200CL_preprocessing_IC.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import matplotlib.pyplot as plt\n",
    "from mpl_toolkits.mplot3d import Axes3D\n",
    "import mpl_toolkits.mplot3d.axes3d as p3\n",
    "from sklearn.decomposition import PCA\n",
    "import scanpy as sc\n",
    "import math\n",
    "\n",
    "import pandas as pd\n",
    "\n",
    "from matplotlib import animation, rc\n",
    "from IPython.display import HTML\n",
    "\n",
    "import sys\n",
    "DATA_PATH = '/home/risitop/OneDrive/Documents/PHD/y1/data/'\n",
    "sys.path.append(DATA_PATH)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "plt.style.use('dark_background')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>IC1</th>\n",
       "      <th>IC2</th>\n",
       "      <th>IC3</th>\n",
       "      <th>IC4</th>\n",
       "      <th>IC5</th>\n",
       "      <th>IC6</th>\n",
       "      <th>IC7</th>\n",
       "      <th>IC8</th>\n",
       "      <th>IC9</th>\n",
       "      <th>IC10</th>\n",
       "      <th>IC11</th>\n",
       "      <th>IC12</th>\n",
       "      <th>IC13</th>\n",
       "      <th>IC14</th>\n",
       "      <th>IC15</th>\n",
       "      <th>Unnamed: 16</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>PROBE</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>CDK1</th>\n",
       "      <td>-0.9190</td>\n",
       "      <td>5.0419</td>\n",
       "      <td>8.2869</td>\n",
       "      <td>-0.9463</td>\n",
       "      <td>0.5935</td>\n",
       "      <td>-0.0419</td>\n",
       "      <td>0.0775</td>\n",
       "      <td>-1.5286</td>\n",
       "      <td>-1.7286</td>\n",
       "      <td>8.2389</td>\n",
       "      <td>-1.3952</td>\n",
       "      <td>0.6260</td>\n",
       "      <td>-0.3849</td>\n",
       "      <td>0.8650</td>\n",
       "      <td>-0.8569</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>UBE2C</th>\n",
       "      <td>0.6697</td>\n",
       "      <td>3.1003</td>\n",
       "      <td>9.5936</td>\n",
       "      <td>-1.6848</td>\n",
       "      <td>-1.2334</td>\n",
       "      <td>-0.0712</td>\n",
       "      <td>-0.1914</td>\n",
       "      <td>4.6683</td>\n",
       "      <td>-0.5717</td>\n",
       "      <td>4.0906</td>\n",
       "      <td>-0.4803</td>\n",
       "      <td>1.1264</td>\n",
       "      <td>-0.3727</td>\n",
       "      <td>0.8197</td>\n",
       "      <td>-0.8002</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>CCNB1</th>\n",
       "      <td>-0.4128</td>\n",
       "      <td>-3.9112</td>\n",
       "      <td>11.4137</td>\n",
       "      <td>0.4421</td>\n",
       "      <td>1.2527</td>\n",
       "      <td>1.1820</td>\n",
       "      <td>-1.3029</td>\n",
       "      <td>6.0085</td>\n",
       "      <td>-1.2580</td>\n",
       "      <td>0.3552</td>\n",
       "      <td>-0.9335</td>\n",
       "      <td>0.2340</td>\n",
       "      <td>1.4414</td>\n",
       "      <td>0.2826</td>\n",
       "      <td>3.3749</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AURKB</th>\n",
       "      <td>-1.3091</td>\n",
       "      <td>4.9938</td>\n",
       "      <td>8.9267</td>\n",
       "      <td>-0.5047</td>\n",
       "      <td>1.0750</td>\n",
       "      <td>0.2742</td>\n",
       "      <td>0.9673</td>\n",
       "      <td>3.2298</td>\n",
       "      <td>-0.3919</td>\n",
       "      <td>4.0472</td>\n",
       "      <td>-2.2181</td>\n",
       "      <td>-1.2844</td>\n",
       "      <td>-0.6276</td>\n",
       "      <td>0.5016</td>\n",
       "      <td>0.7448</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AURKA</th>\n",
       "      <td>-0.1496</td>\n",
       "      <td>-2.8967</td>\n",
       "      <td>11.9240</td>\n",
       "      <td>0.1731</td>\n",
       "      <td>0.9337</td>\n",
       "      <td>0.2881</td>\n",
       "      <td>0.4520</td>\n",
       "      <td>-0.9910</td>\n",
       "      <td>0.2682</td>\n",
       "      <td>-0.3779</td>\n",
       "      <td>0.3459</td>\n",
       "      <td>0.6775</td>\n",
       "      <td>1.6482</td>\n",
       "      <td>0.4719</td>\n",
       "      <td>3.1775</td>\n",
       "      <td>NaN</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>LGALS3</th>\n",
       "      <td>-0.1466</td>\n",
       "      <td>-0.9214</td>\n",
       "      <td>-0.0991</td>\n",
       "      <td>-0.6781</td>\n",
       "      <td>-0.1304</td>\n",
       "      <td>-1.3243</td>\n",
       "      <td>1.0802</td>\n",
       "      <td>0.2069</td>\n",
       "      <td>-0.8436</td>\n",
       "      <td>0.8988</td>\n",
       "      <td>-1.2667</td>\n",
       "      <td>1.4437</td>\n",
       "      <td>0.0509</td>\n",
       "      <td>0.4350</td>\n",
       "      <td>0.8060</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>DOK1</th>\n",
       "      <td>0.4799</td>\n",
       "      <td>0.1539</td>\n",
       "      <td>-0.3843</td>\n",
       "      <td>-0.4367</td>\n",
       "      <td>-0.2834</td>\n",
       "      <td>-0.4136</td>\n",
       "      <td>0.1613</td>\n",
       "      <td>-0.0583</td>\n",
       "      <td>0.2711</td>\n",
       "      <td>-0.1829</td>\n",
       "      <td>-0.7776</td>\n",
       "      <td>-0.4143</td>\n",
       "      <td>0.2355</td>\n",
       "      <td>0.1569</td>\n",
       "      <td>-0.1020</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>MVB12A</th>\n",
       "      <td>-0.6149</td>\n",
       "      <td>-0.3588</td>\n",
       "      <td>-0.5584</td>\n",
       "      <td>-0.6734</td>\n",
       "      <td>1.2381</td>\n",
       "      <td>0.1803</td>\n",
       "      <td>0.2249</td>\n",
       "      <td>-0.0821</td>\n",
       "      <td>-0.0896</td>\n",
       "      <td>0.5334</td>\n",
       "      <td>0.3950</td>\n",
       "      <td>-0.5984</td>\n",
       "      <td>0.1611</td>\n",
       "      <td>-1.5826</td>\n",
       "      <td>-1.0250</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>HRCT1</th>\n",
       "      <td>-0.9159</td>\n",
       "      <td>-0.2209</td>\n",
       "      <td>-0.4397</td>\n",
       "      <td>-0.1543</td>\n",
       "      <td>0.2590</td>\n",
       "      <td>0.2297</td>\n",
       "      <td>0.0160</td>\n",
       "      <td>0.4183</td>\n",
       "      <td>1.3329</td>\n",
       "      <td>0.5509</td>\n",
       "      <td>0.0661</td>\n",
       "      <td>0.1099</td>\n",
       "      <td>1.0450</td>\n",
       "      <td>-0.1599</td>\n",
       "      <td>0.0919</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>ZNF286B</th>\n",
       "      <td>-1.1783</td>\n",
       "      <td>-0.4882</td>\n",
       "      <td>-0.2140</td>\n",
       "      <td>0.2558</td>\n",
       "      <td>-0.3750</td>\n",
       "      <td>-0.8201</td>\n",
       "      <td>-0.6184</td>\n",
       "      <td>-0.2800</td>\n",
       "      <td>0.0307</td>\n",
       "      <td>-0.4195</td>\n",
       "      <td>-0.4247</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.3943</td>\n",
       "      <td>-0.0806</td>\n",
       "      <td>0.6930</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>10000 rows × 16 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            IC1     IC2      IC3     IC4     IC5     IC6     IC7     IC8  \\\n",
       "PROBE                                                                      \n",
       "CDK1    -0.9190  5.0419   8.2869 -0.9463  0.5935 -0.0419  0.0775 -1.5286   \n",
       "UBE2C    0.6697  3.1003   9.5936 -1.6848 -1.2334 -0.0712 -0.1914  4.6683   \n",
       "CCNB1   -0.4128 -3.9112  11.4137  0.4421  1.2527  1.1820 -1.3029  6.0085   \n",
       "AURKB   -1.3091  4.9938   8.9267 -0.5047  1.0750  0.2742  0.9673  3.2298   \n",
       "AURKA   -0.1496 -2.8967  11.9240  0.1731  0.9337  0.2881  0.4520 -0.9910   \n",
       "...         ...     ...      ...     ...     ...     ...     ...     ...   \n",
       "LGALS3  -0.1466 -0.9214  -0.0991 -0.6781 -0.1304 -1.3243  1.0802  0.2069   \n",
       "DOK1     0.4799  0.1539  -0.3843 -0.4367 -0.2834 -0.4136  0.1613 -0.0583   \n",
       "MVB12A  -0.6149 -0.3588  -0.5584 -0.6734  1.2381  0.1803  0.2249 -0.0821   \n",
       "HRCT1   -0.9159 -0.2209  -0.4397 -0.1543  0.2590  0.2297  0.0160  0.4183   \n",
       "ZNF286B -1.1783 -0.4882  -0.2140  0.2558 -0.3750 -0.8201 -0.6184 -0.2800   \n",
       "\n",
       "            IC9    IC10    IC11    IC12    IC13    IC14    IC15  Unnamed: 16  \n",
       "PROBE                                                                         \n",
       "CDK1    -1.7286  8.2389 -1.3952  0.6260 -0.3849  0.8650 -0.8569          NaN  \n",
       "UBE2C   -0.5717  4.0906 -0.4803  1.1264 -0.3727  0.8197 -0.8002          NaN  \n",
       "CCNB1   -1.2580  0.3552 -0.9335  0.2340  1.4414  0.2826  3.3749          NaN  \n",
       "AURKB   -0.3919  4.0472 -2.2181 -1.2844 -0.6276  0.5016  0.7448          NaN  \n",
       "AURKA    0.2682 -0.3779  0.3459  0.6775  1.6482  0.4719  3.1775          NaN  \n",
       "...         ...     ...     ...     ...     ...     ...     ...          ...  \n",
       "LGALS3  -0.8436  0.8988 -1.2667  1.4437  0.0509  0.4350  0.8060          NaN  \n",
       "DOK1     0.2711 -0.1829 -0.7776 -0.4143  0.2355  0.1569 -0.1020          NaN  \n",
       "MVB12A  -0.0896  0.5334  0.3950 -0.5984  0.1611 -1.5826 -1.0250          NaN  \n",
       "HRCT1    1.3329  0.5509  0.0661  0.1099  1.0450 -0.1599  0.0919          NaN  \n",
       "ZNF286B  0.0307 -0.4195 -0.4247  0.0000  0.3943 -0.0806  0.6930          NaN  \n",
       "\n",
       "[10000 rows x 16 columns]"
      ]
     },
     "execution_count": 31,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_gene_weights = pd.read_csv(DATA_PATH + 'CCLE/JHU011_UPPER_AERODIGESTIVE_TRACT_ica_S.xls', sep='\\t', index_col=0)\n",
    "df_gene_weights"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 53513 × 22590\n",
       "    obs: 'Cell_line', 'Cancer_type', 'n_genes', 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt', 'batch'\n",
       "    var: 'n_cells', 'mt', 'n_cells_by_counts', 'mean_counts', 'pct_dropout_by_counts', 'total_counts'"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata = sc.read_h5ad(DATA_PATH + 'CCLE/CPM_data_pp.h5ad')\n",
    "adata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": [
    "def batch_computation(X, f, k=10):\n",
    "    n = len(X)\n",
    "    step = int(n/k)\n",
    "    X_tot = None\n",
    "    for i in range(k+1):\n",
    "        print('Computing batch %i...' % (i + 1))\n",
    "        X_batch = f(X[i*step:(i+1)*step,:])\n",
    "        if X_tot is None:\n",
    "            X_tot = X_batch\n",
    "        else:\n",
    "            X_tot = np.vstack( (X_tot, X_batch) )\n",
    "    return X_tot\n",
    "\n",
    "def compute_ICs(adata, df_S):\n",
    "    \n",
    "    def one_step(X):\n",
    "        X = np.log(X + 1)\n",
    "        X = X - X.mean(axis=0)\n",
    "        return X@df_S.values[:,:-1]\n",
    "    \n",
    "    print('Selecting relevant genes...', end=' ')\n",
    "    IC_genes = [g for g in list(df_S.index) if g in adata.var_names]\n",
    "    print('%i genes retained.' % len(IC_genes))\n",
    "    df_S = df_S.loc[IC_genes,:]\n",
    "    adata_red = adata[:,IC_genes]\n",
    "    X_ICs = batch_computation(adata_red.X, one_step, k=10)\n",
    "    \n",
    "    return pd.DataFrame(\n",
    "        data=X_ICs, \n",
    "        index=adata.obs_names.str.decode('utf-8'), \n",
    "        columns=['IC%i' % (i+1) for i in range(len(X_ICs.T))]\n",
    "    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Selecting relevant genes... 10000 genes retained.\n",
      "Computing batch 1...\n",
      "Computing batch 2...\n",
      "Computing batch 3...\n",
      "Computing batch 4...\n",
      "Computing batch 5...\n",
      "Computing batch 6...\n",
      "Computing batch 7...\n",
      "Computing batch 8...\n",
      "Computing batch 9...\n",
      "Computing batch 10...\n",
      "Computing batch 11...\n"
     ]
    }
   ],
   "source": [
    "df = compute_ICs(adata, df_gene_weights)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "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>IC1</th>\n",
       "      <th>IC2</th>\n",
       "      <th>IC3</th>\n",
       "      <th>IC4</th>\n",
       "      <th>IC5</th>\n",
       "      <th>IC6</th>\n",
       "      <th>IC7</th>\n",
       "      <th>IC8</th>\n",
       "      <th>IC9</th>\n",
       "      <th>IC10</th>\n",
       "      <th>IC11</th>\n",
       "      <th>IC12</th>\n",
       "      <th>IC13</th>\n",
       "      <th>IC14</th>\n",
       "      <th>IC15</th>\n",
       "      <th>Cell_line</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Cells</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
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       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>AAAGATGCAGTTAACC-1-18-0</th>\n",
       "      <td>-459.273019</td>\n",
       "      <td>-99.719000</td>\n",
       "      <td>505.566067</td>\n",
       "      <td>-519.114922</td>\n",
       "      <td>169.847575</td>\n",
       "      <td>424.536166</td>\n",
       "      <td>-299.121371</td>\n",
       "      <td>116.057499</td>\n",
       "      <td>-106.598212</td>\n",
       "      <td>77.995203</td>\n",
       "      <td>5.576831</td>\n",
       "      <td>90.426192</td>\n",
       "      <td>-84.181949</td>\n",
       "      <td>-155.222429</td>\n",
       "      <td>92.378606</td>\n",
       "      <td>JHH7_LIVER</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AACACGTAGACAGACC-1-18-0</th>\n",
       "      <td>-478.774515</td>\n",
       "      <td>178.630990</td>\n",
       "      <td>421.437251</td>\n",
       "      <td>-533.562986</td>\n",
       "      <td>284.366121</td>\n",
       "      <td>214.053055</td>\n",
       "      <td>-677.596930</td>\n",
       "      <td>368.076459</td>\n",
       "      <td>-172.676563</td>\n",
       "      <td>-75.932147</td>\n",
       "      <td>84.548938</td>\n",
       "      <td>59.592393</td>\n",
       "      <td>3.305337</td>\n",
       "      <td>-321.780319</td>\n",
       "      <td>180.195851</td>\n",
       "      <td>JHH7_LIVER</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AACTCAGAGCGACGTA-1-18-0</th>\n",
       "      <td>-1051.309756</td>\n",
       "      <td>556.437037</td>\n",
       "      <td>258.953507</td>\n",
       "      <td>-797.287721</td>\n",
       "      <td>583.002547</td>\n",
       "      <td>420.020011</td>\n",
       "      <td>-776.948234</td>\n",
       "      <td>362.052093</td>\n",
       "      <td>-281.485070</td>\n",
       "      <td>51.031295</td>\n",
       "      <td>70.308815</td>\n",
       "      <td>-59.425816</td>\n",
       "      <td>-110.605379</td>\n",
       "      <td>-369.345908</td>\n",
       "      <td>94.166193</td>\n",
       "      <td>JHH7_LIVER</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AACTCAGAGGTGCTAG-1-18-0</th>\n",
       "      <td>-321.972861</td>\n",
       "      <td>-121.400228</td>\n",
       "      <td>404.064765</td>\n",
       "      <td>-569.280165</td>\n",
       "      <td>104.051543</td>\n",
       "      <td>221.087551</td>\n",
       "      <td>-142.273235</td>\n",
       "      <td>227.717972</td>\n",
       "      <td>-74.066529</td>\n",
       "      <td>65.799318</td>\n",
       "      <td>-22.533060</td>\n",
       "      <td>-14.224675</td>\n",
       "      <td>-187.831258</td>\n",
       "      <td>-241.859425</td>\n",
       "      <td>-5.026453</td>\n",
       "      <td>JHH7_LIVER</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AACTTTCAGATAGGAG-1-18-0</th>\n",
       "      <td>-665.343220</td>\n",
       "      <td>-11.258566</td>\n",
       "      <td>638.515797</td>\n",
       "      <td>-850.381385</td>\n",
       "      <td>116.533049</td>\n",
       "      <td>159.868563</td>\n",
       "      <td>-370.795667</td>\n",
       "      <td>287.936557</td>\n",
       "      <td>-94.601118</td>\n",
       "      <td>62.628048</td>\n",
       "      <td>35.066629</td>\n",
       "      <td>-16.878444</td>\n",
       "      <td>-351.609332</td>\n",
       "      <td>-96.789859</td>\n",
       "      <td>126.303109</td>\n",
       "      <td>JHH7_LIVER</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTCTCCTTCAGCGACC-12-10-21</th>\n",
       "      <td>322.325904</td>\n",
       "      <td>352.770239</td>\n",
       "      <td>60.981889</td>\n",
       "      <td>651.414622</td>\n",
       "      <td>65.253577</td>\n",
       "      <td>-720.220860</td>\n",
       "      <td>464.040302</td>\n",
       "      <td>35.644125</td>\n",
       "      <td>127.001891</td>\n",
       "      <td>317.120433</td>\n",
       "      <td>219.426361</td>\n",
       "      <td>230.793803</td>\n",
       "      <td>173.595164</td>\n",
       "      <td>484.667149</td>\n",
       "      <td>-218.424113</td>\n",
       "      <td>HS729_SOFT_TISSUE</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTGCCGTGTAACGTTC-12-10-21</th>\n",
       "      <td>265.691919</td>\n",
       "      <td>100.153499</td>\n",
       "      <td>108.466144</td>\n",
       "      <td>567.538490</td>\n",
       "      <td>-16.043168</td>\n",
       "      <td>-661.138942</td>\n",
       "      <td>690.405381</td>\n",
       "      <td>-39.719779</td>\n",
       "      <td>124.096445</td>\n",
       "      <td>214.083750</td>\n",
       "      <td>145.419761</td>\n",
       "      <td>220.937859</td>\n",
       "      <td>138.363664</td>\n",
       "      <td>544.678195</td>\n",
       "      <td>-138.847494</td>\n",
       "      <td>HS729_SOFT_TISSUE</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTGTAGGCACATCCAA-12-10-21</th>\n",
       "      <td>-519.169840</td>\n",
       "      <td>396.303187</td>\n",
       "      <td>-208.636064</td>\n",
       "      <td>-322.383344</td>\n",
       "      <td>299.332509</td>\n",
       "      <td>18.559136</td>\n",
       "      <td>-123.652939</td>\n",
       "      <td>-159.495100</td>\n",
       "      <td>-188.274307</td>\n",
       "      <td>364.818837</td>\n",
       "      <td>-0.348277</td>\n",
       "      <td>-44.838243</td>\n",
       "      <td>-145.566006</td>\n",
       "      <td>-63.403952</td>\n",
       "      <td>-33.393872</td>\n",
       "      <td>HS729_SOFT_TISSUE</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTGTAGGTCGCCATAA-12-10-21</th>\n",
       "      <td>444.738501</td>\n",
       "      <td>-773.156501</td>\n",
       "      <td>682.459386</td>\n",
       "      <td>439.485426</td>\n",
       "      <td>-171.622208</td>\n",
       "      <td>-10.604976</td>\n",
       "      <td>75.673812</td>\n",
       "      <td>349.194274</td>\n",
       "      <td>201.423027</td>\n",
       "      <td>-533.556870</td>\n",
       "      <td>-57.012437</td>\n",
       "      <td>60.871715</td>\n",
       "      <td>280.090545</td>\n",
       "      <td>75.046452</td>\n",
       "      <td>-10.435954</td>\n",
       "      <td>HS729_SOFT_TISSUE</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>TTTGGTTGTTAAGATG-12-10-21</th>\n",
       "      <td>74.431363</td>\n",
       "      <td>376.853293</td>\n",
       "      <td>-473.823453</td>\n",
       "      <td>-117.102051</td>\n",
       "      <td>-127.710368</td>\n",
       "      <td>-7.954126</td>\n",
       "      <td>47.979107</td>\n",
       "      <td>-189.699246</td>\n",
       "      <td>-13.148754</td>\n",
       "      <td>168.738012</td>\n",
       "      <td>57.360715</td>\n",
       "      <td>-16.033394</td>\n",
       "      <td>-134.524547</td>\n",
       "      <td>-11.642503</td>\n",
       "      <td>43.829803</td>\n",
       "      <td>HS729_SOFT_TISSUE</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>53513 rows × 16 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                   IC1         IC2         IC3         IC4  \\\n",
       "Cells                                                                        \n",
       "AAAGATGCAGTTAACC-1-18-0    -459.273019  -99.719000  505.566067 -519.114922   \n",
       "AACACGTAGACAGACC-1-18-0    -478.774515  178.630990  421.437251 -533.562986   \n",
       "AACTCAGAGCGACGTA-1-18-0   -1051.309756  556.437037  258.953507 -797.287721   \n",
       "AACTCAGAGGTGCTAG-1-18-0    -321.972861 -121.400228  404.064765 -569.280165   \n",
       "AACTTTCAGATAGGAG-1-18-0    -665.343220  -11.258566  638.515797 -850.381385   \n",
       "...                                ...         ...         ...         ...   \n",
       "TTCTCCTTCAGCGACC-12-10-21   322.325904  352.770239   60.981889  651.414622   \n",
       "TTGCCGTGTAACGTTC-12-10-21   265.691919  100.153499  108.466144  567.538490   \n",
       "TTGTAGGCACATCCAA-12-10-21  -519.169840  396.303187 -208.636064 -322.383344   \n",
       "TTGTAGGTCGCCATAA-12-10-21   444.738501 -773.156501  682.459386  439.485426   \n",
       "TTTGGTTGTTAAGATG-12-10-21    74.431363  376.853293 -473.823453 -117.102051   \n",
       "\n",
       "                                  IC5         IC6         IC7         IC8  \\\n",
       "Cells                                                                       \n",
       "AAAGATGCAGTTAACC-1-18-0    169.847575  424.536166 -299.121371  116.057499   \n",
       "AACACGTAGACAGACC-1-18-0    284.366121  214.053055 -677.596930  368.076459   \n",
       "AACTCAGAGCGACGTA-1-18-0    583.002547  420.020011 -776.948234  362.052093   \n",
       "AACTCAGAGGTGCTAG-1-18-0    104.051543  221.087551 -142.273235  227.717972   \n",
       "AACTTTCAGATAGGAG-1-18-0    116.533049  159.868563 -370.795667  287.936557   \n",
       "...                               ...         ...         ...         ...   \n",
       "TTCTCCTTCAGCGACC-12-10-21   65.253577 -720.220860  464.040302   35.644125   \n",
       "TTGCCGTGTAACGTTC-12-10-21  -16.043168 -661.138942  690.405381  -39.719779   \n",
       "TTGTAGGCACATCCAA-12-10-21  299.332509   18.559136 -123.652939 -159.495100   \n",
       "TTGTAGGTCGCCATAA-12-10-21 -171.622208  -10.604976   75.673812  349.194274   \n",
       "TTTGGTTGTTAAGATG-12-10-21 -127.710368   -7.954126   47.979107 -189.699246   \n",
       "\n",
       "                                  IC9        IC10        IC11        IC12  \\\n",
       "Cells                                                                       \n",
       "AAAGATGCAGTTAACC-1-18-0   -106.598212   77.995203    5.576831   90.426192   \n",
       "AACACGTAGACAGACC-1-18-0   -172.676563  -75.932147   84.548938   59.592393   \n",
       "AACTCAGAGCGACGTA-1-18-0   -281.485070   51.031295   70.308815  -59.425816   \n",
       "AACTCAGAGGTGCTAG-1-18-0    -74.066529   65.799318  -22.533060  -14.224675   \n",
       "AACTTTCAGATAGGAG-1-18-0    -94.601118   62.628048   35.066629  -16.878444   \n",
       "...                               ...         ...         ...         ...   \n",
       "TTCTCCTTCAGCGACC-12-10-21  127.001891  317.120433  219.426361  230.793803   \n",
       "TTGCCGTGTAACGTTC-12-10-21  124.096445  214.083750  145.419761  220.937859   \n",
       "TTGTAGGCACATCCAA-12-10-21 -188.274307  364.818837   -0.348277  -44.838243   \n",
       "TTGTAGGTCGCCATAA-12-10-21  201.423027 -533.556870  -57.012437   60.871715   \n",
       "TTTGGTTGTTAAGATG-12-10-21  -13.148754  168.738012   57.360715  -16.033394   \n",
       "\n",
       "                                 IC13        IC14        IC15  \\\n",
       "Cells                                                           \n",
       "AAAGATGCAGTTAACC-1-18-0    -84.181949 -155.222429   92.378606   \n",
       "AACACGTAGACAGACC-1-18-0      3.305337 -321.780319  180.195851   \n",
       "AACTCAGAGCGACGTA-1-18-0   -110.605379 -369.345908   94.166193   \n",
       "AACTCAGAGGTGCTAG-1-18-0   -187.831258 -241.859425   -5.026453   \n",
       "AACTTTCAGATAGGAG-1-18-0   -351.609332  -96.789859  126.303109   \n",
       "...                               ...         ...         ...   \n",
       "TTCTCCTTCAGCGACC-12-10-21  173.595164  484.667149 -218.424113   \n",
       "TTGCCGTGTAACGTTC-12-10-21  138.363664  544.678195 -138.847494   \n",
       "TTGTAGGCACATCCAA-12-10-21 -145.566006  -63.403952  -33.393872   \n",
       "TTGTAGGTCGCCATAA-12-10-21  280.090545   75.046452  -10.435954   \n",
       "TTTGGTTGTTAAGATG-12-10-21 -134.524547  -11.642503   43.829803   \n",
       "\n",
       "                                   Cell_line  \n",
       "Cells                                         \n",
       "AAAGATGCAGTTAACC-1-18-0           JHH7_LIVER  \n",
       "AACACGTAGACAGACC-1-18-0           JHH7_LIVER  \n",
       "AACTCAGAGCGACGTA-1-18-0           JHH7_LIVER  \n",
       "AACTCAGAGGTGCTAG-1-18-0           JHH7_LIVER  \n",
       "AACTTTCAGATAGGAG-1-18-0           JHH7_LIVER  \n",
       "...                                      ...  \n",
       "TTCTCCTTCAGCGACC-12-10-21  HS729_SOFT_TISSUE  \n",
       "TTGCCGTGTAACGTTC-12-10-21  HS729_SOFT_TISSUE  \n",
       "TTGTAGGCACATCCAA-12-10-21  HS729_SOFT_TISSUE  \n",
       "TTGTAGGTCGCCATAA-12-10-21  HS729_SOFT_TISSUE  \n",
       "TTTGGTTGTTAAGATG-12-10-21  HS729_SOFT_TISSUE  \n",
       "\n",
       "[53513 rows x 16 columns]"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df['Cell_line'] = list(adata.obs['Cell_line'])\n",
    "df['Cells'] = list(adata.obs_names)\n",
    "df = df.set_index('Cells')\n",
    "df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "df.to_csv(DATA_PATH + \"all_tumors_pp_ICs.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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