my_anndata.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "0738f2cf-95d4-44d2-b4c9-0bca8a399a45",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Requirement already satisfied: anndata in /opt/anaconda3/lib/python3.12/site-packages (0.10.8)\n",
      "Requirement already satisfied: array-api-compat!=1.5,>1.4 in /opt/anaconda3/lib/python3.12/site-packages (from anndata) (1.8)\n",
      "Requirement already satisfied: h5py>=3.1 in /opt/anaconda3/lib/python3.12/site-packages (from anndata) (3.11.0)\n",
      "Requirement already satisfied: natsort in /opt/anaconda3/lib/python3.12/site-packages (from anndata) (8.4.0)\n",
      "Requirement already satisfied: numpy>=1.23 in /opt/anaconda3/lib/python3.12/site-packages (from anndata) (1.26.4)\n",
      "Requirement already satisfied: packaging>=20.0 in /opt/anaconda3/lib/python3.12/site-packages (from anndata) (23.2)\n",
      "Requirement already satisfied: pandas!=2.1.0rc0,!=2.1.2,>=1.4 in /opt/anaconda3/lib/python3.12/site-packages (from anndata) (2.2.2)\n",
      "Requirement already satisfied: scipy>1.8 in /opt/anaconda3/lib/python3.12/site-packages (from anndata) (1.13.1)\n",
      "Requirement already satisfied: python-dateutil>=2.8.2 in /opt/anaconda3/lib/python3.12/site-packages (from pandas!=2.1.0rc0,!=2.1.2,>=1.4->anndata) (2.9.0.post0)\n",
      "Requirement already satisfied: pytz>=2020.1 in /opt/anaconda3/lib/python3.12/site-packages (from pandas!=2.1.0rc0,!=2.1.2,>=1.4->anndata) (2024.1)\n",
      "Requirement already satisfied: tzdata>=2022.7 in /opt/anaconda3/lib/python3.12/site-packages (from pandas!=2.1.0rc0,!=2.1.2,>=1.4->anndata) (2023.3)\n",
      "Requirement already satisfied: six>=1.5 in /opt/anaconda3/lib/python3.12/site-packages (from python-dateutil>=2.8.2->pandas!=2.1.0rc0,!=2.1.2,>=1.4->anndata) (1.16.0)\n"
     ]
    }
   ],
   "source": [
    "! pip install anndata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "ba6471a1-bfd9-436e-8c03-0d384078987d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Requirement already satisfied: scanpy in /opt/anaconda3/lib/python3.12/site-packages (1.10.2)\n",
      "Requirement already satisfied: anndata>=0.8 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (0.10.8)\n",
      "Requirement already satisfied: h5py>=3.1 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (3.11.0)\n",
      "Requirement already satisfied: joblib in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (1.4.2)\n",
      "Requirement already satisfied: legacy-api-wrap>=1.4 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (1.4)\n",
      "Requirement already satisfied: matplotlib>=3.6 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (3.8.4)\n",
      "Requirement already satisfied: natsort in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (8.4.0)\n",
      "Requirement already satisfied: networkx>=2.7 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (3.2.1)\n",
      "Requirement already satisfied: numba>=0.56 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (0.59.1)\n",
      "Requirement already satisfied: numpy<2,>=1.23 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (1.26.4)\n",
      "Requirement already satisfied: packaging>=21.3 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (23.2)\n",
      "Requirement already satisfied: pandas>=1.5 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (2.2.2)\n",
      "Requirement already satisfied: patsy in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (0.5.6)\n",
      "Requirement already satisfied: pynndescent>=0.5 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (0.5.13)\n",
      "Requirement already satisfied: scikit-learn>=0.24 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (1.4.2)\n",
      "Requirement already satisfied: scipy>=1.8 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (1.13.1)\n",
      "Requirement already satisfied: seaborn>=0.13 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (0.13.2)\n",
      "Requirement already satisfied: session-info in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (1.0.0)\n",
      "Requirement already satisfied: statsmodels>=0.13 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (0.14.2)\n",
      "Requirement already satisfied: tqdm in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (4.66.4)\n",
      "Requirement already satisfied: umap-learn!=0.5.0,>=0.5 in /opt/anaconda3/lib/python3.12/site-packages (from scanpy) (0.5.6)\n",
      "Requirement already satisfied: array-api-compat!=1.5,>1.4 in /opt/anaconda3/lib/python3.12/site-packages (from anndata>=0.8->scanpy) (1.8)\n",
      "Requirement already satisfied: contourpy>=1.0.1 in /opt/anaconda3/lib/python3.12/site-packages (from matplotlib>=3.6->scanpy) (1.2.0)\n",
      "Requirement already satisfied: cycler>=0.10 in /opt/anaconda3/lib/python3.12/site-packages (from matplotlib>=3.6->scanpy) (0.11.0)\n",
      "Requirement already satisfied: fonttools>=4.22.0 in /opt/anaconda3/lib/python3.12/site-packages (from matplotlib>=3.6->scanpy) (4.51.0)\n",
      "Requirement already satisfied: kiwisolver>=1.3.1 in /opt/anaconda3/lib/python3.12/site-packages (from matplotlib>=3.6->scanpy) (1.4.4)\n",
      "Requirement already satisfied: pillow>=8 in /opt/anaconda3/lib/python3.12/site-packages (from matplotlib>=3.6->scanpy) (10.3.0)\n",
      "Requirement already satisfied: pyparsing>=2.3.1 in /opt/anaconda3/lib/python3.12/site-packages (from matplotlib>=3.6->scanpy) (3.0.9)\n",
      "Requirement already satisfied: python-dateutil>=2.7 in /opt/anaconda3/lib/python3.12/site-packages (from matplotlib>=3.6->scanpy) (2.9.0.post0)\n",
      "Requirement already satisfied: llvmlite<0.43,>=0.42.0dev0 in /opt/anaconda3/lib/python3.12/site-packages (from numba>=0.56->scanpy) (0.42.0)\n",
      "Requirement already satisfied: pytz>=2020.1 in /opt/anaconda3/lib/python3.12/site-packages (from pandas>=1.5->scanpy) (2024.1)\n",
      "Requirement already satisfied: tzdata>=2022.7 in /opt/anaconda3/lib/python3.12/site-packages (from pandas>=1.5->scanpy) (2023.3)\n",
      "Requirement already satisfied: threadpoolctl>=2.0.0 in /opt/anaconda3/lib/python3.12/site-packages (from scikit-learn>=0.24->scanpy) (2.2.0)\n",
      "Requirement already satisfied: six in /opt/anaconda3/lib/python3.12/site-packages (from patsy->scanpy) (1.16.0)\n",
      "Requirement already satisfied: stdlib-list in /opt/anaconda3/lib/python3.12/site-packages (from session-info->scanpy) (0.10.0)\n"
     ]
    }
   ],
   "source": [
    "! pip install scanpy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "bcba518b-76d5-4b9f-a90b-b85c4d63c7ba",
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import numpy as np\n",
    "import pandas as pd\n",
    "import scipy\n",
    "import anndata\n",
    "import scanpy as sc\n",
    "import seaborn as sns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "f132ea58-4fce-4835-af39-24f01291c5e9",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'/Users/sarachitgaran/Desktop/F1L_Internship/Kinkner_2020'"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cwd= os.getcwd()\n",
    "cwd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "4b966f84-e316-4df9-a57e-b27bca7f8efe",
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/var/folders/0j/y04ny1ms5mg2smfny631m8940000gn/T/ipykernel_3479/3242124268.py:3: DtypeWarning: Columns (4,9,10,11,12,13,14,15,16,17,18,19,20) have mixed types. Specify dtype option on import or set low_memory=False.\n",
      "  meta = pd.read_csv(cwd+'/data/Metadata.txt', sep='\\t')\n"
     ]
    },
    {
     "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>CellID</th>\n",
       "      <th>CellLine</th>\n",
       "      <th>Pool</th>\n",
       "      <th>Indication</th>\n",
       "      <th>Genes_expressed</th>\n",
       "      <th>Discrete_cluster_minpts5_eps1.8</th>\n",
       "      <th>Discrete_cluster_minpts5_eps1.5</th>\n",
       "      <th>Discrete_cluster_minpts5_eps1.2</th>\n",
       "      <th>CNA_subclone</th>\n",
       "      <th>SkinPig_score</th>\n",
       "      <th>...</th>\n",
       "      <th>EMTII_score</th>\n",
       "      <th>EMTIII_score</th>\n",
       "      <th>IFNResp_score</th>\n",
       "      <th>p53Sen_score</th>\n",
       "      <th>EpiSen_score</th>\n",
       "      <th>StressResp_score</th>\n",
       "      <th>ProtMatu_score</th>\n",
       "      <th>ProtDegra_score</th>\n",
       "      <th>G1/S_score</th>\n",
       "      <th>G2/M_score</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AAACCTGAGACATAAC-1-18</td>\n",
       "      <td>NCIH2126_LUNG</td>\n",
       "      <td>18</td>\n",
       "      <td>Lung Cancer</td>\n",
       "      <td>4318</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.166</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.935</td>\n",
       "      <td>-0.935</td>\n",
       "      <td>0.13</td>\n",
       "      <td>0.619</td>\n",
       "      <td>1.869</td>\n",
       "      <td>-0.004</td>\n",
       "      <td>0.805</td>\n",
       "      <td>0.896</td>\n",
       "      <td>0.424</td>\n",
       "      <td>-1.125</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AACGTTGTCACCCGAG-1-18</td>\n",
       "      <td>NCIH2126_LUNG</td>\n",
       "      <td>18</td>\n",
       "      <td>Lung Cancer</td>\n",
       "      <td>5200</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.213</td>\n",
       "      <td>...</td>\n",
       "      <td>-1.027</td>\n",
       "      <td>-1.027</td>\n",
       "      <td>0.066</td>\n",
       "      <td>1.049</td>\n",
       "      <td>1.267</td>\n",
       "      <td>0.252</td>\n",
       "      <td>1.299</td>\n",
       "      <td>1.61</td>\n",
       "      <td>0.624</td>\n",
       "      <td>-0.048</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AACTGGTAGACACGAC-1-18</td>\n",
       "      <td>NCIH2126_LUNG</td>\n",
       "      <td>18</td>\n",
       "      <td>Lung Cancer</td>\n",
       "      <td>4004</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.101</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.677</td>\n",
       "      <td>-0.677</td>\n",
       "      <td>0.304</td>\n",
       "      <td>0.822</td>\n",
       "      <td>2.401</td>\n",
       "      <td>0.141</td>\n",
       "      <td>0.451</td>\n",
       "      <td>1.225</td>\n",
       "      <td>-0.795</td>\n",
       "      <td>0.064</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AACTGGTAGGGCTTGA-1-18</td>\n",
       "      <td>NCIH2126_LUNG</td>\n",
       "      <td>18</td>\n",
       "      <td>Lung Cancer</td>\n",
       "      <td>4295</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.014</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.735</td>\n",
       "      <td>-0.735</td>\n",
       "      <td>0.094</td>\n",
       "      <td>0.834</td>\n",
       "      <td>2.282</td>\n",
       "      <td>0.15</td>\n",
       "      <td>0.267</td>\n",
       "      <td>0.892</td>\n",
       "      <td>-0.238</td>\n",
       "      <td>1.118</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>AACTGGTAGTACTTGC-1-18</td>\n",
       "      <td>NCIH2126_LUNG</td>\n",
       "      <td>18</td>\n",
       "      <td>Lung Cancer</td>\n",
       "      <td>4842</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.006</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.821</td>\n",
       "      <td>-0.821</td>\n",
       "      <td>0.034</td>\n",
       "      <td>0.96</td>\n",
       "      <td>1.4</td>\n",
       "      <td>-0.012</td>\n",
       "      <td>-0.276</td>\n",
       "      <td>-0.428</td>\n",
       "      <td>0.267</td>\n",
       "      <td>0.791</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>53509</th>\n",
       "      <td>c4722</td>\n",
       "      <td>JHU006_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>custom</td>\n",
       "      <td>Head and Neck Cancer</td>\n",
       "      <td>3343</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.018</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.505</td>\n",
       "      <td>-0.505</td>\n",
       "      <td>1.657</td>\n",
       "      <td>1.583</td>\n",
       "      <td>3.85</td>\n",
       "      <td>0.539</td>\n",
       "      <td>0.473</td>\n",
       "      <td>0.544</td>\n",
       "      <td>-1.079</td>\n",
       "      <td>-1.349</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53510</th>\n",
       "      <td>c4724</td>\n",
       "      <td>JHU006_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>custom</td>\n",
       "      <td>Head and Neck Cancer</td>\n",
       "      <td>6977</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.098</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.876</td>\n",
       "      <td>-0.876</td>\n",
       "      <td>0.669</td>\n",
       "      <td>1.086</td>\n",
       "      <td>3.046</td>\n",
       "      <td>0.799</td>\n",
       "      <td>0.49</td>\n",
       "      <td>1.319</td>\n",
       "      <td>-0.37</td>\n",
       "      <td>0.057</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53511</th>\n",
       "      <td>c4731</td>\n",
       "      <td>JHU006_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>custom</td>\n",
       "      <td>Head and Neck Cancer</td>\n",
       "      <td>6638</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.112</td>\n",
       "      <td>...</td>\n",
       "      <td>-0.112</td>\n",
       "      <td>-0.112</td>\n",
       "      <td>0.61</td>\n",
       "      <td>0.693</td>\n",
       "      <td>2.289</td>\n",
       "      <td>0.65</td>\n",
       "      <td>0.729</td>\n",
       "      <td>1.143</td>\n",
       "      <td>-0.508</td>\n",
       "      <td>0.501</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53512</th>\n",
       "      <td>c4735</td>\n",
       "      <td>JHU006_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>custom</td>\n",
       "      <td>Head and Neck Cancer</td>\n",
       "      <td>4052</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.244</td>\n",
       "      <td>...</td>\n",
       "      <td>1.981</td>\n",
       "      <td>1.981</td>\n",
       "      <td>0.523</td>\n",
       "      <td>-0.309</td>\n",
       "      <td>0.267</td>\n",
       "      <td>0.822</td>\n",
       "      <td>1.049</td>\n",
       "      <td>0.777</td>\n",
       "      <td>0.296</td>\n",
       "      <td>-0.936</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>53513</th>\n",
       "      <td>c4741</td>\n",
       "      <td>JHU006_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>custom</td>\n",
       "      <td>Head and Neck Cancer</td>\n",
       "      <td>5062</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.054</td>\n",
       "      <td>...</td>\n",
       "      <td>1.337</td>\n",
       "      <td>1.337</td>\n",
       "      <td>0.21</td>\n",
       "      <td>0.39</td>\n",
       "      <td>0.664</td>\n",
       "      <td>0.654</td>\n",
       "      <td>0.533</td>\n",
       "      <td>0.863</td>\n",
       "      <td>-0.551</td>\n",
       "      <td>-1.292</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>53513 rows × 21 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                      CellID                          CellLine    Pool  \\\n",
       "1      AAACCTGAGACATAAC-1-18                     NCIH2126_LUNG      18   \n",
       "2      AACGTTGTCACCCGAG-1-18                     NCIH2126_LUNG      18   \n",
       "3      AACTGGTAGACACGAC-1-18                     NCIH2126_LUNG      18   \n",
       "4      AACTGGTAGGGCTTGA-1-18                     NCIH2126_LUNG      18   \n",
       "5      AACTGGTAGTACTTGC-1-18                     NCIH2126_LUNG      18   \n",
       "...                      ...                               ...     ...   \n",
       "53509                  c4722  JHU006_UPPER_AERODIGESTIVE_TRACT  custom   \n",
       "53510                  c4724  JHU006_UPPER_AERODIGESTIVE_TRACT  custom   \n",
       "53511                  c4731  JHU006_UPPER_AERODIGESTIVE_TRACT  custom   \n",
       "53512                  c4735  JHU006_UPPER_AERODIGESTIVE_TRACT  custom   \n",
       "53513                  c4741  JHU006_UPPER_AERODIGESTIVE_TRACT  custom   \n",
       "\n",
       "                 Indication Genes_expressed Discrete_cluster_minpts5_eps1.8  \\\n",
       "1               Lung Cancer            4318                             NaN   \n",
       "2               Lung Cancer            5200                             NaN   \n",
       "3               Lung Cancer            4004                             NaN   \n",
       "4               Lung Cancer            4295                             NaN   \n",
       "5               Lung Cancer            4842                             NaN   \n",
       "...                     ...             ...                             ...   \n",
       "53509  Head and Neck Cancer            3343                             NaN   \n",
       "53510  Head and Neck Cancer            6977                             NaN   \n",
       "53511  Head and Neck Cancer            6638                             NaN   \n",
       "53512  Head and Neck Cancer            4052                             NaN   \n",
       "53513  Head and Neck Cancer            5062                             NaN   \n",
       "\n",
       "      Discrete_cluster_minpts5_eps1.5 Discrete_cluster_minpts5_eps1.2  \\\n",
       "1                                 NaN                             NaN   \n",
       "2                                 NaN                             NaN   \n",
       "3                                 NaN                             NaN   \n",
       "4                                 NaN                             NaN   \n",
       "5                                 NaN                             NaN   \n",
       "...                               ...                             ...   \n",
       "53509                             NaN                             NaN   \n",
       "53510                             NaN                             NaN   \n",
       "53511                             NaN                             NaN   \n",
       "53512                             NaN                             NaN   \n",
       "53513                             NaN                             NaN   \n",
       "\n",
       "      CNA_subclone SkinPig_score  ... EMTII_score EMTIII_score IFNResp_score  \\\n",
       "1              NaN         0.166  ...      -0.935       -0.935          0.13   \n",
       "2              NaN        -0.213  ...      -1.027       -1.027         0.066   \n",
       "3              NaN        -0.101  ...      -0.677       -0.677         0.304   \n",
       "4              NaN        -0.014  ...      -0.735       -0.735         0.094   \n",
       "5              NaN         0.006  ...      -0.821       -0.821         0.034   \n",
       "...            ...           ...  ...         ...          ...           ...   \n",
       "53509          NaN         0.018  ...      -0.505       -0.505         1.657   \n",
       "53510          NaN        -0.098  ...      -0.876       -0.876         0.669   \n",
       "53511          NaN        -0.112  ...      -0.112       -0.112          0.61   \n",
       "53512          NaN        -0.244  ...       1.981        1.981         0.523   \n",
       "53513          NaN        -0.054  ...       1.337        1.337          0.21   \n",
       "\n",
       "      p53Sen_score EpiSen_score StressResp_score ProtMatu_score  \\\n",
       "1            0.619        1.869           -0.004          0.805   \n",
       "2            1.049        1.267            0.252          1.299   \n",
       "3            0.822        2.401            0.141          0.451   \n",
       "4            0.834        2.282             0.15          0.267   \n",
       "5             0.96          1.4           -0.012         -0.276   \n",
       "...            ...          ...              ...            ...   \n",
       "53509        1.583         3.85            0.539          0.473   \n",
       "53510        1.086        3.046            0.799           0.49   \n",
       "53511        0.693        2.289             0.65          0.729   \n",
       "53512       -0.309        0.267            0.822          1.049   \n",
       "53513         0.39        0.664            0.654          0.533   \n",
       "\n",
       "      ProtDegra_score G1/S_score G2/M_score  \n",
       "1               0.896      0.424     -1.125  \n",
       "2                1.61      0.624     -0.048  \n",
       "3               1.225     -0.795      0.064  \n",
       "4               0.892     -0.238      1.118  \n",
       "5              -0.428      0.267      0.791  \n",
       "...               ...        ...        ...  \n",
       "53509           0.544     -1.079     -1.349  \n",
       "53510           1.319      -0.37      0.057  \n",
       "53511           1.143     -0.508      0.501  \n",
       "53512           0.777      0.296     -0.936  \n",
       "53513           0.863     -0.551     -1.292  \n",
       "\n",
       "[53513 rows x 21 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# read metdata. drop the first row. renames columns\n",
    "cwd= os.getcwd()\n",
    "meta = pd.read_csv(cwd+'/data/Metadata.txt', sep='\\t')\n",
    "meta.drop([0], axis=0, inplace=True)\n",
    "meta.rename(columns={'NAME':'CellID', 'Cell_line':'CellLine', 'Pool_ID':'Pool', 'Cancer_type':'Indication'}, inplace=True)\n",
    "meta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "915d912b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "        text-align: right;\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>0</th>\n",
       "      <th>1</th>\n",
       "      <th>2</th>\n",
       "      <th>3</th>\n",
       "      <th>4</th>\n",
       "      <th>5</th>\n",
       "      <th>6</th>\n",
       "      <th>7</th>\n",
       "      <th>8</th>\n",
       "      <th>9</th>\n",
       "      <th>...</th>\n",
       "      <th>56973</th>\n",
       "      <th>56974</th>\n",
       "      <th>56975</th>\n",
       "      <th>56976</th>\n",
       "      <th>56977</th>\n",
       "      <th>56978</th>\n",
       "      <th>56979</th>\n",
       "      <th>56980</th>\n",
       "      <th>56981</th>\n",
       "      <th>56982</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>NaN</td>\n",
       "      <td>AAACCTGAGACATAAC-1-18</td>\n",
       "      <td>AAACCTGCACAACGCC-1-18</td>\n",
       "      <td>AAACCTGCAGACAAGC-1-18</td>\n",
       "      <td>AAACCTGCAGCTCGAC-1-18</td>\n",
       "      <td>AAACCTGCATGGATGG-1-18</td>\n",
       "      <td>AAACCTGGTACGAAAT-1-18</td>\n",
       "      <td>AAACGGGAGATACACA-1-18</td>\n",
       "      <td>AAACGGGCAGGTGCCT-1-18</td>\n",
       "      <td>AAACGGGGTTTAGGAA-1-18</td>\n",
       "      <td>...</td>\n",
       "      <td>c4781</td>\n",
       "      <td>c4784</td>\n",
       "      <td>c4785</td>\n",
       "      <td>c4786</td>\n",
       "      <td>c4787</td>\n",
       "      <td>c4788</td>\n",
       "      <td>c4789</td>\n",
       "      <td>c4793</td>\n",
       "      <td>c4800</td>\n",
       "      <td>c4812</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Cell_line</td>\n",
       "      <td>NCIH2126_LUNG</td>\n",
       "      <td>SW579_THYROID</td>\n",
       "      <td>C32_SKIN</td>\n",
       "      <td>SW579_THYROID</td>\n",
       "      <td>NCIH446_LUNG</td>\n",
       "      <td>HEC251_ENDOMETRIUM</td>\n",
       "      <td>MFE319_ENDOMETRIUM</td>\n",
       "      <td>SKNAS_AUTONOMIC_GANGLIA</td>\n",
       "      <td>NCIH2452_PLEURA</td>\n",
       "      <td>...</td>\n",
       "      <td>SCC25_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>SCC25_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>SCC25_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>SCC25_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>93VU_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>JHU029_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>JHU029_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Pool_ID</td>\n",
       "      <td>18</td>\n",
       "      <td>18</td>\n",
       "      <td>18</td>\n",
       "      <td>18</td>\n",
       "      <td>18</td>\n",
       "      <td>18</td>\n",
       "      <td>18</td>\n",
       "      <td>18</td>\n",
       "      <td>18</td>\n",
       "      <td>...</td>\n",
       "      <td>custom</td>\n",
       "      <td>custom</td>\n",
       "      <td>custom</td>\n",
       "      <td>custom</td>\n",
       "      <td>custom</td>\n",
       "      <td>custom</td>\n",
       "      <td>custom</td>\n",
       "      <td>custom</td>\n",
       "      <td>custom</td>\n",
       "      <td>custom</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>A1BG</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>A1BG-AS1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>5</th>\n",
       "      <td>A1CF</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>6</th>\n",
       "      <td>A2M</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>7</th>\n",
       "      <td>A2M-AS1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>8</th>\n",
       "      <td>A2ML1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>9</th>\n",
       "      <td>A2ML1-AS1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>10 rows × 56983 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       0                      1                      2      \\\n",
       "0        NaN  AAACCTGAGACATAAC-1-18  AAACCTGCACAACGCC-1-18   \n",
       "1  Cell_line          NCIH2126_LUNG          SW579_THYROID   \n",
       "2    Pool_ID                     18                     18   \n",
       "3       A1BG                      0                      1   \n",
       "4   A1BG-AS1                      0                      0   \n",
       "5       A1CF                      0                      0   \n",
       "6        A2M                      0                      0   \n",
       "7    A2M-AS1                      0                      0   \n",
       "8      A2ML1                      0                      0   \n",
       "9  A2ML1-AS1                      0                      0   \n",
       "\n",
       "                   3                      4                      5      \\\n",
       "0  AAACCTGCAGACAAGC-1-18  AAACCTGCAGCTCGAC-1-18  AAACCTGCATGGATGG-1-18   \n",
       "1               C32_SKIN          SW579_THYROID           NCIH446_LUNG   \n",
       "2                     18                     18                     18   \n",
       "3                      1                      1                      0   \n",
       "4                      0                      0                      0   \n",
       "5                      0                      0                      0   \n",
       "6                      0                      0                      0   \n",
       "7                      0                      0                      0   \n",
       "8                      0                      0                      0   \n",
       "9                      0                      0                      0   \n",
       "\n",
       "                   6                      7                        8      \\\n",
       "0  AAACCTGGTACGAAAT-1-18  AAACGGGAGATACACA-1-18    AAACGGGCAGGTGCCT-1-18   \n",
       "1     HEC251_ENDOMETRIUM     MFE319_ENDOMETRIUM  SKNAS_AUTONOMIC_GANGLIA   \n",
       "2                     18                     18                       18   \n",
       "3                      2                      0                        0   \n",
       "4                      0                      0                        0   \n",
       "5                      0                      0                        0   \n",
       "6                      0                      0                        0   \n",
       "7                      0                      0                        0   \n",
       "8                      0                      0                        0   \n",
       "9                      0                      0                        0   \n",
       "\n",
       "                   9      ...                            56973  \\\n",
       "0  AAACGGGGTTTAGGAA-1-18  ...                            c4781   \n",
       "1        NCIH2452_PLEURA  ...  SCC25_UPPER_AERODIGESTIVE_TRACT   \n",
       "2                     18  ...                           custom   \n",
       "3                      0  ...                                0   \n",
       "4                      0  ...                                0   \n",
       "5                      0  ...                                0   \n",
       "6                      0  ...                                0   \n",
       "7                      0  ...                                0   \n",
       "8                      0  ...                                0   \n",
       "9                      0  ...                                0   \n",
       "\n",
       "                             56974                            56975  \\\n",
       "0                            c4784                            c4785   \n",
       "1  SCC25_UPPER_AERODIGESTIVE_TRACT  SCC25_UPPER_AERODIGESTIVE_TRACT   \n",
       "2                           custom                           custom   \n",
       "3                                0                                0   \n",
       "4                                0                                0   \n",
       "5                                0                                0   \n",
       "6                                0                                0   \n",
       "7                                0                                0   \n",
       "8                                0                                0   \n",
       "9                                0                                0   \n",
       "\n",
       "                             56976                           56977  \\\n",
       "0                            c4786                           c4787   \n",
       "1  SCC25_UPPER_AERODIGESTIVE_TRACT  93VU_UPPER_AERODIGESTIVE_TRACT   \n",
       "2                           custom                          custom   \n",
       "3                                0                               0   \n",
       "4                                0                               0   \n",
       "5                                0                               0   \n",
       "6                                0                               0   \n",
       "7                                0                               0   \n",
       "8                                0                               0   \n",
       "9                                0                               0   \n",
       "\n",
       "                              56978                           56979  \\\n",
       "0                             c4788                           c4789   \n",
       "1  JHU029_UPPER_AERODIGESTIVE_TRACT  SCC9_UPPER_AERODIGESTIVE_TRACT   \n",
       "2                            custom                          custom   \n",
       "3                                 1                               0   \n",
       "4                                 0                               0   \n",
       "5                                 0                               0   \n",
       "6                                 0                               0   \n",
       "7                                 0                               0   \n",
       "8                                 0                               0   \n",
       "9                                 0                               0   \n",
       "\n",
       "                              56980                           56981  \\\n",
       "0                             c4793                           c4800   \n",
       "1  JHU029_UPPER_AERODIGESTIVE_TRACT  SCC9_UPPER_AERODIGESTIVE_TRACT   \n",
       "2                            custom                          custom   \n",
       "3                                 0                               0   \n",
       "4                                 0                               0   \n",
       "5                                 0                               0   \n",
       "6                                 0                               0   \n",
       "7                                 0                               1   \n",
       "8                                 0                               0   \n",
       "9                                 0                               0   \n",
       "\n",
       "                            56982  \n",
       "0                           c4812  \n",
       "1  SCC9_UPPER_AERODIGESTIVE_TRACT  \n",
       "2                          custom  \n",
       "3                               1  \n",
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       "\n",
       "[10 rows x 56983 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# the first three rows are CellID, CellLine, and Pool\n",
    "# only need the first row, CellID\n",
    "pd.read_csv(cwd+'/data/UMIcount_data.txt', nrows=10, sep='\\t', header=None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
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     "height": 161
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    "executionInfo": {
     "elapsed": 595,
     "status": "ok",
     "timestamp": 1703199075524,
     "user": {
      "displayName": "Dean Lee",
      "userId": "08770626040323150090"
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    "id": "ee7766fb",
    "outputId": "0e3de2e9-fb82-49c2-f4e8-0810c399bbcc"
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    "counts_cellid = pd.read_csv(cwd+'/data/UMIcount_data.txt', nrows=1, sep='\\t', header=None)\n",
    "counts_cellid = counts_cellid.transpose()\n",
    "counts_cellid.drop([0], inplace=True)\n",
    "counts_cellid"
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  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "b19809bb",
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     "text": [
      "CPU times: user 6min 37s, sys: 29.7 s, total: 7min 7s\n",
      "Wall time: 7min 48s\n"
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     "execution_count": 10,
     "metadata": {},
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   "source": [
    "%%time\n",
    "counts = pd.read_csv(cwd+'/data/UMIcount_data.txt', sep='\\t', skiprows=3, header=None, index_col=0)\n",
    "counts = counts.transpose()\n",
    "counts"
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  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "5f66e7bc",
   "metadata": {},
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       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>6</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCACAACGCC-1-18</th>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCAGACAAGC-1-18</th>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCAGCTCGAC-1-18</th>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCATGGATGG-1-18</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
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       "      <td>0</td>\n",
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       "    </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>c4788</th>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>4</td>\n",
       "      <td>4</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>c4789</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>c4793</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>c4800</th>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>c4812</th>\n",
       "      <td>1</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>2</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>53513 rows × 30314 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "0                      A1BG  A1BG-AS1  A1CF  A2M  A2M-AS1  A2ML1  A2ML1-AS1  \\\n",
       "AAACCTGAGACATAAC-1-18     0         0     0    0        0      0          0   \n",
       "AAACCTGCACAACGCC-1-18     1         0     0    0        0      0          0   \n",
       "AAACCTGCAGACAAGC-1-18     1         0     0    0        0      0          0   \n",
       "AAACCTGCAGCTCGAC-1-18     1         0     0    0        0      0          0   \n",
       "AAACCTGCATGGATGG-1-18     0         0     0    0        0      0          0   \n",
       "...                     ...       ...   ...  ...      ...    ...        ...   \n",
       "c4788                     1         0     0    0        0      0          0   \n",
       "c4789                     0         0     0    0        0      0          0   \n",
       "c4793                     0         0     0    0        0      0          0   \n",
       "c4800                     0         0     0    0        1      0          0   \n",
       "c4812                     1         0     0    0        0      0          0   \n",
       "\n",
       "0                      A2ML1-AS2  A3GALT2  A4GALT  ...  PRICKLE4  RABL6  \\\n",
       "AAACCTGAGACATAAC-1-18          0        0       0  ...         0      6   \n",
       "AAACCTGCACAACGCC-1-18          0        0       1  ...         0      1   \n",
       "AAACCTGCAGACAAGC-1-18          0        0       0  ...         0      2   \n",
       "AAACCTGCAGCTCGAC-1-18          0        0       0  ...         0      0   \n",
       "AAACCTGCATGGATGG-1-18          0        0       0  ...         0      0   \n",
       "...                          ...      ...     ...  ...       ...    ...   \n",
       "c4788                          0        0       0  ...         0      2   \n",
       "c4789                          0        0       0  ...         0      1   \n",
       "c4793                          0        0       0  ...         0      0   \n",
       "c4800                          0        0       0  ...         0      0   \n",
       "c4812                          0        0       0  ...         0      2   \n",
       "\n",
       "0                      RAET1E-AS1  RGS5  SERPINA3  SPATA13  TBC1D26  TIMM10B  \\\n",
       "AAACCTGAGACATAAC-1-18           0     0         0        0        0        1   \n",
       "AAACCTGCACAACGCC-1-18           0     0         0        0        0        0   \n",
       "AAACCTGCAGACAAGC-1-18           0     0         0        1        0        0   \n",
       "AAACCTGCAGCTCGAC-1-18           0     0         0        0        0        0   \n",
       "AAACCTGCATGGATGG-1-18           0     0         0        0        0        0   \n",
       "...                           ...   ...       ...      ...      ...      ...   \n",
       "c4788                           0     0         0        0        0        4   \n",
       "c4789                           0     0         0        0        0        1   \n",
       "c4793                           0     0         0        0        0        1   \n",
       "c4800                           0     0         0        0        0        1   \n",
       "c4812                           0     0         0        0        0        0   \n",
       "\n",
       "0                      TMBIM4  TMEM256-PLSCR3  \n",
       "AAACCTGAGACATAAC-1-18       0               0  \n",
       "AAACCTGCACAACGCC-1-18       0               0  \n",
       "AAACCTGCAGACAAGC-1-18       0               0  \n",
       "AAACCTGCAGCTCGAC-1-18       0               0  \n",
       "AAACCTGCATGGATGG-1-18       0               0  \n",
       "...                       ...             ...  \n",
       "c4788                       4               0  \n",
       "c4789                       0               0  \n",
       "c4793                       0               0  \n",
       "c4800                       0               0  \n",
       "c4812                       2               0  \n",
       "\n",
       "[53513 rows x 30314 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "counts.index = counts_cellid[0]\n",
    "counts.index.name = None\n",
    "a = counts.index.isin(meta['CellID'])\n",
    "counts = counts[a]\n",
    "counts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "2986c96b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>CellLine</th>\n",
       "      <th>Pool</th>\n",
       "      <th>Indication</th>\n",
       "      <th>Genes_expressed</th>\n",
       "      <th>Discrete_cluster_minpts5_eps1.8</th>\n",
       "      <th>Discrete_cluster_minpts5_eps1.5</th>\n",
       "      <th>Discrete_cluster_minpts5_eps1.2</th>\n",
       "      <th>CNA_subclone</th>\n",
       "      <th>SkinPig_score</th>\n",
       "      <th>EMTI_score</th>\n",
       "      <th>EMTII_score</th>\n",
       "      <th>EMTIII_score</th>\n",
       "      <th>IFNResp_score</th>\n",
       "      <th>p53Sen_score</th>\n",
       "      <th>EpiSen_score</th>\n",
       "      <th>StressResp_score</th>\n",
       "      <th>ProtMatu_score</th>\n",
       "      <th>ProtDegra_score</th>\n",
       "      <th>G1/S_score</th>\n",
       "      <th>G2/M_score</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>AAACCTGAGACATAAC-1-18</th>\n",
       "      <td>NCIH2126_LUNG</td>\n",
       "      <td>18</td>\n",
       "      <td>Lung Cancer</td>\n",
       "      <td>4318</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>0.166</td>\n",
       "      <td>-0.045</td>\n",
       "      <td>-0.935</td>\n",
       "      <td>-0.935</td>\n",
       "      <td>0.13</td>\n",
       "      <td>0.619</td>\n",
       "      <td>1.869</td>\n",
       "      <td>-0.004</td>\n",
       "      <td>0.805</td>\n",
       "      <td>0.896</td>\n",
       "      <td>0.424</td>\n",
       "      <td>-1.125</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCACAACGCC-1-18</th>\n",
       "      <td>SW579_THYROID</td>\n",
       "      <td>18</td>\n",
       "      <td>Thyroid Cancer</td>\n",
       "      <td>5021</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SW579_THYROID_1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.056</td>\n",
       "      <td>0.776</td>\n",
       "      <td>0.953</td>\n",
       "      <td>0.953</td>\n",
       "      <td>-0.266</td>\n",
       "      <td>-0.334</td>\n",
       "      <td>-1.125</td>\n",
       "      <td>-0.039</td>\n",
       "      <td>-0.243</td>\n",
       "      <td>-0.642</td>\n",
       "      <td>-0.173</td>\n",
       "      <td>1.365</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCAGACAAGC-1-18</th>\n",
       "      <td>C32_SKIN</td>\n",
       "      <td>18</td>\n",
       "      <td>Skin Cancer</td>\n",
       "      <td>3047</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>1.092</td>\n",
       "      <td>0.617</td>\n",
       "      <td>-0.034</td>\n",
       "      <td>-0.034</td>\n",
       "      <td>0.318</td>\n",
       "      <td>0.57</td>\n",
       "      <td>-0.165</td>\n",
       "      <td>0.074</td>\n",
       "      <td>0.25</td>\n",
       "      <td>0.096</td>\n",
       "      <td>-0.367</td>\n",
       "      <td>-1.135</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCAGCTCGAC-1-18</th>\n",
       "      <td>SW579_THYROID</td>\n",
       "      <td>18</td>\n",
       "      <td>Thyroid Cancer</td>\n",
       "      <td>2765</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SW579_THYROID_1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.601</td>\n",
       "      <td>1.038</td>\n",
       "      <td>1.952</td>\n",
       "      <td>1.952</td>\n",
       "      <td>0.341</td>\n",
       "      <td>-0.253</td>\n",
       "      <td>-0.552</td>\n",
       "      <td>0.921</td>\n",
       "      <td>2.876</td>\n",
       "      <td>1.645</td>\n",
       "      <td>0.226</td>\n",
       "      <td>0.469</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>AAACCTGCATGGATGG-1-18</th>\n",
       "      <td>NCIH446_LUNG</td>\n",
       "      <td>18</td>\n",
       "      <td>Lung Cancer</td>\n",
       "      <td>2064</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.251</td>\n",
       "      <td>-0.325</td>\n",
       "      <td>0.258</td>\n",
       "      <td>0.258</td>\n",
       "      <td>-0.044</td>\n",
       "      <td>-1.256</td>\n",
       "      <td>-0.367</td>\n",
       "      <td>-0.317</td>\n",
       "      <td>0.79</td>\n",
       "      <td>1.925</td>\n",
       "      <td>0.138</td>\n",
       "      <td>-0.384</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
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       "      <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>c4788</th>\n",
       "      <td>JHU029_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>custom</td>\n",
       "      <td>Head and Neck Cancer</td>\n",
       "      <td>5929</td>\n",
       "      <td>JHU029_UPPER_AERODIGESTIVE_TRACT_1</td>\n",
       "      <td>JHU029_UPPER_AERODIGESTIVE_TRACT_1</td>\n",
       "      <td>JHU029_UPPER_AERODIGESTIVE_TRACT_1</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.317</td>\n",
       "      <td>-0.39</td>\n",
       "      <td>0.023</td>\n",
       "      <td>0.023</td>\n",
       "      <td>-0.1</td>\n",
       "      <td>-0.604</td>\n",
       "      <td>-0.358</td>\n",
       "      <td>-0.123</td>\n",
       "      <td>0.067</td>\n",
       "      <td>0.804</td>\n",
       "      <td>0.135</td>\n",
       "      <td>0.264</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>c4789</th>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>custom</td>\n",
       "      <td>Head and Neck Cancer</td>\n",
       "      <td>3531</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT_2</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT_2</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT_2</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT_2</td>\n",
       "      <td>0.238</td>\n",
       "      <td>1.176</td>\n",
       "      <td>2.094</td>\n",
       "      <td>2.094</td>\n",
       "      <td>0.014</td>\n",
       "      <td>-0.045</td>\n",
       "      <td>-0.05</td>\n",
       "      <td>0.214</td>\n",
       "      <td>0.238</td>\n",
       "      <td>-0.514</td>\n",
       "      <td>-1.021</td>\n",
       "      <td>-1.243</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>c4793</th>\n",
       "      <td>JHU029_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>custom</td>\n",
       "      <td>Head and Neck Cancer</td>\n",
       "      <td>4029</td>\n",
       "      <td>JHU029_UPPER_AERODIGESTIVE_TRACT_1</td>\n",
       "      <td>JHU029_UPPER_AERODIGESTIVE_TRACT_3</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>-0.164</td>\n",
       "      <td>-0.163</td>\n",
       "      <td>-0.405</td>\n",
       "      <td>-0.405</td>\n",
       "      <td>0.01</td>\n",
       "      <td>-0.008</td>\n",
       "      <td>0.045</td>\n",
       "      <td>0.265</td>\n",
       "      <td>0.054</td>\n",
       "      <td>-0.466</td>\n",
       "      <td>0.345</td>\n",
       "      <td>0.804</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>c4800</th>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>custom</td>\n",
       "      <td>Head and Neck Cancer</td>\n",
       "      <td>4009</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT_1</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT_1</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT_4</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT_1</td>\n",
       "      <td>0.205</td>\n",
       "      <td>0.217</td>\n",
       "      <td>0.833</td>\n",
       "      <td>0.833</td>\n",
       "      <td>-0.257</td>\n",
       "      <td>-0.856</td>\n",
       "      <td>-0.593</td>\n",
       "      <td>0.152</td>\n",
       "      <td>0.022</td>\n",
       "      <td>0.684</td>\n",
       "      <td>0.684</td>\n",
       "      <td>0.624</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>c4812</th>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT</td>\n",
       "      <td>custom</td>\n",
       "      <td>Head and Neck Cancer</td>\n",
       "      <td>3428</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT_2</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT_2</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT_2</td>\n",
       "      <td>SCC9_UPPER_AERODIGESTIVE_TRACT_1</td>\n",
       "      <td>0.196</td>\n",
       "      <td>0.64</td>\n",
       "      <td>1.253</td>\n",
       "      <td>1.253</td>\n",
       "      <td>-0.098</td>\n",
       "      <td>-0.589</td>\n",
       "      <td>0.011</td>\n",
       "      <td>-0.01</td>\n",
       "      <td>0.265</td>\n",
       "      <td>-0.381</td>\n",
       "      <td>-1.253</td>\n",
       "      <td>-1.277</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>53513 rows × 20 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                               CellLine    Pool  \\\n",
       "AAACCTGAGACATAAC-1-18                     NCIH2126_LUNG      18   \n",
       "AAACCTGCACAACGCC-1-18                     SW579_THYROID      18   \n",
       "AAACCTGCAGACAAGC-1-18                          C32_SKIN      18   \n",
       "AAACCTGCAGCTCGAC-1-18                     SW579_THYROID      18   \n",
       "AAACCTGCATGGATGG-1-18                      NCIH446_LUNG      18   \n",
       "...                                                 ...     ...   \n",
       "c4788                  JHU029_UPPER_AERODIGESTIVE_TRACT  custom   \n",
       "c4789                    SCC9_UPPER_AERODIGESTIVE_TRACT  custom   \n",
       "c4793                  JHU029_UPPER_AERODIGESTIVE_TRACT  custom   \n",
       "c4800                    SCC9_UPPER_AERODIGESTIVE_TRACT  custom   \n",
       "c4812                    SCC9_UPPER_AERODIGESTIVE_TRACT  custom   \n",
       "\n",
       "                                 Indication Genes_expressed  \\\n",
       "AAACCTGAGACATAAC-1-18           Lung Cancer            4318   \n",
       "AAACCTGCACAACGCC-1-18        Thyroid Cancer            5021   \n",
       "AAACCTGCAGACAAGC-1-18           Skin Cancer            3047   \n",
       "AAACCTGCAGCTCGAC-1-18        Thyroid Cancer            2765   \n",
       "AAACCTGCATGGATGG-1-18           Lung Cancer            2064   \n",
       "...                                     ...             ...   \n",
       "c4788                  Head and Neck Cancer            5929   \n",
       "c4789                  Head and Neck Cancer            3531   \n",
       "c4793                  Head and Neck Cancer            4029   \n",
       "c4800                  Head and Neck Cancer            4009   \n",
       "c4812                  Head and Neck Cancer            3428   \n",
       "\n",
       "                          Discrete_cluster_minpts5_eps1.8  \\\n",
       "AAACCTGAGACATAAC-1-18                                 NaN   \n",
       "AAACCTGCACAACGCC-1-18                                 NaN   \n",
       "AAACCTGCAGACAAGC-1-18                                 NaN   \n",
       "AAACCTGCAGCTCGAC-1-18                                 NaN   \n",
       "AAACCTGCATGGATGG-1-18                                 NaN   \n",
       "...                                                   ...   \n",
       "c4788                  JHU029_UPPER_AERODIGESTIVE_TRACT_1   \n",
       "c4789                    SCC9_UPPER_AERODIGESTIVE_TRACT_2   \n",
       "c4793                  JHU029_UPPER_AERODIGESTIVE_TRACT_1   \n",
       "c4800                    SCC9_UPPER_AERODIGESTIVE_TRACT_1   \n",
       "c4812                    SCC9_UPPER_AERODIGESTIVE_TRACT_2   \n",
       "\n",
       "                          Discrete_cluster_minpts5_eps1.5  \\\n",
       "AAACCTGAGACATAAC-1-18                                 NaN   \n",
       "AAACCTGCACAACGCC-1-18                                 NaN   \n",
       "AAACCTGCAGACAAGC-1-18                                 NaN   \n",
       "AAACCTGCAGCTCGAC-1-18                                 NaN   \n",
       "AAACCTGCATGGATGG-1-18                                 NaN   \n",
       "...                                                   ...   \n",
       "c4788                  JHU029_UPPER_AERODIGESTIVE_TRACT_1   \n",
       "c4789                    SCC9_UPPER_AERODIGESTIVE_TRACT_2   \n",
       "c4793                  JHU029_UPPER_AERODIGESTIVE_TRACT_3   \n",
       "c4800                    SCC9_UPPER_AERODIGESTIVE_TRACT_1   \n",
       "c4812                    SCC9_UPPER_AERODIGESTIVE_TRACT_2   \n",
       "\n",
       "                          Discrete_cluster_minpts5_eps1.2  \\\n",
       "AAACCTGAGACATAAC-1-18                                 NaN   \n",
       "AAACCTGCACAACGCC-1-18                     SW579_THYROID_1   \n",
       "AAACCTGCAGACAAGC-1-18                                 NaN   \n",
       "AAACCTGCAGCTCGAC-1-18                     SW579_THYROID_1   \n",
       "AAACCTGCATGGATGG-1-18                                 NaN   \n",
       "...                                                   ...   \n",
       "c4788                  JHU029_UPPER_AERODIGESTIVE_TRACT_1   \n",
       "c4789                    SCC9_UPPER_AERODIGESTIVE_TRACT_2   \n",
       "c4793                                                 NaN   \n",
       "c4800                    SCC9_UPPER_AERODIGESTIVE_TRACT_4   \n",
       "c4812                    SCC9_UPPER_AERODIGESTIVE_TRACT_2   \n",
       "\n",
       "                                           CNA_subclone SkinPig_score  \\\n",
       "AAACCTGAGACATAAC-1-18                               NaN         0.166   \n",
       "AAACCTGCACAACGCC-1-18                               NaN        -0.056   \n",
       "AAACCTGCAGACAAGC-1-18                               NaN         1.092   \n",
       "AAACCTGCAGCTCGAC-1-18                               NaN        -0.601   \n",
       "AAACCTGCATGGATGG-1-18                               NaN        -0.251   \n",
       "...                                                 ...           ...   \n",
       "c4788                                               NaN        -0.317   \n",
       "c4789                  SCC9_UPPER_AERODIGESTIVE_TRACT_2         0.238   \n",
       "c4793                                               NaN        -0.164   \n",
       "c4800                  SCC9_UPPER_AERODIGESTIVE_TRACT_1         0.205   \n",
       "c4812                  SCC9_UPPER_AERODIGESTIVE_TRACT_1         0.196   \n",
       "\n",
       "                      EMTI_score EMTII_score EMTIII_score IFNResp_score  \\\n",
       "AAACCTGAGACATAAC-1-18     -0.045      -0.935       -0.935          0.13   \n",
       "AAACCTGCACAACGCC-1-18      0.776       0.953        0.953        -0.266   \n",
       "AAACCTGCAGACAAGC-1-18      0.617      -0.034       -0.034         0.318   \n",
       "AAACCTGCAGCTCGAC-1-18      1.038       1.952        1.952         0.341   \n",
       "AAACCTGCATGGATGG-1-18     -0.325       0.258        0.258        -0.044   \n",
       "...                          ...         ...          ...           ...   \n",
       "c4788                      -0.39       0.023        0.023          -0.1   \n",
       "c4789                      1.176       2.094        2.094         0.014   \n",
       "c4793                     -0.163      -0.405       -0.405          0.01   \n",
       "c4800                      0.217       0.833        0.833        -0.257   \n",
       "c4812                       0.64       1.253        1.253        -0.098   \n",
       "\n",
       "                      p53Sen_score EpiSen_score StressResp_score  \\\n",
       "AAACCTGAGACATAAC-1-18        0.619        1.869           -0.004   \n",
       "AAACCTGCACAACGCC-1-18       -0.334       -1.125           -0.039   \n",
       "AAACCTGCAGACAAGC-1-18         0.57       -0.165            0.074   \n",
       "AAACCTGCAGCTCGAC-1-18       -0.253       -0.552            0.921   \n",
       "AAACCTGCATGGATGG-1-18       -1.256       -0.367           -0.317   \n",
       "...                            ...          ...              ...   \n",
       "c4788                       -0.604       -0.358           -0.123   \n",
       "c4789                       -0.045        -0.05            0.214   \n",
       "c4793                       -0.008        0.045            0.265   \n",
       "c4800                       -0.856       -0.593            0.152   \n",
       "c4812                       -0.589        0.011            -0.01   \n",
       "\n",
       "                      ProtMatu_score ProtDegra_score G1/S_score G2/M_score  \n",
       "AAACCTGAGACATAAC-1-18          0.805           0.896      0.424     -1.125  \n",
       "AAACCTGCACAACGCC-1-18         -0.243          -0.642     -0.173      1.365  \n",
       "AAACCTGCAGACAAGC-1-18           0.25           0.096     -0.367     -1.135  \n",
       "AAACCTGCAGCTCGAC-1-18          2.876           1.645      0.226      0.469  \n",
       "AAACCTGCATGGATGG-1-18           0.79           1.925      0.138     -0.384  \n",
       "...                              ...             ...        ...        ...  \n",
       "c4788                          0.067           0.804      0.135      0.264  \n",
       "c4789                          0.238          -0.514     -1.021     -1.243  \n",
       "c4793                          0.054          -0.466      0.345      0.804  \n",
       "c4800                          0.022           0.684      0.684      0.624  \n",
       "c4812                          0.265          -0.381     -1.253     -1.277  \n",
       "\n",
       "[53513 rows x 20 columns]"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "meta = meta.set_index('CellID')\n",
    "meta = meta.reindex(index=counts.index)\n",
    "meta"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "9ae50965",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "counts.index.equals(meta.index)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "6505a9fa",
   "metadata": {
    "id": "6505a9fa"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 53513 × 30314\n",
       "    obs: 'CellLine', 'Pool', 'Indication', 'Genes_expressed', 'Discrete_cluster_minpts5_eps1.8', 'Discrete_cluster_minpts5_eps1.5', 'Discrete_cluster_minpts5_eps1.2', 'CNA_subclone', 'SkinPig_score', 'EMTI_score', 'EMTII_score', 'EMTIII_score', 'IFNResp_score', 'p53Sen_score', 'EpiSen_score', 'StressResp_score', 'ProtMatu_score', 'ProtDegra_score', 'G1/S_score', 'G2/M_score'"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "adata = anndata.AnnData(X=scipy.sparse.csr_matrix(counts),\n",
    "                        obs=meta,\n",
    "                        var=counts.columns.to_frame())\n",
    "del counts\n",
    "adata.var.drop(columns=[0], inplace=True)\n",
    "adata.var.index.name = None\n",
    "adata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "f9e14080",
   "metadata": {},
   "outputs": [],
   "source": [
    "adata.obs['CellLine'] = adata.obs['CellLine'].astype(str)\n",
    "adata.obs['Pool'] = adata.obs['Pool'].astype(str)\n",
    "adata.obs['Indication'] = adata.obs['Indication'].astype(str)\n",
    "adata.obs['Genes_expressed'] = adata.obs['Genes_expressed'].astype(int)\n",
    "adata.obs['Discrete_cluster_minpts5_eps1.8'] = adata.obs['Discrete_cluster_minpts5_eps1.8'].astype(str)\n",
    "adata.obs['Discrete_cluster_minpts5_eps1.5'] = adata.obs['Discrete_cluster_minpts5_eps1.5'].astype(str)\n",
    "adata.obs['Discrete_cluster_minpts5_eps1.2'] = adata.obs['Discrete_cluster_minpts5_eps1.2'].astype(str)\n",
    "adata.obs['CNA_subclone'] = adata.obs['CNA_subclone'].astype(str)\n",
    "adata.obs['SkinPig_score'] = adata.obs['SkinPig_score'].astype(float)\n",
    "adata.obs['EMTI_score'] = adata.obs['EMTI_score'].astype(float)\n",
    "adata.obs['EMTII_score'] = adata.obs['EMTII_score'].astype(float)\n",
    "adata.obs['EMTIII_score'] = adata.obs['EMTIII_score'].astype(float)\n",
    "adata.obs['IFNResp_score'] = adata.obs['IFNResp_score'].astype(float)\n",
    "adata.obs['p53Sen_score'] = adata.obs['p53Sen_score'].astype(float)\n",
    "adata.obs['EpiSen_score'] = adata.obs['EpiSen_score'].astype(float)\n",
    "adata.obs['StressResp_score'] = adata.obs['StressResp_score'].astype(float)\n",
    "adata.obs['ProtMatu_score'] = adata.obs['ProtMatu_score'].astype(float)\n",
    "adata.obs['ProtDegra_score'] = adata.obs['ProtDegra_score'].astype(float)\n",
    "adata.obs['G1/S_score'] = adata.obs['G1/S_score'].astype(float)\n",
    "adata.obs['G2/M_score'] = adata.obs['G2/M_score'].astype(float)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "f07c050e",
   "metadata": {
    "id": "f07c050e"
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "AnnData object with n_obs × n_vars = 53513 × 23081\n",
       "    obs: 'CellLine', 'Pool', 'Indication', 'Genes_expressed', 'Discrete_cluster_minpts5_eps1.8', 'Discrete_cluster_minpts5_eps1.5', 'Discrete_cluster_minpts5_eps1.2', 'CNA_subclone', 'SkinPig_score', 'EMTI_score', 'EMTII_score', 'EMTIII_score', 'IFNResp_score', 'p53Sen_score', 'EpiSen_score', 'StressResp_score', 'ProtMatu_score', 'ProtDegra_score', 'G1/S_score', 'G2/M_score', 'n_genes'\n",
       "    var: 'n_cells'"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sc.pp.filter_genes(adata, min_cells=10)\n",
    "sc.pp.filter_cells(adata, min_genes=200)\n",
    "adata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "7caa8473",
   "metadata": {},
   "outputs": [],
   "source": [
    "adata.write(cwd+'/outs/240701_kinker_anndata.h5ad')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "5e02893e-cdab-4e27-8f0f-7d429127b9f0",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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