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       "      <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>10.00</td>\n",
       "      <td>COc1cc(O)cc(\\C=C\\c2ccccc2)c1</td>\n",
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       "      <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>0.015408</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",
       "      <td>10.00</td>\n",
       "      <td>COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...</td>\n",
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       "      <td>-0.020058</td>\n",
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       "      <td>-0.086168</td>\n",
       "      <td>-0.090049</td>\n",
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       "      <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",
       "      <td>4.39</td>\n",
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      ],
      "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_Mito_3_0  \\\n",
       "0                    -0.228257  ...                           -0.010427   \n",
       "1                     0.050313  ...                           -0.058560   \n",
       "2                    -0.033444  ...                            0.029891   \n",
       "3                    -0.215598  ...                            0.015408   \n",
       "4                    -0.090049  ...                            0.118873   \n",
       "\n",
       "   Nuclei_Texture_SumEntropy_RNA_5_0  Nuclei_Texture_SumVariance_ER_10_0  \\\n",
       "0                           0.118997                            0.006318   \n",
       "1                           0.065822                           -0.089380   \n",
       "2                           0.079777                            0.020954   \n",
       "3                           0.339100                            0.031178   \n",
       "4                           0.415623                            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_mmoles_per_liter2  \\\n",
       "0                          0.066800                        6.05   \n",
       "1                          0.174417                       10.00   \n",
       "2                          0.115051                       10.00   \n",
       "3                          0.322316                       10.00   \n",
       "4                          0.437593                        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 605 columns]"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "CP_CSV_matched_filter = CP_CSV_matched_filter.drop(columns=['Metadata_pert_mfc_id','Metadata_pert_type', 'control_type', 'Metadata_Sample_Dose', \\\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": null,
   "metadata": {},
   "outputs": [
    {
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       "      <th></th>\n",
       "      <th>Metadata_mmoles_per_liter2</th>\n",
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       "      <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",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>10.00</td>\n",
       "      <td>COc1cc(O)cc(\\C=C\\c2ccccc2)c1</td>\n",
       "      <td>24277</td>\n",
       "      <td>-0.130346</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",
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       "      <td>0.097992</td>\n",
       "      <td>0.230331</td>\n",
       "      <td>0.029891</td>\n",
       "      <td>0.079777</td>\n",
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       "      <td>-0.089633</td>\n",
       "      <td>0.075818</td>\n",
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       "      <th>3</th>\n",
       "      <td>10.00</td>\n",
       "      <td>COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...</td>\n",
       "      <td>24277</td>\n",
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       "      <td>-0.055084</td>\n",
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       "      <td>0.503035</td>\n",
       "      <td>0.154239</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",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4.39</td>\n",
       "      <td>CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...</td>\n",
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       "      <td>0.426826</td>\n",
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      ],
      "text/plain": [
       "   Metadata_mmoles_per_liter2  \\\n",
       "0                        6.05   \n",
       "1                       10.00   \n",
       "2                       10.00   \n",
       "3                       10.00   \n",
       "4                        4.39   \n",
       "\n",
       "                                              SMILES  Metadata_Plate  \\\n",
       "0                     CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC           24277   \n",
       "1       COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C           24277   \n",
       "2                       COc1cc(O)cc(\\C=C\\c2ccccc2)c1           24277   \n",
       "3  COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...           24277   \n",
       "4  CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...           24277   \n",
       "\n",
       "   Cells_AreaShape_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",
       "   Cells_AreaShape_Solidity  ...  Nuclei_Texture_SumEntropy_DNA_10_0  \\\n",
       "0                  0.072795  ...                            0.099029   \n",
       "1                  0.145941  ...                           -0.042474   \n",
       "2                  0.094736  ...                            0.097992   \n",
       "3                  0.154239  ...                            0.389063   \n",
       "4                  0.214587  ...                            0.610344   \n",
       "\n",
       "   Nuclei_Texture_SumEntropy_ER_10_0  Nuclei_Texture_SumEntropy_Mito_3_0  \\\n",
       "0                           0.271039                           -0.010427   \n",
       "1                           0.254293                           -0.058560   \n",
       "2                           0.230331                            0.029891   \n",
       "3                           0.208347                            0.015408   \n",
       "4                           0.426826                            0.118873   \n",
       "\n",
       "   Nuclei_Texture_SumEntropy_RNA_5_0  Nuclei_Texture_SumVariance_ER_10_0  \\\n",
       "0                           0.118997                            0.006318   \n",
       "1                           0.065822                           -0.089380   \n",
       "2                           0.079777                            0.020954   \n",
       "3                           0.339100                            0.031178   \n",
       "4                           0.415623                            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  \n",
       "0                          0.066800  \n",
       "1                          0.174417  \n",
       "2                          0.115051  \n",
       "3                          0.322316  \n",
       "4                          0.437593  \n",
       "\n",
       "[5 rows x 605 columns]"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# 把最后2列移动到前面2列\n",
    "\n",
    "cols = CP_CSV_matched_filter.columns.tolist()\n",
    "cols = cols[-2:] + cols[:-2]\n",
    "CP_CSV_matched_filter = CP_CSV_matched_filter[cols]\n",
    "CP_CSV_matched_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "(18540, 605)\n"
     ]
    },
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>dose</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>Cells_AreaShape_Solidity</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>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>0.072795</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>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>0.145941</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>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>0.094736</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>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>0.154239</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>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>0.214587</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",
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       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 605 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "    dose                                             SMILES  Metadata_Plate  \\\n",
       "0   6.05                     CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC           24277   \n",
       "1  10.00       COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C           24277   \n",
       "2  10.00                       COc1cc(O)cc(\\C=C\\c2ccccc2)c1           24277   \n",
       "3  10.00  COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]...           24277   \n",
       "4   4.39  CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@...           24277   \n",
       "\n",
       "   Cells_AreaShape_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",
       "   Cells_AreaShape_Solidity  ...  Nuclei_Texture_SumEntropy_DNA_10_0  \\\n",
       "0                  0.072795  ...                            0.099029   \n",
       "1                  0.145941  ...                           -0.042474   \n",
       "2                  0.094736  ...                            0.097992   \n",
       "3                  0.154239  ...                            0.389063   \n",
       "4                  0.214587  ...                            0.610344   \n",
       "\n",
       "   Nuclei_Texture_SumEntropy_ER_10_0  Nuclei_Texture_SumEntropy_Mito_3_0  \\\n",
       "0                           0.271039                           -0.010427   \n",
       "1                           0.254293                           -0.058560   \n",
       "2                           0.230331                            0.029891   \n",
       "3                           0.208347                            0.015408   \n",
       "4                           0.426826                            0.118873   \n",
       "\n",
       "   Nuclei_Texture_SumEntropy_RNA_5_0  Nuclei_Texture_SumVariance_ER_10_0  \\\n",
       "0                           0.118997                            0.006318   \n",
       "1                           0.065822                           -0.089380   \n",
       "2                           0.079777                            0.020954   \n",
       "3                           0.339100                            0.031178   \n",
       "4                           0.415623                            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  \n",
       "0                          0.066800  \n",
       "1                          0.174417  \n",
       "2                          0.115051  \n",
       "3                          0.322316  \n",
       "4                          0.437593  \n",
       "\n",
       "[5 rows x 605 columns]"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# 改名：Metadata_mmoles_per_liter2列改为does\n",
    "CP_CSV_matched_filter = CP_CSV_matched_filter.rename(columns={'Metadata_mmoles_per_liter2': 'dose', 'Metadata_pert_iname2': 'pert_iname'})\n",
    "\n",
    "print(CP_CSV_matched_filter.shape)\n",
    "CP_CSV_matched_filter.head()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "CP_CSV_matched_filter.to_csv('./CP_data.csv', index=False)    \n",
    "\n",
    "# CP_CSV_matched_filter.to_parquet('./CP_data.parquet', index=False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 下面就不用看了，是基因表达部分的"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# 处理基因表达"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "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>221227_x_at</th>\n",
       "      <th>212345_s_at</th>\n",
       "      <th>218597_s_at</th>\n",
       "      <th>217140_s_at</th>\n",
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       "      <th>214404_x_at</th>\n",
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       "      <th>201225_s_at</th>\n",
       "      <th>202535_at</th>\n",
       "      <th>219499_at</th>\n",
       "      <th>...</th>\n",
       "      <th>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": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GE_CSV.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>221227_x_at</th>\n",
       "      <th>212345_s_at</th>\n",
       "      <th>218597_s_at</th>\n",
       "      <th>217140_s_at</th>\n",
       "      <th>209253_at</th>\n",
       "      <th>214404_x_at</th>\n",
       "      <th>219888_at</th>\n",
       "      <th>201225_s_at</th>\n",
       "      <th>202535_at</th>\n",
       "      <th>219499_at</th>\n",
       "      <th>...</th>\n",
       "      <th>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>BROAD_CPD_ID</th>\n",
       "      <th>CPD_NAME</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>BRD-K07762753</td>\n",
       "      <td>aminopurvalanol A</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>BRD-K09991945</td>\n",
       "      <td>GSK-3 inhibitor II</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>BRD-K46678324</td>\n",
       "      <td>RHO-kinase inhibitor II</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>BRD-K67860401</td>\n",
       "      <td>GSK-3beta inhibitor VIII</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>BRD-K52620403</td>\n",
       "      <td>STO 609</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   BROAD_CPD_ID  \\\n",
       "0   0.340382     0.498778   0.352152    0.53591    0.52484  BRD-K07762753   \n",
       "1  -0.024428    -0.225122   0.533052   -0.19329   -0.25436  BRD-K09991945   \n",
       "2   0.005919    -0.408722  -0.057177   -0.25699    0.31004  BRD-K46678324   \n",
       "3  -0.040848    -0.251122   0.040732    0.17091   -0.05144  BRD-K67860401   \n",
       "4  -0.303418     0.474878  -0.022947   -0.28589    0.06423  BRD-K52620403   \n",
       "\n",
       "                   CPD_NAME                                         CPD_SMILES  \n",
       "0         aminopurvalanol A  CC(C)[C@H](CO)Nc1nc(Nc2cc(N)cc(Cl)c2)c2ncn(C(C...  \n",
       "1        GSK-3 inhibitor II                    Ic1cccc(CSc2nnc(o2)-c2ccncc2)c1  \n",
       "2   RHO-kinase inhibitor II                Clc1cc(Cl)c(NC(=O)Nc2ccncc2)c(Cl)c1  \n",
       "3  GSK-3beta inhibitor VIII          COc1ccc(CNC(=O)Nc2ncc(s2)[N+]([O-])=O)cc1  \n",
       "4                   STO 609           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','det_plate', 'pert_id', 'pert_dose'])\n",
    "GE_CSV_filter.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "      <th></th>\n",
       "      <th>BROAD_CPD_ID</th>\n",
       "      <th>CPD_NAME</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",
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       "      <th>214404_x_at</th>\n",
       "      <th>219888_at</th>\n",
       "      <th>...</th>\n",
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       "      <th>211071_s_at</th>\n",
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>BRD-K07762753</td>\n",
       "      <td>aminopurvalanol A</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>BRD-K09991945</td>\n",
       "      <td>GSK-3 inhibitor II</td>\n",
       "      <td>Ic1cccc(CSc2nnc(o2)-c2ccncc2)c1</td>\n",
       "      <td>0.043264</td>\n",
       "      <td>-0.264945</td>\n",
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       "      <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>BRD-K46678324</td>\n",
       "      <td>RHO-kinase inhibitor II</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>BRD-K67860401</td>\n",
       "      <td>GSK-3beta inhibitor VIII</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>BRD-K52620403</td>\n",
       "      <td>STO 609</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": [
       "    BROAD_CPD_ID                  CPD_NAME  \\\n",
       "0  BRD-K07762753         aminopurvalanol A   \n",
       "1  BRD-K09991945        GSK-3 inhibitor II   \n",
       "2  BRD-K46678324   RHO-kinase inhibitor II   \n",
       "3  BRD-K67860401  GSK-3beta inhibitor VIII   \n",
       "4  BRD-K52620403                   STO 609   \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": [
    "GE_CSV_filter.to_csv('./GE_data.csv', index=False)    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(6929, 980)"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "GE_CSV_filter.shape"
   ]
  }
 ],
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