{ "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" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "(18540, 606) (6929, 980)\n" ] }, { "data": { "text/html": [ "
| \n", " | pert_dose | \n", "det_plate | \n", "CPD_SMILES | \n", "221227_x_at | \n", "212345_s_at | \n", "218597_s_at | \n", "217140_s_at | \n", "209253_at | \n", "214404_x_at | \n", "219888_at | \n", "... | \n", "218397_at | \n", "202996_at | \n", "204608_at | \n", "211071_s_at | \n", "203341_at | \n", "202801_at | \n", "206414_s_at | \n", "204978_at | \n", "205379_at | \n", "203897_at | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "50.0 | \n", "PAC001_U2OS_6H_X1_B1_UNI4445L | \n", "CC(C)[C@H](CO)Nc1nc(Nc2cc(N)cc(Cl)c2)c2ncn(C(C... | \n", "-0.118505 | \n", "-0.293445 | \n", "-0.294088 | \n", "0.292745 | \n", "-0.145896 | \n", "0.97358 | \n", "0.247915 | \n", "... | \n", "-0.529905 | \n", "0.804992 | \n", "0.430269 | \n", "-0.97559 | \n", "-1.740605 | \n", "0.340382 | \n", "0.498778 | \n", "0.352152 | \n", "0.53591 | \n", "0.52484 | \n", "
| 1 | \n", "12.7 | \n", "PAC001_U2OS_6H_X1_B1_UNI4445L | \n", "Ic1cccc(CSc2nnc(o2)-c2ccncc2)c1 | \n", "0.043264 | \n", "-0.264945 | \n", "-0.000633 | \n", "0.000935 | \n", "0.177604 | \n", "-0.50472 | \n", "0.214315 | \n", "... | \n", "0.228895 | \n", "-0.381308 | \n", "0.556969 | \n", "0.25051 | \n", "-0.025625 | \n", "-0.024428 | \n", "-0.225122 | \n", "0.533052 | \n", "-0.19329 | \n", "-0.25436 | \n", "
| 2 | \n", "50.0 | \n", "PAC001_U2OS_6H_X1_B1_UNI4445L | \n", "Clc1cc(Cl)c(NC(=O)Nc2ccncc2)c(Cl)c1 | \n", "-0.070805 | \n", "0.195755 | \n", "0.004606 | \n", "-0.040855 | \n", "-0.067346 | \n", "-0.19872 | \n", "-0.053195 | \n", "... | \n", "-0.031795 | \n", "-0.051728 | \n", "-0.017741 | \n", "0.05681 | \n", "0.130695 | \n", "0.005919 | \n", "-0.408722 | \n", "-0.057177 | \n", "-0.25699 | \n", "0.31004 | \n", "
| 3 | \n", "16.2 | \n", "PAC001_U2OS_6H_X1_B1_UNI4445L | \n", "COc1ccc(CNC(=O)Nc2ncc(s2)[N+]([O-])=O)cc1 | \n", "0.027165 | \n", "-0.149545 | \n", "0.173113 | \n", "-0.100695 | \n", "-0.309296 | \n", "-0.20782 | \n", "-0.323985 | \n", "... | \n", "-0.013787 | \n", "-0.177608 | \n", "0.219869 | \n", "-0.16129 | \n", "0.365195 | \n", "-0.040848 | \n", "-0.251122 | \n", "0.040732 | \n", "0.17091 | \n", "-0.05144 | \n", "
| 4 | \n", "12.5 | \n", "PAC001_U2OS_6H_X1_B1_UNI4445L | \n", "OC(=O)c1ccc2c3nc4ccccc4n3c(=O)c3cccc1c23 | \n", "0.303294 | \n", "0.254455 | \n", "-0.055418 | \n", "-0.053635 | \n", "0.000455 | \n", "-0.10908 | \n", "0.031425 | \n", "... | \n", "-0.052585 | \n", "-0.196108 | \n", "0.245469 | \n", "0.00784 | \n", "0.093595 | \n", "-0.303418 | \n", "0.474878 | \n", "-0.022947 | \n", "-0.28589 | \n", "0.06423 | \n", "
5 rows × 980 columns
\n", "| \n", " | dose | \n", "Plate | \n", "SMILES | \n", "221227_x_at | \n", "212345_s_at | \n", "218597_s_at | \n", "217140_s_at | \n", "209253_at | \n", "214404_x_at | \n", "219888_at | \n", "... | \n", "218397_at | \n", "202996_at | \n", "204608_at | \n", "211071_s_at | \n", "203341_at | \n", "202801_at | \n", "206414_s_at | \n", "204978_at | \n", "205379_at | \n", "203897_at | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "50.0 | \n", "PAC001_U2OS_6H_X1_B1_UNI4445L | \n", "CC(C)[C@H](CO)Nc1nc(Nc2cc(N)cc(Cl)c2)c2ncn(C(C... | \n", "-0.118505 | \n", "-0.293445 | \n", "-0.294088 | \n", "0.292745 | \n", "-0.145896 | \n", "0.97358 | \n", "0.247915 | \n", "... | \n", "-0.529905 | \n", "0.804992 | \n", "0.430269 | \n", "-0.97559 | \n", "-1.740605 | \n", "0.340382 | \n", "0.498778 | \n", "0.352152 | \n", "0.53591 | \n", "0.52484 | \n", "
| 1 | \n", "12.7 | \n", "PAC001_U2OS_6H_X1_B1_UNI4445L | \n", "Ic1cccc(CSc2nnc(o2)-c2ccncc2)c1 | \n", "0.043264 | \n", "-0.264945 | \n", "-0.000633 | \n", "0.000935 | \n", "0.177604 | \n", "-0.50472 | \n", "0.214315 | \n", "... | \n", "0.228895 | \n", "-0.381308 | \n", "0.556969 | \n", "0.25051 | \n", "-0.025625 | \n", "-0.024428 | \n", "-0.225122 | \n", "0.533052 | \n", "-0.19329 | \n", "-0.25436 | \n", "
| 2 | \n", "50.0 | \n", "PAC001_U2OS_6H_X1_B1_UNI4445L | \n", "Clc1cc(Cl)c(NC(=O)Nc2ccncc2)c(Cl)c1 | \n", "-0.070805 | \n", "0.195755 | \n", "0.004606 | \n", "-0.040855 | \n", "-0.067346 | \n", "-0.19872 | \n", "-0.053195 | \n", "... | \n", "-0.031795 | \n", "-0.051728 | \n", "-0.017741 | \n", "0.05681 | \n", "0.130695 | \n", "0.005919 | \n", "-0.408722 | \n", "-0.057177 | \n", "-0.25699 | \n", "0.31004 | \n", "
| 3 | \n", "16.2 | \n", "PAC001_U2OS_6H_X1_B1_UNI4445L | \n", "COc1ccc(CNC(=O)Nc2ncc(s2)[N+]([O-])=O)cc1 | \n", "0.027165 | \n", "-0.149545 | \n", "0.173113 | \n", "-0.100695 | \n", "-0.309296 | \n", "-0.20782 | \n", "-0.323985 | \n", "... | \n", "-0.013787 | \n", "-0.177608 | \n", "0.219869 | \n", "-0.16129 | \n", "0.365195 | \n", "-0.040848 | \n", "-0.251122 | \n", "0.040732 | \n", "0.17091 | \n", "-0.05144 | \n", "
| 4 | \n", "12.5 | \n", "PAC001_U2OS_6H_X1_B1_UNI4445L | \n", "OC(=O)c1ccc2c3nc4ccccc4n3c(=O)c3cccc1c23 | \n", "0.303294 | \n", "0.254455 | \n", "-0.055418 | \n", "-0.053635 | \n", "0.000455 | \n", "-0.10908 | \n", "0.031425 | \n", "... | \n", "-0.052585 | \n", "-0.196108 | \n", "0.245469 | \n", "0.00784 | \n", "0.093595 | \n", "-0.303418 | \n", "0.474878 | \n", "-0.022947 | \n", "-0.28589 | \n", "0.06423 | \n", "
5 rows × 980 columns
\n", "| \n", " | dose | \n", "SMILES | \n", "Plate | \n", "Cells_AreaShape_Center_X | \n", "Cells_AreaShape_Compactness | \n", "Cells_AreaShape_Extent | \n", "Cells_AreaShape_FormFactor | \n", "Cells_AreaShape_Orientation | \n", "Cells_AreaShape_Perimeter | \n", "Cells_AreaShape_Solidity | \n", "... | \n", "Nuclei_Texture_SumEntropy_DNA_10_0 | \n", "Nuclei_Texture_SumEntropy_ER_10_0 | \n", "Nuclei_Texture_SumEntropy_Mito_3_0 | \n", "Nuclei_Texture_SumEntropy_RNA_5_0 | \n", "Nuclei_Texture_SumVariance_ER_10_0 | \n", "Nuclei_Texture_SumVariance_RNA_10_0 | \n", "Nuclei_Texture_Variance_AGP_10_0 | \n", "Nuclei_Texture_Variance_ER_10_0 | \n", "Nuclei_Texture_Variance_Mito_10_0 | \n", "Nuclei_Texture_Variance_RNA_10_0 | \n", "
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "6.05 | \n", "CCCOc1cc(N)ccc1C(=O)OCCN(CC)CC | \n", "24277 | \n", "-0.070346 | \n", "0.256710 | \n", "-0.114990 | \n", "-0.237090 | \n", "-0.037928 | \n", "0.525950 | \n", "0.072795 | \n", "... | \n", "0.099029 | \n", "0.271039 | \n", "-0.010427 | \n", "0.118997 | \n", "0.006318 | \n", "-0.024573 | \n", "-0.362861 | \n", "-0.199743 | \n", "-0.329832 | \n", "0.066800 | \n", "
| 1 | \n", "10.00 | \n", "COc1cc(C)cc(OC)c1[C@@H]1C=C(C)CC[C@H]1C(C)=C | \n", "24277 | \n", "0.041380 | \n", "0.050962 | \n", "0.051053 | \n", "-0.033733 | \n", "0.064711 | \n", "0.298818 | \n", "0.145941 | \n", "... | \n", "-0.042474 | \n", "0.254293 | \n", "-0.058560 | \n", "0.065822 | \n", "-0.089380 | \n", "-0.041392 | \n", "-0.220610 | \n", "-0.154711 | \n", "-0.116072 | \n", "0.174417 | \n", "
| 2 | \n", "10.00 | \n", "COc1cc(O)cc(\\C=C\\c2ccccc2)c1 | \n", "24277 | \n", "-0.130346 | \n", "-0.098185 | \n", "0.044212 | \n", "0.164668 | \n", "-0.130904 | \n", "0.001828 | \n", "0.094736 | \n", "... | \n", "0.097992 | \n", "0.230331 | \n", "0.029891 | \n", "0.079777 | \n", "0.020954 | \n", "-0.089633 | \n", "0.075818 | \n", "-0.021001 | \n", "-0.028661 | \n", "0.115051 | \n", "
| 3 | \n", "10.00 | \n", "COc1c(O)cc2C(=O)O[C@H]3[C@@H](O)[C@H](O)[C@@H]... | \n", "24277 | \n", "-0.316555 | \n", "0.410722 | \n", "-0.236208 | \n", "-0.055084 | \n", "-0.099876 | \n", "0.503035 | \n", "0.154239 | \n", "... | \n", "0.389063 | \n", "0.208347 | \n", "0.015408 | \n", "0.339100 | \n", "0.031178 | \n", "0.103611 | \n", "-0.070876 | \n", "-0.044751 | \n", "-0.009591 | \n", "0.322316 | \n", "
| 4 | \n", "4.39 | \n", "CCOc1ccc2ccccc2c1C(=O)N[C@H]1[C@H]2SC(C)(C)[C@... | \n", "24277 | \n", "-0.047587 | \n", "0.248559 | \n", "-0.020058 | \n", "0.085772 | \n", "0.096394 | \n", "0.545575 | \n", "0.214587 | \n", "... | \n", "0.610344 | \n", "0.426826 | \n", "0.118873 | \n", "0.415623 | \n", "0.339794 | \n", "0.238471 | \n", "-0.157253 | \n", "-0.002357 | \n", "-0.057382 | \n", "0.437593 | \n", "
5 rows × 605 columns
\n", "