numbat_preprocess.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "4b77328a",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:26:00.932322Z",
     "start_time": "2023-07-16T02:26:00.742722Z"
    }
   },
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "e78ee89f",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:26:02.083761Z",
     "start_time": "2023-07-16T02:26:02.076333Z"
    }
   },
   "outputs": [],
   "source": [
    "t_cell_clusters = [0, 3, 7, 19, 45]\n",
    "b_cell_clusters = [1, 11, 24, 25, 35, 36, 40]\n",
    "nk_cell_clusters = [2, 15, 30]\n",
    "myeloid_clusters = [4, 8, 21, 26, 28, 29]\n",
    "aml_clusters = [14, 23, 41, 42]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "21b3fba7",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:26:02.861657Z",
     "start_time": "2023-07-16T02:26:02.718785Z"
    }
   },
   "outputs": [
    {
     "data": {
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       "\n",
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       "    }\n",
       "\n",
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       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGAGAGCTATA</th>\n",
       "      <td>GD1_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>21</td>\n",
       "      <td>AAACCTGAGAGCTATA-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGAGAGGTTAT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorGD</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGAGGTTAT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGAGGAGCGTT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorEL</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGGAGCGTT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGAGGATTCGG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGGATTCGG-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGAGTCCTCCT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGTCCTCCT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCATCGAGGTAG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCGAGGTAG-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCATCTTCAACT</th>\n",
       "      <td>MS4_</td>\n",
       "      <td>tumorGD</td>\n",
       "      <td>22</td>\n",
       "      <td>TTTGTCATCTTCAACT-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCATCTTCCTTC</th>\n",
       "      <td>MS4_</td>\n",
       "      <td>donorMS</td>\n",
       "      <td>28</td>\n",
       "      <td>TTTGTCATCTTCCTTC-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCATCTTCGGTC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>doublet</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCTTCGGTC-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCATCTTGCCGT</th>\n",
       "      <td>MS4_</td>\n",
       "      <td>donorMS</td>\n",
       "      <td>4</td>\n",
       "      <td>TTTGTCATCTTGCCGT-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>104154 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                        ref_sample donor_id  cluster_number  \\\n",
       "KMA1_AAACCTGAGAGCTATA         GD1_  doublet              21   \n",
       "KMA1_AAACCTGAGAGGTTAT  not in data  tumorGD              -1   \n",
       "KMA1_AAACCTGAGGAGCGTT  not in data  donorEL              -1   \n",
       "KMA1_AAACCTGAGGATTCGG  not in data  donorLB              -1   \n",
       "KMA1_AAACCTGAGTCCTCCT  not in data  donorLB              -1   \n",
       "...                            ...      ...             ...   \n",
       "KMA7_TTTGTCATCGAGGTAG  not in data  donorKC              -1   \n",
       "KMA7_TTTGTCATCTTCAACT         MS4_  tumorGD              22   \n",
       "KMA7_TTTGTCATCTTCCTTC         MS4_  donorMS              28   \n",
       "KMA7_TTTGTCATCTTCGGTC  not in data  doublet              -1   \n",
       "KMA7_TTTGTCATCTTGCCGT         MS4_  donorMS               4   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA1_AAACCTGAGAGCTATA  AAACCTGAGAGCTATA-1  KMA1  \n",
       "KMA1_AAACCTGAGAGGTTAT  AAACCTGAGAGGTTAT-1  KMA1  \n",
       "KMA1_AAACCTGAGGAGCGTT  AAACCTGAGGAGCGTT-1  KMA1  \n",
       "KMA1_AAACCTGAGGATTCGG  AAACCTGAGGATTCGG-1  KMA1  \n",
       "KMA1_AAACCTGAGTCCTCCT  AAACCTGAGTCCTCCT-1  KMA1  \n",
       "...                                   ...   ...  \n",
       "KMA7_TTTGTCATCGAGGTAG  TTTGTCATCGAGGTAG-1  KMA7  \n",
       "KMA7_TTTGTCATCTTCAACT  TTTGTCATCTTCAACT-1  KMA7  \n",
       "KMA7_TTTGTCATCTTCCTTC  TTTGTCATCTTCCTTC-1  KMA7  \n",
       "KMA7_TTTGTCATCTTCGGTC  TTTGTCATCTTCGGTC-1  KMA7  \n",
       "KMA7_TTTGTCATCTTGCCGT  TTTGTCATCTTGCCGT-1  KMA7  \n",
       "\n",
       "[104154 rows x 5 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cells_df = pd.read_csv('data/vireo_labels_allpools.csv', index_col='Unnamed: 0')\n",
    "cells_df['pool'] = cells_df.index.str.slice(0, 4)\n",
    "cells_df['barcode'] += '-1'\n",
    "cells_df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b1c55c4f",
   "metadata": {
    "heading_collapsed": true
   },
   "source": [
    "### KMA5, AH2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "4e1f5e77",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T02:15:16.582965Z",
     "start_time": "2023-07-14T02:15:16.554264Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGAGAGGGATA</th>\n",
       "      <td>AH2_</td>\n",
       "      <td>donorAH</td>\n",
       "      <td>3</td>\n",
       "      <td>AAACCTGAGAGGGATA-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGAGAGTGAGA</th>\n",
       "      <td>AH2_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>11</td>\n",
       "      <td>AAACCTGAGAGTGAGA-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGAGGCATGTG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>doublet</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGGCATGTG-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGAGGCGCTCT</th>\n",
       "      <td>AH2_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>18</td>\n",
       "      <td>AAACCTGAGGCGCTCT-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGCAAACTGCT</th>\n",
       "      <td>KC2_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>4</td>\n",
       "      <td>AAACCTGCAAACTGCT-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCATCATTGCGA</th>\n",
       "      <td>KC2_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>4</td>\n",
       "      <td>TTTGTCATCATTGCGA-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCATCGCAAGCC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCGCAAGCC-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCATCGCCAGCA</th>\n",
       "      <td>MS2_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>28</td>\n",
       "      <td>TTTGTCATCGCCAGCA-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCATCTCTGCTG</th>\n",
       "      <td>AH2_</td>\n",
       "      <td>donorAH</td>\n",
       "      <td>0</td>\n",
       "      <td>TTTGTCATCTCTGCTG-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCATCTGCAAGT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCTGCAAGT-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>11952 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                        ref_sample    donor_id  cluster_number  \\\n",
       "KMA5_AAACCTGAGAGGGATA         AH2_     donorAH               3   \n",
       "KMA5_AAACCTGAGAGTGAGA         AH2_     doublet              11   \n",
       "KMA5_AAACCTGAGGCATGTG  not in data     doublet              -1   \n",
       "KMA5_AAACCTGAGGCGCTCT         AH2_  unassigned              18   \n",
       "KMA5_AAACCTGCAAACTGCT         KC2_     donorKC               4   \n",
       "...                            ...         ...             ...   \n",
       "KMA5_TTTGTCATCATTGCGA         KC2_     donorKC               4   \n",
       "KMA5_TTTGTCATCGCAAGCC  not in data  unassigned              -1   \n",
       "KMA5_TTTGTCATCGCCAGCA         MS2_  unassigned              28   \n",
       "KMA5_TTTGTCATCTCTGCTG         AH2_     donorAH               0   \n",
       "KMA5_TTTGTCATCTGCAAGT  not in data     donorKC              -1   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA5_AAACCTGAGAGGGATA  AAACCTGAGAGGGATA-1  KMA5  \n",
       "KMA5_AAACCTGAGAGTGAGA  AAACCTGAGAGTGAGA-1  KMA5  \n",
       "KMA5_AAACCTGAGGCATGTG  AAACCTGAGGCATGTG-1  KMA5  \n",
       "KMA5_AAACCTGAGGCGCTCT  AAACCTGAGGCGCTCT-1  KMA5  \n",
       "KMA5_AAACCTGCAAACTGCT  AAACCTGCAAACTGCT-1  KMA5  \n",
       "...                                   ...   ...  \n",
       "KMA5_TTTGTCATCATTGCGA  TTTGTCATCATTGCGA-1  KMA5  \n",
       "KMA5_TTTGTCATCGCAAGCC  TTTGTCATCGCAAGCC-1  KMA5  \n",
       "KMA5_TTTGTCATCGCCAGCA  TTTGTCATCGCCAGCA-1  KMA5  \n",
       "KMA5_TTTGTCATCTCTGCTG  TTTGTCATCTCTGCTG-1  KMA5  \n",
       "KMA5_TTTGTCATCTGCAAGT  TTTGTCATCTGCAAGT-1  KMA5  \n",
       "\n",
       "[11952 rows x 5 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pool_df = cells_df[cells_df['pool'] == 'KMA5']\n",
    "pool_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "8d261072",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T02:15:23.720553Z",
     "start_time": "2023-07-14T02:15:23.708668Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "unassigned    3411\n",
       "donorAH       3248\n",
       "doublet       2593\n",
       "donorKC       1532\n",
       "donorMS        715\n",
       "tumorAH        332\n",
       "tumorKC         56\n",
       "tumorMS         53\n",
       "donorLB         12\n",
       "Name: donor_id, dtype: int64"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pool_df['donor_id'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "9d157eb7",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T02:16:52.431359Z",
     "start_time": "2023-07-14T02:16:52.410006Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA5_AAAGATGAGCCAGAAC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAAGATGAGCCAGAAC-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAAGCAACACATTCGA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAAGCAACACATTCGA-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAAGTAGAGTGTCTCA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAAGTAGAGTGTCTCA-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AACACGTTCGCATGGC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>AACACGTTCGCATGGC-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AACTCAGGTCGGATCC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>AACTCAGGTCGGATCC-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTATGCCACATGGGA</th>\n",
       "      <td>LB5_</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>23</td>\n",
       "      <td>TTTATGCCACATGGGA-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGGTTCATGCATGT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGGTTCATGCATGT-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGGTTTCAACTCTT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGGTTTCAACTCTT-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCAAGGCAGTCA</th>\n",
       "      <td>AH2_</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>29</td>\n",
       "      <td>TTTGTCAAGGCAGTCA-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCAGTTGCGCAC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCAGTTGCGCAC-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>191 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                        ref_sample donor_id  cluster_number  \\\n",
       "KMA5_AAAGATGAGCCAGAAC  not in data  tumorAH              -1   \n",
       "KMA5_AAAGCAACACATTCGA  not in data  tumorAH              -1   \n",
       "KMA5_AAAGTAGAGTGTCTCA  not in data  tumorAH              -1   \n",
       "KMA5_AACACGTTCGCATGGC  not in data  tumorAH              -1   \n",
       "KMA5_AACTCAGGTCGGATCC  not in data  tumorAH              -1   \n",
       "...                            ...      ...             ...   \n",
       "KMA5_TTTATGCCACATGGGA         LB5_  tumorAH              23   \n",
       "KMA5_TTTGGTTCATGCATGT  not in data  tumorAH              -1   \n",
       "KMA5_TTTGGTTTCAACTCTT  not in data  tumorAH              -1   \n",
       "KMA5_TTTGTCAAGGCAGTCA         AH2_  tumorAH              29   \n",
       "KMA5_TTTGTCAGTTGCGCAC  not in data  tumorAH              -1   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA5_AAAGATGAGCCAGAAC  AAAGATGAGCCAGAAC-1  KMA5  \n",
       "KMA5_AAAGCAACACATTCGA  AAAGCAACACATTCGA-1  KMA5  \n",
       "KMA5_AAAGTAGAGTGTCTCA  AAAGTAGAGTGTCTCA-1  KMA5  \n",
       "KMA5_AACACGTTCGCATGGC  AACACGTTCGCATGGC-1  KMA5  \n",
       "KMA5_AACTCAGGTCGGATCC  AACTCAGGTCGGATCC-1  KMA5  \n",
       "...                                   ...   ...  \n",
       "KMA5_TTTATGCCACATGGGA  TTTATGCCACATGGGA-1  KMA5  \n",
       "KMA5_TTTGGTTCATGCATGT  TTTGGTTCATGCATGT-1  KMA5  \n",
       "KMA5_TTTGGTTTCAACTCTT  TTTGGTTTCAACTCTT-1  KMA5  \n",
       "KMA5_TTTGTCAAGGCAGTCA  TTTGTCAAGGCAGTCA-1  KMA5  \n",
       "KMA5_TTTGTCAGTTGCGCAC  TTTGTCAGTTGCGCAC-1  KMA5  \n",
       "\n",
       "[191 rows x 5 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sample_df = pool_df[pool_df['donor_id'] == 'tumorAH']\n",
    "myeloid_aml_cells_df = sample_df[sample_df['cluster_number'].isin(\n",
    "                            myeloid_clusters + aml_clusters + [-1])]\n",
    "myeloid_aml_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "0912a8ce",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T02:17:52.025985Z",
     "start_time": "2023-07-14T02:17:52.003646Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>barcode</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA5_AAAGATGAGCCAGAAC</th>\n",
       "      <td>AAAGATGAGCCAGAAC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAAGCAACACATTCGA</th>\n",
       "      <td>AAAGCAACACATTCGA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAAGTAGAGTGTCTCA</th>\n",
       "      <td>AAAGTAGAGTGTCTCA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AACACGTTCGCATGGC</th>\n",
       "      <td>AACACGTTCGCATGGC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AACTCAGGTCGGATCC</th>\n",
       "      <td>AACTCAGGTCGGATCC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTATGCCACATGGGA</th>\n",
       "      <td>TTTATGCCACATGGGA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGGTTCATGCATGT</th>\n",
       "      <td>TTTGGTTCATGCATGT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGGTTTCAACTCTT</th>\n",
       "      <td>TTTGGTTTCAACTCTT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCAAGGCAGTCA</th>\n",
       "      <td>TTTGTCAAGGCAGTCA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCAGTTGCGCAC</th>\n",
       "      <td>TTTGTCAGTTGCGCAC-1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>191 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                  barcode\n",
       "KMA5_AAAGATGAGCCAGAAC  AAAGATGAGCCAGAAC-1\n",
       "KMA5_AAAGCAACACATTCGA  AAAGCAACACATTCGA-1\n",
       "KMA5_AAAGTAGAGTGTCTCA  AAAGTAGAGTGTCTCA-1\n",
       "KMA5_AACACGTTCGCATGGC  AACACGTTCGCATGGC-1\n",
       "KMA5_AACTCAGGTCGGATCC  AACTCAGGTCGGATCC-1\n",
       "...                                   ...\n",
       "KMA5_TTTATGCCACATGGGA  TTTATGCCACATGGGA-1\n",
       "KMA5_TTTGGTTCATGCATGT  TTTGGTTCATGCATGT-1\n",
       "KMA5_TTTGGTTTCAACTCTT  TTTGGTTTCAACTCTT-1\n",
       "KMA5_TTTGTCAAGGCAGTCA  TTTGTCAAGGCAGTCA-1\n",
       "KMA5_TTTGTCAGTTGCGCAC  TTTGTCAGTTGCGCAC-1\n",
       "\n",
       "[191 rows x 1 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "myeloid_aml_cells_barcodes = myeloid_aml_cells_df[['barcode']]\n",
    "myeloid_aml_cells_barcodes.to_csv('data/AH2/myeloid_aml_cells_barcodes.tsv', \n",
    "                                  index=False, header=False)\n",
    "myeloid_aml_cells_barcodes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "96940df1",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T02:18:01.523246Z",
     "start_time": "2023-07-14T02:18:01.502755Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGAGAGGGATA</th>\n",
       "      <td>AH2_</td>\n",
       "      <td>donorAH</td>\n",
       "      <td>3</td>\n",
       "      <td>AAACCTGAGAGGGATA-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGAGAGTGAGA</th>\n",
       "      <td>AH2_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>11</td>\n",
       "      <td>AAACCTGAGAGTGAGA-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGCAGCCTGTG</th>\n",
       "      <td>AH2_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>24</td>\n",
       "      <td>AAACCTGCAGCCTGTG-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGCAGGTGGAT</th>\n",
       "      <td>AH2_</td>\n",
       "      <td>donorAH</td>\n",
       "      <td>0</td>\n",
       "      <td>AAACCTGCAGGTGGAT-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGGTAGAGGAA</th>\n",
       "      <td>KC2_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>0</td>\n",
       "      <td>AAACCTGGTAGAGGAA-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGGTTTCTACTTAC</th>\n",
       "      <td>MS2_</td>\n",
       "      <td>donorMS</td>\n",
       "      <td>1</td>\n",
       "      <td>TTTGGTTTCTACTTAC-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCAAGTGAACAT</th>\n",
       "      <td>AH2_</td>\n",
       "      <td>donorAH</td>\n",
       "      <td>25</td>\n",
       "      <td>TTTGTCAAGTGAACAT-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCACAAATTGCC</th>\n",
       "      <td>AH2_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>36</td>\n",
       "      <td>TTTGTCACAAATTGCC-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCACAGTAGAGC</th>\n",
       "      <td>AH2_</td>\n",
       "      <td>donorAH</td>\n",
       "      <td>15</td>\n",
       "      <td>TTTGTCACAGTAGAGC-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCATCTCTGCTG</th>\n",
       "      <td>AH2_</td>\n",
       "      <td>donorAH</td>\n",
       "      <td>0</td>\n",
       "      <td>TTTGTCATCTCTGCTG-1</td>\n",
       "      <td>KMA5</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3243 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                      ref_sample    donor_id  cluster_number  \\\n",
       "KMA5_AAACCTGAGAGGGATA       AH2_     donorAH               3   \n",
       "KMA5_AAACCTGAGAGTGAGA       AH2_     doublet              11   \n",
       "KMA5_AAACCTGCAGCCTGTG       AH2_  unassigned              24   \n",
       "KMA5_AAACCTGCAGGTGGAT       AH2_     donorAH               0   \n",
       "KMA5_AAACCTGGTAGAGGAA       KC2_  unassigned               0   \n",
       "...                          ...         ...             ...   \n",
       "KMA5_TTTGGTTTCTACTTAC       MS2_     donorMS               1   \n",
       "KMA5_TTTGTCAAGTGAACAT       AH2_     donorAH              25   \n",
       "KMA5_TTTGTCACAAATTGCC       AH2_     doublet              36   \n",
       "KMA5_TTTGTCACAGTAGAGC       AH2_     donorAH              15   \n",
       "KMA5_TTTGTCATCTCTGCTG       AH2_     donorAH               0   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA5_AAACCTGAGAGGGATA  AAACCTGAGAGGGATA-1  KMA5  \n",
       "KMA5_AAACCTGAGAGTGAGA  AAACCTGAGAGTGAGA-1  KMA5  \n",
       "KMA5_AAACCTGCAGCCTGTG  AAACCTGCAGCCTGTG-1  KMA5  \n",
       "KMA5_AAACCTGCAGGTGGAT  AAACCTGCAGGTGGAT-1  KMA5  \n",
       "KMA5_AAACCTGGTAGAGGAA  AAACCTGGTAGAGGAA-1  KMA5  \n",
       "...                                   ...   ...  \n",
       "KMA5_TTTGGTTTCTACTTAC  TTTGGTTTCTACTTAC-1  KMA5  \n",
       "KMA5_TTTGTCAAGTGAACAT  TTTGTCAAGTGAACAT-1  KMA5  \n",
       "KMA5_TTTGTCACAAATTGCC  TTTGTCACAAATTGCC-1  KMA5  \n",
       "KMA5_TTTGTCACAGTAGAGC  TTTGTCACAGTAGAGC-1  KMA5  \n",
       "KMA5_TTTGTCATCTCTGCTG  TTTGTCATCTCTGCTG-1  KMA5  \n",
       "\n",
       "[3243 rows x 5 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = pool_df[pool_df['cluster_number'].\\\n",
    "                    isin(t_cell_clusters + b_cell_clusters + nk_cell_clusters)]\n",
    "normal_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "a4b72049",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T02:18:55.516595Z",
     "start_time": "2023-07-14T02:18:55.502921Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0     1023\n",
       "1      465\n",
       "3      308\n",
       "2      303\n",
       "7      277\n",
       "11     224\n",
       "45     171\n",
       "25     158\n",
       "36     107\n",
       "24      77\n",
       "15      59\n",
       "40      47\n",
       "30      15\n",
       "35       8\n",
       "19       1\n",
       "Name: cluster_number, dtype: int64"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cluster_counts = normal_cells_df['cluster_number'].value_counts()\n",
    "cluster_counts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "a5b27275",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T02:20:14.672777Z",
     "start_time": "2023-07-14T02:20:14.654769Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0     1023\n",
       "1      465\n",
       "3      308\n",
       "2      303\n",
       "7      277\n",
       "11     224\n",
       "45     171\n",
       "25     158\n",
       "36     107\n",
       "24      77\n",
       "15      59\n",
       "40      47\n",
       "30      15\n",
       "35       8\n",
       "Name: cluster_number, dtype: int64"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = normal_cells_df[normal_cells_df['cluster_number'].isin(\n",
    "                    cluster_counts[cluster_counts > 1].index)]\n",
    "\n",
    "cluster_counts = normal_cells_df['cluster_number'].value_counts()\n",
    "cluster_counts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "808c5d7f",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T02:20:39.885759Z",
     "start_time": "2023-07-14T02:20:39.859435Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>cell</th>\n",
       "      <th>group</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGAGAGGGATA</th>\n",
       "      <td>AAACCTGAGAGGGATA-1</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGAGAGTGAGA</th>\n",
       "      <td>AAACCTGAGAGTGAGA-1</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGCAGCCTGTG</th>\n",
       "      <td>AAACCTGCAGCCTGTG-1</td>\n",
       "      <td>24</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGCAGGTGGAT</th>\n",
       "      <td>AAACCTGCAGGTGGAT-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_AAACCTGGTAGAGGAA</th>\n",
       "      <td>AAACCTGGTAGAGGAA-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGGTTTCTACTTAC</th>\n",
       "      <td>TTTGGTTTCTACTTAC-1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCAAGTGAACAT</th>\n",
       "      <td>TTTGTCAAGTGAACAT-1</td>\n",
       "      <td>25</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCACAAATTGCC</th>\n",
       "      <td>TTTGTCACAAATTGCC-1</td>\n",
       "      <td>36</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCACAGTAGAGC</th>\n",
       "      <td>TTTGTCACAGTAGAGC-1</td>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA5_TTTGTCATCTCTGCTG</th>\n",
       "      <td>TTTGTCATCTCTGCTG-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3242 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                     cell  group\n",
       "KMA5_AAACCTGAGAGGGATA  AAACCTGAGAGGGATA-1      3\n",
       "KMA5_AAACCTGAGAGTGAGA  AAACCTGAGAGTGAGA-1     11\n",
       "KMA5_AAACCTGCAGCCTGTG  AAACCTGCAGCCTGTG-1     24\n",
       "KMA5_AAACCTGCAGGTGGAT  AAACCTGCAGGTGGAT-1      0\n",
       "KMA5_AAACCTGGTAGAGGAA  AAACCTGGTAGAGGAA-1      0\n",
       "...                                   ...    ...\n",
       "KMA5_TTTGGTTTCTACTTAC  TTTGGTTTCTACTTAC-1      1\n",
       "KMA5_TTTGTCAAGTGAACAT  TTTGTCAAGTGAACAT-1     25\n",
       "KMA5_TTTGTCACAAATTGCC  TTTGTCACAAATTGCC-1     36\n",
       "KMA5_TTTGTCACAGTAGAGC  TTTGTCACAGTAGAGC-1     15\n",
       "KMA5_TTTGTCATCTCTGCTG  TTTGTCATCTCTGCTG-1      0\n",
       "\n",
       "[3242 rows x 2 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = normal_cells_df[['barcode', 'cluster_number']]\n",
    "normal_cells_df.columns = ['cell', 'group']\n",
    "normal_cells_df.to_csv('data/AH2/normal_cells_annotations.csv', index=False)\n",
    "normal_cells_df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3b74fc7b",
   "metadata": {
    "heading_collapsed": true
   },
   "source": [
    "### KMA6, JS2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "8e98bbf6",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-13T19:04:54.413225Z",
     "start_time": "2023-07-13T19:04:54.379142Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGAGAATGTTG</th>\n",
       "      <td>KC3_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>14</td>\n",
       "      <td>AAACCTGAGAATGTTG-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGAGACTGGGT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGACTGGGT-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGAGCTGAAAT</th>\n",
       "      <td>KC3_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>14</td>\n",
       "      <td>AAACCTGAGCTGAAAT-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGAGGCCCGTT</th>\n",
       "      <td>KC3_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>0</td>\n",
       "      <td>AAACCTGAGGCCCGTT-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGAGTGCTGCC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGTGCTGCC-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCAGTTGGACCC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCAGTTGGACCC-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCATCCATGAAC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCCATGAAC-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCATCGCTAGCG</th>\n",
       "      <td>JS2_</td>\n",
       "      <td>donorJS</td>\n",
       "      <td>15</td>\n",
       "      <td>TTTGTCATCGCTAGCG-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCATCTTGCAAG</th>\n",
       "      <td>KC3_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>14</td>\n",
       "      <td>TTTGTCATCTTGCAAG-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCATCTTGGGTA</th>\n",
       "      <td>JS2_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>28</td>\n",
       "      <td>TTTGTCATCTTGGGTA-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>13229 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                        ref_sample    donor_id  cluster_number  \\\n",
       "KMA6_AAACCTGAGAATGTTG         KC3_     doublet              14   \n",
       "KMA6_AAACCTGAGACTGGGT  not in data     donorKC              -1   \n",
       "KMA6_AAACCTGAGCTGAAAT         KC3_     doublet              14   \n",
       "KMA6_AAACCTGAGGCCCGTT         KC3_     donorKC               0   \n",
       "KMA6_AAACCTGAGTGCTGCC  not in data  unassigned              -1   \n",
       "...                            ...         ...             ...   \n",
       "KMA6_TTTGTCAGTTGGACCC  not in data     donorKC              -1   \n",
       "KMA6_TTTGTCATCCATGAAC  not in data     donorKC              -1   \n",
       "KMA6_TTTGTCATCGCTAGCG         JS2_     donorJS              15   \n",
       "KMA6_TTTGTCATCTTGCAAG         KC3_     doublet              14   \n",
       "KMA6_TTTGTCATCTTGGGTA         JS2_  unassigned              28   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA6_AAACCTGAGAATGTTG  AAACCTGAGAATGTTG-1  KMA6  \n",
       "KMA6_AAACCTGAGACTGGGT  AAACCTGAGACTGGGT-1  KMA6  \n",
       "KMA6_AAACCTGAGCTGAAAT  AAACCTGAGCTGAAAT-1  KMA6  \n",
       "KMA6_AAACCTGAGGCCCGTT  AAACCTGAGGCCCGTT-1  KMA6  \n",
       "KMA6_AAACCTGAGTGCTGCC  AAACCTGAGTGCTGCC-1  KMA6  \n",
       "...                                   ...   ...  \n",
       "KMA6_TTTGTCAGTTGGACCC  TTTGTCAGTTGGACCC-1  KMA6  \n",
       "KMA6_TTTGTCATCCATGAAC  TTTGTCATCCATGAAC-1  KMA6  \n",
       "KMA6_TTTGTCATCGCTAGCG  TTTGTCATCGCTAGCG-1  KMA6  \n",
       "KMA6_TTTGTCATCTTGCAAG  TTTGTCATCTTGCAAG-1  KMA6  \n",
       "KMA6_TTTGTCATCTTGGGTA  TTTGTCATCTTGGGTA-1  KMA6  \n",
       "\n",
       "[13229 rows x 5 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pool_df = cells_df[cells_df['pool'] == 'KMA6']\n",
    "pool_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "5f4bd436",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-13T19:05:22.049014Z",
     "start_time": "2023-07-13T19:05:22.039238Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "unassigned    3403\n",
       "doublet       3191\n",
       "donorLB       2109\n",
       "donorKC       2063\n",
       "donorMS       1419\n",
       "donorJS        571\n",
       "tumorJS        473\n",
       "Name: donor_id, dtype: int64"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pool_df['donor_id'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "83120655",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-13T19:05:27.661596Z",
     "start_time": "2023-07-13T19:05:27.642984Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGCAGTCGATT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGCAGTCGATT-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACGGGCAATGGAGC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACGGGCAATGGAGC-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACGGGCATTGGTAC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACGGGCATTGGTAC-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACGGGCATTTCAGG</th>\n",
       "      <td>JS2_</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>14</td>\n",
       "      <td>AAACGGGCATTTCAGG-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAAGCAAAGCACCGTC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAAGCAAAGCACCGTC-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTCCTCGTCTCTTAT</th>\n",
       "      <td>JS2_</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>8</td>\n",
       "      <td>TTTCCTCGTCTCTTAT-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGCGCAGCAATATG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGCGCAGCAATATG-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGCGCCACATCTTT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGCGCCACATCTTT-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGGTTTCTCATTCA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGGTTTCTCATTCA-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCAGTTCGTTGA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCAGTTCGTTGA-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>352 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                        ref_sample donor_id  cluster_number  \\\n",
       "KMA6_AAACCTGCAGTCGATT  not in data  tumorJS              -1   \n",
       "KMA6_AAACGGGCAATGGAGC  not in data  tumorJS              -1   \n",
       "KMA6_AAACGGGCATTGGTAC  not in data  tumorJS              -1   \n",
       "KMA6_AAACGGGCATTTCAGG         JS2_  tumorJS              14   \n",
       "KMA6_AAAGCAAAGCACCGTC  not in data  tumorJS              -1   \n",
       "...                            ...      ...             ...   \n",
       "KMA6_TTTCCTCGTCTCTTAT         JS2_  tumorJS               8   \n",
       "KMA6_TTTGCGCAGCAATATG  not in data  tumorJS              -1   \n",
       "KMA6_TTTGCGCCACATCTTT  not in data  tumorJS              -1   \n",
       "KMA6_TTTGGTTTCTCATTCA  not in data  tumorJS              -1   \n",
       "KMA6_TTTGTCAGTTCGTTGA  not in data  tumorJS              -1   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA6_AAACCTGCAGTCGATT  AAACCTGCAGTCGATT-1  KMA6  \n",
       "KMA6_AAACGGGCAATGGAGC  AAACGGGCAATGGAGC-1  KMA6  \n",
       "KMA6_AAACGGGCATTGGTAC  AAACGGGCATTGGTAC-1  KMA6  \n",
       "KMA6_AAACGGGCATTTCAGG  AAACGGGCATTTCAGG-1  KMA6  \n",
       "KMA6_AAAGCAAAGCACCGTC  AAAGCAAAGCACCGTC-1  KMA6  \n",
       "...                                   ...   ...  \n",
       "KMA6_TTTCCTCGTCTCTTAT  TTTCCTCGTCTCTTAT-1  KMA6  \n",
       "KMA6_TTTGCGCAGCAATATG  TTTGCGCAGCAATATG-1  KMA6  \n",
       "KMA6_TTTGCGCCACATCTTT  TTTGCGCCACATCTTT-1  KMA6  \n",
       "KMA6_TTTGGTTTCTCATTCA  TTTGGTTTCTCATTCA-1  KMA6  \n",
       "KMA6_TTTGTCAGTTCGTTGA  TTTGTCAGTTCGTTGA-1  KMA6  \n",
       "\n",
       "[352 rows x 5 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sample_df = pool_df[pool_df['donor_id'] == 'tumorJS']\n",
    "myeloid_aml_cells_df = sample_df[sample_df['cluster_number'].isin(\n",
    "                            myeloid_clusters + aml_clusters + [-1])]\n",
    "myeloid_aml_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "b1dd6499",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-13T19:07:34.237229Z",
     "start_time": "2023-07-13T19:07:34.213060Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "\n",
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       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>barcode</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGCAGTCGATT</th>\n",
       "      <td>AAACCTGCAGTCGATT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACGGGCAATGGAGC</th>\n",
       "      <td>AAACGGGCAATGGAGC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACGGGCATTGGTAC</th>\n",
       "      <td>AAACGGGCATTGGTAC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACGGGCATTTCAGG</th>\n",
       "      <td>AAACGGGCATTTCAGG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAAGCAAAGCACCGTC</th>\n",
       "      <td>AAAGCAAAGCACCGTC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTCCTCGTCTCTTAT</th>\n",
       "      <td>TTTCCTCGTCTCTTAT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGCGCAGCAATATG</th>\n",
       "      <td>TTTGCGCAGCAATATG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGCGCCACATCTTT</th>\n",
       "      <td>TTTGCGCCACATCTTT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGGTTTCTCATTCA</th>\n",
       "      <td>TTTGGTTTCTCATTCA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCAGTTCGTTGA</th>\n",
       "      <td>TTTGTCAGTTCGTTGA-1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>352 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                  barcode\n",
       "KMA6_AAACCTGCAGTCGATT  AAACCTGCAGTCGATT-1\n",
       "KMA6_AAACGGGCAATGGAGC  AAACGGGCAATGGAGC-1\n",
       "KMA6_AAACGGGCATTGGTAC  AAACGGGCATTGGTAC-1\n",
       "KMA6_AAACGGGCATTTCAGG  AAACGGGCATTTCAGG-1\n",
       "KMA6_AAAGCAAAGCACCGTC  AAAGCAAAGCACCGTC-1\n",
       "...                                   ...\n",
       "KMA6_TTTCCTCGTCTCTTAT  TTTCCTCGTCTCTTAT-1\n",
       "KMA6_TTTGCGCAGCAATATG  TTTGCGCAGCAATATG-1\n",
       "KMA6_TTTGCGCCACATCTTT  TTTGCGCCACATCTTT-1\n",
       "KMA6_TTTGGTTTCTCATTCA  TTTGGTTTCTCATTCA-1\n",
       "KMA6_TTTGTCAGTTCGTTGA  TTTGTCAGTTCGTTGA-1\n",
       "\n",
       "[352 rows x 1 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "myeloid_aml_cells_barcodes = myeloid_aml_cells_df[['barcode']]\n",
    "myeloid_aml_cells_barcodes.to_csv('data/JS2/myeloid_aml_cells_barcodes.tsv', \n",
    "                                  index=False, header=False)\n",
    "myeloid_aml_cells_barcodes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "d0d7e879",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-13T19:13:26.381955Z",
     "start_time": "2023-07-13T19:13:26.361609Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
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       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGAGGCCCGTT</th>\n",
       "      <td>KC3_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>0</td>\n",
       "      <td>AAACCTGAGGCCCGTT-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGCACGGCTAC</th>\n",
       "      <td>MS3_</td>\n",
       "      <td>donorMS</td>\n",
       "      <td>0</td>\n",
       "      <td>AAACCTGCACGGCTAC-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGCACTTAAGC</th>\n",
       "      <td>LB6_</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>2</td>\n",
       "      <td>AAACCTGCACTTAAGC-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGGTTTACTCT</th>\n",
       "      <td>LB6_</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>19</td>\n",
       "      <td>AAACCTGGTTTACTCT-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGTCTCTAAGG</th>\n",
       "      <td>LB6_</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>19</td>\n",
       "      <td>AAACCTGTCTCTAAGG-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCAAGAAGGTTT</th>\n",
       "      <td>LB6_</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>2</td>\n",
       "      <td>TTTGTCAAGAAGGTTT-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCAAGACTAAGT</th>\n",
       "      <td>KC3_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>0</td>\n",
       "      <td>TTTGTCAAGACTAAGT-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCACACAGTCGC</th>\n",
       "      <td>LB6_</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>2</td>\n",
       "      <td>TTTGTCACACAGTCGC-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCAGTTCCACAA</th>\n",
       "      <td>KC3_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>0</td>\n",
       "      <td>TTTGTCAGTTCCACAA-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCATCGCTAGCG</th>\n",
       "      <td>JS2_</td>\n",
       "      <td>donorJS</td>\n",
       "      <td>15</td>\n",
       "      <td>TTTGTCATCGCTAGCG-1</td>\n",
       "      <td>KMA6</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2350 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                      ref_sample donor_id  cluster_number             barcode  \\\n",
       "KMA6_AAACCTGAGGCCCGTT       KC3_  donorKC               0  AAACCTGAGGCCCGTT-1   \n",
       "KMA6_AAACCTGCACGGCTAC       MS3_  donorMS               0  AAACCTGCACGGCTAC-1   \n",
       "KMA6_AAACCTGCACTTAAGC       LB6_  donorLB               2  AAACCTGCACTTAAGC-1   \n",
       "KMA6_AAACCTGGTTTACTCT       LB6_  donorLB              19  AAACCTGGTTTACTCT-1   \n",
       "KMA6_AAACCTGTCTCTAAGG       LB6_  donorLB              19  AAACCTGTCTCTAAGG-1   \n",
       "...                          ...      ...             ...                 ...   \n",
       "KMA6_TTTGTCAAGAAGGTTT       LB6_  donorLB               2  TTTGTCAAGAAGGTTT-1   \n",
       "KMA6_TTTGTCAAGACTAAGT       KC3_  donorKC               0  TTTGTCAAGACTAAGT-1   \n",
       "KMA6_TTTGTCACACAGTCGC       LB6_  donorLB               2  TTTGTCACACAGTCGC-1   \n",
       "KMA6_TTTGTCAGTTCCACAA       KC3_  donorKC               0  TTTGTCAGTTCCACAA-1   \n",
       "KMA6_TTTGTCATCGCTAGCG       JS2_  donorJS              15  TTTGTCATCGCTAGCG-1   \n",
       "\n",
       "                       pool  \n",
       "KMA6_AAACCTGAGGCCCGTT  KMA6  \n",
       "KMA6_AAACCTGCACGGCTAC  KMA6  \n",
       "KMA6_AAACCTGCACTTAAGC  KMA6  \n",
       "KMA6_AAACCTGGTTTACTCT  KMA6  \n",
       "KMA6_AAACCTGTCTCTAAGG  KMA6  \n",
       "...                     ...  \n",
       "KMA6_TTTGTCAAGAAGGTTT  KMA6  \n",
       "KMA6_TTTGTCAAGACTAAGT  KMA6  \n",
       "KMA6_TTTGTCACACAGTCGC  KMA6  \n",
       "KMA6_TTTGTCAGTTCCACAA  KMA6  \n",
       "KMA6_TTTGTCATCGCTAGCG  KMA6  \n",
       "\n",
       "[2350 rows x 5 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = pool_df[pool_df['cluster_number'].\\\n",
    "                    isin(t_cell_clusters + b_cell_clusters + nk_cell_clusters)]\n",
    "normal_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "0410ab99",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-13T19:14:49.296808Z",
     "start_time": "2023-07-13T19:14:49.282392Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2     643\n",
       "0     489\n",
       "19    411\n",
       "1     400\n",
       "45    125\n",
       "3     114\n",
       "7      57\n",
       "15     30\n",
       "40     30\n",
       "35     19\n",
       "30     10\n",
       "36      8\n",
       "11      6\n",
       "25      5\n",
       "24      3\n",
       "Name: cluster_number, dtype: int64"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df['cluster_number'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "f5fcec3a",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-13T19:15:49.737238Z",
     "start_time": "2023-07-13T19:15:49.714159Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>cell</th>\n",
       "      <th>group</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGAGGCCCGTT</th>\n",
       "      <td>AAACCTGAGGCCCGTT-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGCACGGCTAC</th>\n",
       "      <td>AAACCTGCACGGCTAC-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGCACTTAAGC</th>\n",
       "      <td>AAACCTGCACTTAAGC-1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGGTTTACTCT</th>\n",
       "      <td>AAACCTGGTTTACTCT-1</td>\n",
       "      <td>19</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_AAACCTGTCTCTAAGG</th>\n",
       "      <td>AAACCTGTCTCTAAGG-1</td>\n",
       "      <td>19</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCAAGAAGGTTT</th>\n",
       "      <td>TTTGTCAAGAAGGTTT-1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCAAGACTAAGT</th>\n",
       "      <td>TTTGTCAAGACTAAGT-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCACACAGTCGC</th>\n",
       "      <td>TTTGTCACACAGTCGC-1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCAGTTCCACAA</th>\n",
       "      <td>TTTGTCAGTTCCACAA-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA6_TTTGTCATCGCTAGCG</th>\n",
       "      <td>TTTGTCATCGCTAGCG-1</td>\n",
       "      <td>15</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>2350 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                     cell  group\n",
       "KMA6_AAACCTGAGGCCCGTT  AAACCTGAGGCCCGTT-1      0\n",
       "KMA6_AAACCTGCACGGCTAC  AAACCTGCACGGCTAC-1      0\n",
       "KMA6_AAACCTGCACTTAAGC  AAACCTGCACTTAAGC-1      2\n",
       "KMA6_AAACCTGGTTTACTCT  AAACCTGGTTTACTCT-1     19\n",
       "KMA6_AAACCTGTCTCTAAGG  AAACCTGTCTCTAAGG-1     19\n",
       "...                                   ...    ...\n",
       "KMA6_TTTGTCAAGAAGGTTT  TTTGTCAAGAAGGTTT-1      2\n",
       "KMA6_TTTGTCAAGACTAAGT  TTTGTCAAGACTAAGT-1      0\n",
       "KMA6_TTTGTCACACAGTCGC  TTTGTCACACAGTCGC-1      2\n",
       "KMA6_TTTGTCAGTTCCACAA  TTTGTCAGTTCCACAA-1      0\n",
       "KMA6_TTTGTCATCGCTAGCG  TTTGTCATCGCTAGCG-1     15\n",
       "\n",
       "[2350 rows x 2 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = normal_cells_df[['barcode', 'cluster_number']]\n",
    "normal_cells_df.columns = ['cell', 'group']\n",
    "normal_cells_df.to_csv('data/JS2/normal_cells_annotations.csv', index=False)\n",
    "normal_cells_df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9d5f1e2d",
   "metadata": {
    "heading_collapsed": true
   },
   "source": [
    "### KMA3, EL3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "afc43ac8",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:35:45.635506Z",
     "start_time": "2023-07-14T16:35:45.601362Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA3_AAACCTGAGAATAGGG</th>\n",
       "      <td>EL3_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>14</td>\n",
       "      <td>AAACCTGAGAATAGGG-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAACCTGAGACTCGGA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGACTCGGA-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAACCTGAGAGGGATA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGAGGGATA-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAACCTGAGATGGGTC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>doublet</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGATGGGTC-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAACCTGAGCCACGCT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGCCACGCT-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGTCATCCTGCCAT</th>\n",
       "      <td>LB3_</td>\n",
       "      <td>donorEL</td>\n",
       "      <td>3</td>\n",
       "      <td>TTTGTCATCCTGCCAT-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGTCATCCTTGACC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCCTTGACC-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGTCATCGCATGAT</th>\n",
       "      <td>EL3_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>41</td>\n",
       "      <td>TTTGTCATCGCATGAT-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGTCATCGGGAGTA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCGGGAGTA-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGTCATCTAGAGTC</th>\n",
       "      <td>EL3_</td>\n",
       "      <td>tumorLB</td>\n",
       "      <td>41</td>\n",
       "      <td>TTTGTCATCTAGAGTC-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>27532 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                        ref_sample    donor_id  cluster_number  \\\n",
       "KMA3_AAACCTGAGAATAGGG         EL3_  unassigned              14   \n",
       "KMA3_AAACCTGAGACTCGGA  not in data  unassigned              -1   \n",
       "KMA3_AAACCTGAGAGGGATA  not in data  unassigned              -1   \n",
       "KMA3_AAACCTGAGATGGGTC  not in data     doublet              -1   \n",
       "KMA3_AAACCTGAGCCACGCT  not in data  unassigned              -1   \n",
       "...                            ...         ...             ...   \n",
       "KMA3_TTTGTCATCCTGCCAT         LB3_     donorEL               3   \n",
       "KMA3_TTTGTCATCCTTGACC  not in data  unassigned              -1   \n",
       "KMA3_TTTGTCATCGCATGAT         EL3_  unassigned              41   \n",
       "KMA3_TTTGTCATCGGGAGTA  not in data  unassigned              -1   \n",
       "KMA3_TTTGTCATCTAGAGTC         EL3_     tumorLB              41   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA3_AAACCTGAGAATAGGG  AAACCTGAGAATAGGG-1  KMA3  \n",
       "KMA3_AAACCTGAGACTCGGA  AAACCTGAGACTCGGA-1  KMA3  \n",
       "KMA3_AAACCTGAGAGGGATA  AAACCTGAGAGGGATA-1  KMA3  \n",
       "KMA3_AAACCTGAGATGGGTC  AAACCTGAGATGGGTC-1  KMA3  \n",
       "KMA3_AAACCTGAGCCACGCT  AAACCTGAGCCACGCT-1  KMA3  \n",
       "...                                   ...   ...  \n",
       "KMA3_TTTGTCATCCTGCCAT  TTTGTCATCCTGCCAT-1  KMA3  \n",
       "KMA3_TTTGTCATCCTTGACC  TTTGTCATCCTTGACC-1  KMA3  \n",
       "KMA3_TTTGTCATCGCATGAT  TTTGTCATCGCATGAT-1  KMA3  \n",
       "KMA3_TTTGTCATCGGGAGTA  TTTGTCATCGGGAGTA-1  KMA3  \n",
       "KMA3_TTTGTCATCTAGAGTC  TTTGTCATCTAGAGTC-1  KMA3  \n",
       "\n",
       "[27532 rows x 5 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pool_df = cells_df[cells_df['pool'] == 'KMA3']\n",
    "pool_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "c89308e0",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:35:49.151798Z",
     "start_time": "2023-07-14T16:35:49.139858Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "unassigned    17375\n",
       "doublet        5820\n",
       "tumorLB        1435\n",
       "donorEL         905\n",
       "tumorEL         857\n",
       "donorKC         843\n",
       "donorAM         133\n",
       "tumorAM         111\n",
       "tumorKC          53\n",
       "Name: donor_id, dtype: int64"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pool_df['donor_id'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "8cd1758c",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:36:06.071358Z",
     "start_time": "2023-07-14T16:36:06.048588Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA3_AAACGGGCAGACGCTC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorEL</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACGGGCAGACGCTC-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAACGGGTCACCATAG</th>\n",
       "      <td>LB3_</td>\n",
       "      <td>tumorEL</td>\n",
       "      <td>23</td>\n",
       "      <td>AAACGGGTCACCATAG-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGATGCATGCGCAC</th>\n",
       "      <td>LB3_</td>\n",
       "      <td>tumorEL</td>\n",
       "      <td>23</td>\n",
       "      <td>AAAGATGCATGCGCAC-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGATGTCATTGCGA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorEL</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAAGATGTCATTGCGA-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGCAAGTCCGTCAG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorEL</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAAGCAAGTCCGTCAG-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGCGCGTCAGGACA</th>\n",
       "      <td>LB3_</td>\n",
       "      <td>tumorEL</td>\n",
       "      <td>23</td>\n",
       "      <td>TTTGCGCGTCAGGACA-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGCGCGTCGACTAT</th>\n",
       "      <td>LB3_</td>\n",
       "      <td>tumorEL</td>\n",
       "      <td>23</td>\n",
       "      <td>TTTGCGCGTCGACTAT-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGCGCGTGAGGGTT</th>\n",
       "      <td>LB3_</td>\n",
       "      <td>tumorEL</td>\n",
       "      <td>23</td>\n",
       "      <td>TTTGCGCGTGAGGGTT-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGTCAGTAGCGTCC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorEL</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCAGTAGCGTCC-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGTCAGTTTAAGCC</th>\n",
       "      <td>LB3_</td>\n",
       "      <td>tumorEL</td>\n",
       "      <td>23</td>\n",
       "      <td>TTTGTCAGTTTAAGCC-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>852 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                        ref_sample donor_id  cluster_number  \\\n",
       "KMA3_AAACGGGCAGACGCTC  not in data  tumorEL              -1   \n",
       "KMA3_AAACGGGTCACCATAG         LB3_  tumorEL              23   \n",
       "KMA3_AAAGATGCATGCGCAC         LB3_  tumorEL              23   \n",
       "KMA3_AAAGATGTCATTGCGA  not in data  tumorEL              -1   \n",
       "KMA3_AAAGCAAGTCCGTCAG  not in data  tumorEL              -1   \n",
       "...                            ...      ...             ...   \n",
       "KMA3_TTTGCGCGTCAGGACA         LB3_  tumorEL              23   \n",
       "KMA3_TTTGCGCGTCGACTAT         LB3_  tumorEL              23   \n",
       "KMA3_TTTGCGCGTGAGGGTT         LB3_  tumorEL              23   \n",
       "KMA3_TTTGTCAGTAGCGTCC  not in data  tumorEL              -1   \n",
       "KMA3_TTTGTCAGTTTAAGCC         LB3_  tumorEL              23   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA3_AAACGGGCAGACGCTC  AAACGGGCAGACGCTC-1  KMA3  \n",
       "KMA3_AAACGGGTCACCATAG  AAACGGGTCACCATAG-1  KMA3  \n",
       "KMA3_AAAGATGCATGCGCAC  AAAGATGCATGCGCAC-1  KMA3  \n",
       "KMA3_AAAGATGTCATTGCGA  AAAGATGTCATTGCGA-1  KMA3  \n",
       "KMA3_AAAGCAAGTCCGTCAG  AAAGCAAGTCCGTCAG-1  KMA3  \n",
       "...                                   ...   ...  \n",
       "KMA3_TTTGCGCGTCAGGACA  TTTGCGCGTCAGGACA-1  KMA3  \n",
       "KMA3_TTTGCGCGTCGACTAT  TTTGCGCGTCGACTAT-1  KMA3  \n",
       "KMA3_TTTGCGCGTGAGGGTT  TTTGCGCGTGAGGGTT-1  KMA3  \n",
       "KMA3_TTTGTCAGTAGCGTCC  TTTGTCAGTAGCGTCC-1  KMA3  \n",
       "KMA3_TTTGTCAGTTTAAGCC  TTTGTCAGTTTAAGCC-1  KMA3  \n",
       "\n",
       "[852 rows x 5 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sample_df = pool_df[pool_df['donor_id'] == 'tumorEL']\n",
    "myeloid_aml_cells_df = sample_df[sample_df['cluster_number'].isin(\n",
    "                            myeloid_clusters + aml_clusters + [-1])]\n",
    "myeloid_aml_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "17158ca1",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:36:38.116585Z",
     "start_time": "2023-07-14T16:36:38.098724Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>barcode</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA3_AAACGGGCAGACGCTC</th>\n",
       "      <td>AAACGGGCAGACGCTC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAACGGGTCACCATAG</th>\n",
       "      <td>AAACGGGTCACCATAG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGATGCATGCGCAC</th>\n",
       "      <td>AAAGATGCATGCGCAC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGATGTCATTGCGA</th>\n",
       "      <td>AAAGATGTCATTGCGA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGCAAGTCCGTCAG</th>\n",
       "      <td>AAAGCAAGTCCGTCAG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGCGCGTCAGGACA</th>\n",
       "      <td>TTTGCGCGTCAGGACA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGCGCGTCGACTAT</th>\n",
       "      <td>TTTGCGCGTCGACTAT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGCGCGTGAGGGTT</th>\n",
       "      <td>TTTGCGCGTGAGGGTT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGTCAGTAGCGTCC</th>\n",
       "      <td>TTTGTCAGTAGCGTCC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGTCAGTTTAAGCC</th>\n",
       "      <td>TTTGTCAGTTTAAGCC-1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>852 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                  barcode\n",
       "KMA3_AAACGGGCAGACGCTC  AAACGGGCAGACGCTC-1\n",
       "KMA3_AAACGGGTCACCATAG  AAACGGGTCACCATAG-1\n",
       "KMA3_AAAGATGCATGCGCAC  AAAGATGCATGCGCAC-1\n",
       "KMA3_AAAGATGTCATTGCGA  AAAGATGTCATTGCGA-1\n",
       "KMA3_AAAGCAAGTCCGTCAG  AAAGCAAGTCCGTCAG-1\n",
       "...                                   ...\n",
       "KMA3_TTTGCGCGTCAGGACA  TTTGCGCGTCAGGACA-1\n",
       "KMA3_TTTGCGCGTCGACTAT  TTTGCGCGTCGACTAT-1\n",
       "KMA3_TTTGCGCGTGAGGGTT  TTTGCGCGTGAGGGTT-1\n",
       "KMA3_TTTGTCAGTAGCGTCC  TTTGTCAGTAGCGTCC-1\n",
       "KMA3_TTTGTCAGTTTAAGCC  TTTGTCAGTTTAAGCC-1\n",
       "\n",
       "[852 rows x 1 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "myeloid_aml_cells_barcodes = myeloid_aml_cells_df[['barcode']]\n",
    "myeloid_aml_cells_barcodes.to_csv('data/EL3/myeloid_aml_cells_barcodes.tsv', \n",
    "                                  index=False, header=False)\n",
    "myeloid_aml_cells_barcodes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "029870f8",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:36:48.918760Z",
     "start_time": "2023-07-14T16:36:48.896645Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA3_AAACGGGGTCTCTCTG</th>\n",
       "      <td>KC1_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>0</td>\n",
       "      <td>AAACGGGGTCTCTCTG-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGATGAGCACACAG</th>\n",
       "      <td>AM1_</td>\n",
       "      <td>tumorEL</td>\n",
       "      <td>36</td>\n",
       "      <td>AAAGATGAGCACACAG-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGATGCACGTCTCT</th>\n",
       "      <td>KC1_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>0</td>\n",
       "      <td>AAAGATGCACGTCTCT-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGATGGTTCAGTAC</th>\n",
       "      <td>KC1_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>11</td>\n",
       "      <td>AAAGATGGTTCAGTAC-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGCAATCCTGTAGA</th>\n",
       "      <td>KC1_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>0</td>\n",
       "      <td>AAAGCAATCCTGTAGA-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGGTTGTAAGGATT</th>\n",
       "      <td>LB3_</td>\n",
       "      <td>donorEL</td>\n",
       "      <td>3</td>\n",
       "      <td>TTTGGTTGTAAGGATT-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGGTTGTCCAAGTT</th>\n",
       "      <td>LB3_</td>\n",
       "      <td>donorEL</td>\n",
       "      <td>2</td>\n",
       "      <td>TTTGGTTGTCCAAGTT-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGGTTTCCCTAATT</th>\n",
       "      <td>KC1_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>7</td>\n",
       "      <td>TTTGGTTTCCCTAATT-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGTCAAGGCTAGGT</th>\n",
       "      <td>KC1_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>0</td>\n",
       "      <td>TTTGTCAAGGCTAGGT-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGTCATCCTGCCAT</th>\n",
       "      <td>LB3_</td>\n",
       "      <td>donorEL</td>\n",
       "      <td>3</td>\n",
       "      <td>TTTGTCATCCTGCCAT-1</td>\n",
       "      <td>KMA3</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1055 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                      ref_sample    donor_id  cluster_number  \\\n",
       "KMA3_AAACGGGGTCTCTCTG       KC1_     doublet               0   \n",
       "KMA3_AAAGATGAGCACACAG       AM1_     tumorEL              36   \n",
       "KMA3_AAAGATGCACGTCTCT       KC1_     doublet               0   \n",
       "KMA3_AAAGATGGTTCAGTAC       KC1_     donorKC              11   \n",
       "KMA3_AAAGCAATCCTGTAGA       KC1_     doublet               0   \n",
       "...                          ...         ...             ...   \n",
       "KMA3_TTTGGTTGTAAGGATT       LB3_     donorEL               3   \n",
       "KMA3_TTTGGTTGTCCAAGTT       LB3_     donorEL               2   \n",
       "KMA3_TTTGGTTTCCCTAATT       KC1_  unassigned               7   \n",
       "KMA3_TTTGTCAAGGCTAGGT       KC1_     doublet               0   \n",
       "KMA3_TTTGTCATCCTGCCAT       LB3_     donorEL               3   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA3_AAACGGGGTCTCTCTG  AAACGGGGTCTCTCTG-1  KMA3  \n",
       "KMA3_AAAGATGAGCACACAG  AAAGATGAGCACACAG-1  KMA3  \n",
       "KMA3_AAAGATGCACGTCTCT  AAAGATGCACGTCTCT-1  KMA3  \n",
       "KMA3_AAAGATGGTTCAGTAC  AAAGATGGTTCAGTAC-1  KMA3  \n",
       "KMA3_AAAGCAATCCTGTAGA  AAAGCAATCCTGTAGA-1  KMA3  \n",
       "...                                   ...   ...  \n",
       "KMA3_TTTGGTTGTAAGGATT  TTTGGTTGTAAGGATT-1  KMA3  \n",
       "KMA3_TTTGGTTGTCCAAGTT  TTTGGTTGTCCAAGTT-1  KMA3  \n",
       "KMA3_TTTGGTTTCCCTAATT  TTTGGTTTCCCTAATT-1  KMA3  \n",
       "KMA3_TTTGTCAAGGCTAGGT  TTTGTCAAGGCTAGGT-1  KMA3  \n",
       "KMA3_TTTGTCATCCTGCCAT  TTTGTCATCCTGCCAT-1  KMA3  \n",
       "\n",
       "[1055 rows x 5 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = pool_df[pool_df['cluster_number'].\\\n",
    "                    isin(t_cell_clusters + b_cell_clusters + nk_cell_clusters)]\n",
    "normal_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "91f66b15",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:36:53.470459Z",
     "start_time": "2023-07-14T16:36:53.455905Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0     374\n",
       "1     239\n",
       "3      85\n",
       "2      81\n",
       "7      69\n",
       "11     55\n",
       "15     32\n",
       "25     30\n",
       "19     28\n",
       "36     24\n",
       "30     22\n",
       "24     11\n",
       "35      3\n",
       "40      2\n",
       "Name: cluster_number, dtype: int64"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df['cluster_number'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "4c3fcf55",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:37:03.829309Z",
     "start_time": "2023-07-14T16:37:03.805140Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>cell</th>\n",
       "      <th>group</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA3_AAACGGGGTCTCTCTG</th>\n",
       "      <td>AAACGGGGTCTCTCTG-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGATGAGCACACAG</th>\n",
       "      <td>AAAGATGAGCACACAG-1</td>\n",
       "      <td>36</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGATGCACGTCTCT</th>\n",
       "      <td>AAAGATGCACGTCTCT-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGATGGTTCAGTAC</th>\n",
       "      <td>AAAGATGGTTCAGTAC-1</td>\n",
       "      <td>11</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_AAAGCAATCCTGTAGA</th>\n",
       "      <td>AAAGCAATCCTGTAGA-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGGTTGTAAGGATT</th>\n",
       "      <td>TTTGGTTGTAAGGATT-1</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGGTTGTCCAAGTT</th>\n",
       "      <td>TTTGGTTGTCCAAGTT-1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGGTTTCCCTAATT</th>\n",
       "      <td>TTTGGTTTCCCTAATT-1</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGTCAAGGCTAGGT</th>\n",
       "      <td>TTTGTCAAGGCTAGGT-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA3_TTTGTCATCCTGCCAT</th>\n",
       "      <td>TTTGTCATCCTGCCAT-1</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1055 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                     cell  group\n",
       "KMA3_AAACGGGGTCTCTCTG  AAACGGGGTCTCTCTG-1      0\n",
       "KMA3_AAAGATGAGCACACAG  AAAGATGAGCACACAG-1     36\n",
       "KMA3_AAAGATGCACGTCTCT  AAAGATGCACGTCTCT-1      0\n",
       "KMA3_AAAGATGGTTCAGTAC  AAAGATGGTTCAGTAC-1     11\n",
       "KMA3_AAAGCAATCCTGTAGA  AAAGCAATCCTGTAGA-1      0\n",
       "...                                   ...    ...\n",
       "KMA3_TTTGGTTGTAAGGATT  TTTGGTTGTAAGGATT-1      3\n",
       "KMA3_TTTGGTTGTCCAAGTT  TTTGGTTGTCCAAGTT-1      2\n",
       "KMA3_TTTGGTTTCCCTAATT  TTTGGTTTCCCTAATT-1      7\n",
       "KMA3_TTTGTCAAGGCTAGGT  TTTGTCAAGGCTAGGT-1      0\n",
       "KMA3_TTTGTCATCCTGCCAT  TTTGTCATCCTGCCAT-1      3\n",
       "\n",
       "[1055 rows x 2 columns]"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = normal_cells_df[['barcode', 'cluster_number']]\n",
    "normal_cells_df.columns = ['cell', 'group']\n",
    "normal_cells_df.to_csv('data/EL3/normal_cells_annotations.csv', index=False)\n",
    "normal_cells_df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "4cbb8e53",
   "metadata": {
    "heading_collapsed": true
   },
   "source": [
    "### KMA2, AH1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "96110053",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:35:45.635506Z",
     "start_time": "2023-07-14T16:35:45.601362Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACCTGAGACCGGAT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>doublet</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGACCGGAT-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACCTGAGACTAGAT</th>\n",
       "      <td>GD2_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>28</td>\n",
       "      <td>AAACCTGAGACTAGAT-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACCTGAGAGCTATA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGAGCTATA-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACCTGAGAGCTGGT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>doublet</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGAGCTGGT-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACCTGAGGCTCTTA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>doublet</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGGCTCTTA-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGTCAGTTTGCATG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>doublet</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCAGTTTGCATG-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGTCATCAAACGGG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorEL</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCAAACGGG-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGTCATCACAAACC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCACAAACC-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGTCATCCGTACAA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCCGTACAA-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGTCATCTGCGGCA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCTGCGGCA-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>10702 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                        ref_sample    donor_id  cluster_number  \\\n",
       "KMA2_AAACCTGAGACCGGAT  not in data     doublet              -1   \n",
       "KMA2_AAACCTGAGACTAGAT         GD2_  unassigned              28   \n",
       "KMA2_AAACCTGAGAGCTATA  not in data  unassigned              -1   \n",
       "KMA2_AAACCTGAGAGCTGGT  not in data     doublet              -1   \n",
       "KMA2_AAACCTGAGGCTCTTA  not in data     doublet              -1   \n",
       "...                            ...         ...             ...   \n",
       "KMA2_TTTGTCAGTTTGCATG  not in data     doublet              -1   \n",
       "KMA2_TTTGTCATCAAACGGG  not in data     donorEL              -1   \n",
       "KMA2_TTTGTCATCACAAACC  not in data     donorLB              -1   \n",
       "KMA2_TTTGTCATCCGTACAA  not in data     donorLB              -1   \n",
       "KMA2_TTTGTCATCTGCGGCA  not in data  unassigned              -1   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA2_AAACCTGAGACCGGAT  AAACCTGAGACCGGAT-1  KMA2  \n",
       "KMA2_AAACCTGAGACTAGAT  AAACCTGAGACTAGAT-1  KMA2  \n",
       "KMA2_AAACCTGAGAGCTATA  AAACCTGAGAGCTATA-1  KMA2  \n",
       "KMA2_AAACCTGAGAGCTGGT  AAACCTGAGAGCTGGT-1  KMA2  \n",
       "KMA2_AAACCTGAGGCTCTTA  AAACCTGAGGCTCTTA-1  KMA2  \n",
       "...                                   ...   ...  \n",
       "KMA2_TTTGTCAGTTTGCATG  TTTGTCAGTTTGCATG-1  KMA2  \n",
       "KMA2_TTTGTCATCAAACGGG  TTTGTCATCAAACGGG-1  KMA2  \n",
       "KMA2_TTTGTCATCACAAACC  TTTGTCATCACAAACC-1  KMA2  \n",
       "KMA2_TTTGTCATCCGTACAA  TTTGTCATCCGTACAA-1  KMA2  \n",
       "KMA2_TTTGTCATCTGCGGCA  TTTGTCATCTGCGGCA-1  KMA2  \n",
       "\n",
       "[10702 rows x 5 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pool_df = cells_df[cells_df['pool'] == 'KMA2']\n",
    "pool_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "39d7e69f",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:35:49.151798Z",
     "start_time": "2023-07-14T16:35:49.139858Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "donorEL       3177\n",
       "doublet       2974\n",
       "unassigned    1958\n",
       "donorLB       1587\n",
       "tumorGD        709\n",
       "donorAH        175\n",
       "tumorAH        110\n",
       "donorGD         12\n",
       "Name: donor_id, dtype: int64"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pool_df['donor_id'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "7e7d8fa8",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:36:06.071358Z",
     "start_time": "2023-07-14T16:36:06.048588Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
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       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA2_AACGTTGGTACAGTGG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>AACGTTGGTACAGTGG-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AACTCTTCACAAGACG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>AACTCTTCACAAGACG-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAGCCGCGTCAGAATA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAGCCGCGTCAGAATA-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAGGAGCTCGGTGTCG</th>\n",
       "      <td>AH1_</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>14</td>\n",
       "      <td>AAGGAGCTCGGTGTCG-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_ACACTGAAGTTAACGA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>ACACTGAAGTTAACGA-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TGTGGTAAGCGGATCA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>TGTGGTAAGCGGATCA-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTGAACGTCTACTTAC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTGAACGTCTACTTAC-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTATGCGTCGAGTTT</th>\n",
       "      <td>AH1_</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>14</td>\n",
       "      <td>TTTATGCGTCGAGTTT-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTATGCGTTCCACGG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTATGCGTTCCACGG-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGGTTTCCTCGCAT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGGTTTCCTCGCAT-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>86 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                        ref_sample donor_id  cluster_number  \\\n",
       "KMA2_AACGTTGGTACAGTGG  not in data  tumorAH              -1   \n",
       "KMA2_AACTCTTCACAAGACG  not in data  tumorAH              -1   \n",
       "KMA2_AAGCCGCGTCAGAATA  not in data  tumorAH              -1   \n",
       "KMA2_AAGGAGCTCGGTGTCG         AH1_  tumorAH              14   \n",
       "KMA2_ACACTGAAGTTAACGA  not in data  tumorAH              -1   \n",
       "...                            ...      ...             ...   \n",
       "KMA2_TGTGGTAAGCGGATCA  not in data  tumorAH              -1   \n",
       "KMA2_TTGAACGTCTACTTAC  not in data  tumorAH              -1   \n",
       "KMA2_TTTATGCGTCGAGTTT         AH1_  tumorAH              14   \n",
       "KMA2_TTTATGCGTTCCACGG  not in data  tumorAH              -1   \n",
       "KMA2_TTTGGTTTCCTCGCAT  not in data  tumorAH              -1   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA2_AACGTTGGTACAGTGG  AACGTTGGTACAGTGG-1  KMA2  \n",
       "KMA2_AACTCTTCACAAGACG  AACTCTTCACAAGACG-1  KMA2  \n",
       "KMA2_AAGCCGCGTCAGAATA  AAGCCGCGTCAGAATA-1  KMA2  \n",
       "KMA2_AAGGAGCTCGGTGTCG  AAGGAGCTCGGTGTCG-1  KMA2  \n",
       "KMA2_ACACTGAAGTTAACGA  ACACTGAAGTTAACGA-1  KMA2  \n",
       "...                                   ...   ...  \n",
       "KMA2_TGTGGTAAGCGGATCA  TGTGGTAAGCGGATCA-1  KMA2  \n",
       "KMA2_TTGAACGTCTACTTAC  TTGAACGTCTACTTAC-1  KMA2  \n",
       "KMA2_TTTATGCGTCGAGTTT  TTTATGCGTCGAGTTT-1  KMA2  \n",
       "KMA2_TTTATGCGTTCCACGG  TTTATGCGTTCCACGG-1  KMA2  \n",
       "KMA2_TTTGGTTTCCTCGCAT  TTTGGTTTCCTCGCAT-1  KMA2  \n",
       "\n",
       "[86 rows x 5 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sample_df = pool_df[pool_df['donor_id'] == 'tumorAH']\n",
    "myeloid_aml_cells_df = sample_df[sample_df['cluster_number'].isin(\n",
    "                            myeloid_clusters + aml_clusters + [-1])]\n",
    "myeloid_aml_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "9917533c",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:36:38.116585Z",
     "start_time": "2023-07-14T16:36:38.098724Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>barcode</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA2_AACGTTGGTACAGTGG</th>\n",
       "      <td>AACGTTGGTACAGTGG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AACTCTTCACAAGACG</th>\n",
       "      <td>AACTCTTCACAAGACG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAGCCGCGTCAGAATA</th>\n",
       "      <td>AAGCCGCGTCAGAATA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAGGAGCTCGGTGTCG</th>\n",
       "      <td>AAGGAGCTCGGTGTCG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_ACACTGAAGTTAACGA</th>\n",
       "      <td>ACACTGAAGTTAACGA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TGTGGTAAGCGGATCA</th>\n",
       "      <td>TGTGGTAAGCGGATCA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTGAACGTCTACTTAC</th>\n",
       "      <td>TTGAACGTCTACTTAC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTATGCGTCGAGTTT</th>\n",
       "      <td>TTTATGCGTCGAGTTT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTATGCGTTCCACGG</th>\n",
       "      <td>TTTATGCGTTCCACGG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGGTTTCCTCGCAT</th>\n",
       "      <td>TTTGGTTTCCTCGCAT-1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>86 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                  barcode\n",
       "KMA2_AACGTTGGTACAGTGG  AACGTTGGTACAGTGG-1\n",
       "KMA2_AACTCTTCACAAGACG  AACTCTTCACAAGACG-1\n",
       "KMA2_AAGCCGCGTCAGAATA  AAGCCGCGTCAGAATA-1\n",
       "KMA2_AAGGAGCTCGGTGTCG  AAGGAGCTCGGTGTCG-1\n",
       "KMA2_ACACTGAAGTTAACGA  ACACTGAAGTTAACGA-1\n",
       "...                                   ...\n",
       "KMA2_TGTGGTAAGCGGATCA  TGTGGTAAGCGGATCA-1\n",
       "KMA2_TTGAACGTCTACTTAC  TTGAACGTCTACTTAC-1\n",
       "KMA2_TTTATGCGTCGAGTTT  TTTATGCGTCGAGTTT-1\n",
       "KMA2_TTTATGCGTTCCACGG  TTTATGCGTTCCACGG-1\n",
       "KMA2_TTTGGTTTCCTCGCAT  TTTGGTTTCCTCGCAT-1\n",
       "\n",
       "[86 rows x 1 columns]"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "myeloid_aml_cells_barcodes = myeloid_aml_cells_df[['barcode']]\n",
    "myeloid_aml_cells_barcodes.to_csv('data/AH1/myeloid_aml_cells_barcodes.tsv', \n",
    "                                  index=False, header=False)\n",
    "myeloid_aml_cells_barcodes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "081f14fe",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:36:48.918760Z",
     "start_time": "2023-07-14T16:36:48.896645Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACCTGCAAAGGCGT</th>\n",
       "      <td>EL2_</td>\n",
       "      <td>donorEL</td>\n",
       "      <td>1</td>\n",
       "      <td>AAACCTGCAAAGGCGT-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACCTGCATAGACTC</th>\n",
       "      <td>LB2_</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>0</td>\n",
       "      <td>AAACCTGCATAGACTC-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACCTGCATTCCTGC</th>\n",
       "      <td>EL2_</td>\n",
       "      <td>donorEL</td>\n",
       "      <td>7</td>\n",
       "      <td>AAACCTGCATTCCTGC-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACCTGGTTAAAGAC</th>\n",
       "      <td>EL2_</td>\n",
       "      <td>donorEL</td>\n",
       "      <td>3</td>\n",
       "      <td>AAACCTGGTTAAAGAC-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACGGGGTTGGACCC</th>\n",
       "      <td>EL2_</td>\n",
       "      <td>donorEL</td>\n",
       "      <td>7</td>\n",
       "      <td>AAACGGGGTTGGACCC-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGCGCGTACCCAAT</th>\n",
       "      <td>EL2_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>35</td>\n",
       "      <td>TTTGCGCGTACCCAAT-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGCGCTCCAAACAC</th>\n",
       "      <td>EL2_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>1</td>\n",
       "      <td>TTTGCGCTCCAAACAC-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGGTTGTCTGCCAG</th>\n",
       "      <td>EL2_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>35</td>\n",
       "      <td>TTTGGTTGTCTGCCAG-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGTCACACATAACC</th>\n",
       "      <td>EL2_</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>36</td>\n",
       "      <td>TTTGTCACACATAACC-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGTCACATGGAATA</th>\n",
       "      <td>LB2_</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>0</td>\n",
       "      <td>TTTGTCACATGGAATA-1</td>\n",
       "      <td>KMA2</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1330 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                      ref_sample    donor_id  cluster_number  \\\n",
       "KMA2_AAACCTGCAAAGGCGT       EL2_     donorEL               1   \n",
       "KMA2_AAACCTGCATAGACTC       LB2_     donorLB               0   \n",
       "KMA2_AAACCTGCATTCCTGC       EL2_     donorEL               7   \n",
       "KMA2_AAACCTGGTTAAAGAC       EL2_     donorEL               3   \n",
       "KMA2_AAACGGGGTTGGACCC       EL2_     donorEL               7   \n",
       "...                          ...         ...             ...   \n",
       "KMA2_TTTGCGCGTACCCAAT       EL2_  unassigned              35   \n",
       "KMA2_TTTGCGCTCCAAACAC       EL2_  unassigned               1   \n",
       "KMA2_TTTGGTTGTCTGCCAG       EL2_  unassigned              35   \n",
       "KMA2_TTTGTCACACATAACC       EL2_     tumorAH              36   \n",
       "KMA2_TTTGTCACATGGAATA       LB2_     donorLB               0   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA2_AAACCTGCAAAGGCGT  AAACCTGCAAAGGCGT-1  KMA2  \n",
       "KMA2_AAACCTGCATAGACTC  AAACCTGCATAGACTC-1  KMA2  \n",
       "KMA2_AAACCTGCATTCCTGC  AAACCTGCATTCCTGC-1  KMA2  \n",
       "KMA2_AAACCTGGTTAAAGAC  AAACCTGGTTAAAGAC-1  KMA2  \n",
       "KMA2_AAACGGGGTTGGACCC  AAACGGGGTTGGACCC-1  KMA2  \n",
       "...                                   ...   ...  \n",
       "KMA2_TTTGCGCGTACCCAAT  TTTGCGCGTACCCAAT-1  KMA2  \n",
       "KMA2_TTTGCGCTCCAAACAC  TTTGCGCTCCAAACAC-1  KMA2  \n",
       "KMA2_TTTGGTTGTCTGCCAG  TTTGGTTGTCTGCCAG-1  KMA2  \n",
       "KMA2_TTTGTCACACATAACC  TTTGTCACACATAACC-1  KMA2  \n",
       "KMA2_TTTGTCACATGGAATA  TTTGTCACATGGAATA-1  KMA2  \n",
       "\n",
       "[1330 rows x 5 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = pool_df[pool_df['cluster_number'].\\\n",
    "                    isin(t_cell_clusters + b_cell_clusters + nk_cell_clusters)]\n",
    "normal_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "c185c16e",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:36:53.470459Z",
     "start_time": "2023-07-14T16:36:53.455905Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2     379\n",
       "1     213\n",
       "3     174\n",
       "0     160\n",
       "35     96\n",
       "7      84\n",
       "45     78\n",
       "36     50\n",
       "40     25\n",
       "19     24\n",
       "15     21\n",
       "25      8\n",
       "30      6\n",
       "11      6\n",
       "24      6\n",
       "Name: cluster_number, dtype: int64"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df['cluster_number'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "5a5cf432",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-14T16:37:03.829309Z",
     "start_time": "2023-07-14T16:37:03.805140Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>cell</th>\n",
       "      <th>group</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACCTGCAAAGGCGT</th>\n",
       "      <td>AAACCTGCAAAGGCGT-1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACCTGCATAGACTC</th>\n",
       "      <td>AAACCTGCATAGACTC-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACCTGCATTCCTGC</th>\n",
       "      <td>AAACCTGCATTCCTGC-1</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACCTGGTTAAAGAC</th>\n",
       "      <td>AAACCTGGTTAAAGAC-1</td>\n",
       "      <td>3</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_AAACGGGGTTGGACCC</th>\n",
       "      <td>AAACGGGGTTGGACCC-1</td>\n",
       "      <td>7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGCGCGTACCCAAT</th>\n",
       "      <td>TTTGCGCGTACCCAAT-1</td>\n",
       "      <td>35</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGCGCTCCAAACAC</th>\n",
       "      <td>TTTGCGCTCCAAACAC-1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGGTTGTCTGCCAG</th>\n",
       "      <td>TTTGGTTGTCTGCCAG-1</td>\n",
       "      <td>35</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGTCACACATAACC</th>\n",
       "      <td>TTTGTCACACATAACC-1</td>\n",
       "      <td>36</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA2_TTTGTCACATGGAATA</th>\n",
       "      <td>TTTGTCACATGGAATA-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1330 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                     cell  group\n",
       "KMA2_AAACCTGCAAAGGCGT  AAACCTGCAAAGGCGT-1      1\n",
       "KMA2_AAACCTGCATAGACTC  AAACCTGCATAGACTC-1      0\n",
       "KMA2_AAACCTGCATTCCTGC  AAACCTGCATTCCTGC-1      7\n",
       "KMA2_AAACCTGGTTAAAGAC  AAACCTGGTTAAAGAC-1      3\n",
       "KMA2_AAACGGGGTTGGACCC  AAACGGGGTTGGACCC-1      7\n",
       "...                                   ...    ...\n",
       "KMA2_TTTGCGCGTACCCAAT  TTTGCGCGTACCCAAT-1     35\n",
       "KMA2_TTTGCGCTCCAAACAC  TTTGCGCTCCAAACAC-1      1\n",
       "KMA2_TTTGGTTGTCTGCCAG  TTTGGTTGTCTGCCAG-1     35\n",
       "KMA2_TTTGTCACACATAACC  TTTGTCACACATAACC-1     36\n",
       "KMA2_TTTGTCACATGGAATA  TTTGTCACATGGAATA-1      0\n",
       "\n",
       "[1330 rows x 2 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = normal_cells_df[['barcode', 'cluster_number']]\n",
    "normal_cells_df.columns = ['cell', 'group']\n",
    "normal_cells_df.to_csv('data/AH1/normal_cells_annotations.csv', index=False)\n",
    "normal_cells_df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "ef50742d",
   "metadata": {
    "heading_collapsed": true
   },
   "source": [
    "### KMA1, JS1"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "2707acab",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:26:42.817143Z",
     "start_time": "2023-07-16T02:26:42.784813Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "\n",
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGAGAGCTATA</th>\n",
       "      <td>GD1_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>21</td>\n",
       "      <td>AAACCTGAGAGCTATA-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGAGAGGTTAT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorGD</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGAGGTTAT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGAGGAGCGTT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorEL</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGGAGCGTT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGAGGATTCGG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGGATTCGG-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGAGTCCTCCT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGTCCTCCT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCATCGCATGGC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>doublet</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCGCATGGC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCATCGGCCGAT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCGGCCGAT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCATCTAAGCCA</th>\n",
       "      <td>GD1_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>1</td>\n",
       "      <td>TTTGTCATCTAAGCCA-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCATCTGCTGTC</th>\n",
       "      <td>GD1_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>21</td>\n",
       "      <td>TTTGTCATCTGCTGTC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCATCTGTCTAT</th>\n",
       "      <td>GD1_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>21</td>\n",
       "      <td>TTTGTCATCTGTCTAT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>17334 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                        ref_sample donor_id  cluster_number  \\\n",
       "KMA1_AAACCTGAGAGCTATA         GD1_  doublet              21   \n",
       "KMA1_AAACCTGAGAGGTTAT  not in data  tumorGD              -1   \n",
       "KMA1_AAACCTGAGGAGCGTT  not in data  donorEL              -1   \n",
       "KMA1_AAACCTGAGGATTCGG  not in data  donorLB              -1   \n",
       "KMA1_AAACCTGAGTCCTCCT  not in data  donorLB              -1   \n",
       "...                            ...      ...             ...   \n",
       "KMA1_TTTGTCATCGCATGGC  not in data  doublet              -1   \n",
       "KMA1_TTTGTCATCGGCCGAT  not in data  donorJS              -1   \n",
       "KMA1_TTTGTCATCTAAGCCA         GD1_  doublet               1   \n",
       "KMA1_TTTGTCATCTGCTGTC         GD1_  doublet              21   \n",
       "KMA1_TTTGTCATCTGTCTAT         GD1_  doublet              21   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA1_AAACCTGAGAGCTATA  AAACCTGAGAGCTATA-1  KMA1  \n",
       "KMA1_AAACCTGAGAGGTTAT  AAACCTGAGAGGTTAT-1  KMA1  \n",
       "KMA1_AAACCTGAGGAGCGTT  AAACCTGAGGAGCGTT-1  KMA1  \n",
       "KMA1_AAACCTGAGGATTCGG  AAACCTGAGGATTCGG-1  KMA1  \n",
       "KMA1_AAACCTGAGTCCTCCT  AAACCTGAGTCCTCCT-1  KMA1  \n",
       "...                                   ...   ...  \n",
       "KMA1_TTTGTCATCGCATGGC  TTTGTCATCGCATGGC-1  KMA1  \n",
       "KMA1_TTTGTCATCGGCCGAT  TTTGTCATCGGCCGAT-1  KMA1  \n",
       "KMA1_TTTGTCATCTAAGCCA  TTTGTCATCTAAGCCA-1  KMA1  \n",
       "KMA1_TTTGTCATCTGCTGTC  TTTGTCATCTGCTGTC-1  KMA1  \n",
       "KMA1_TTTGTCATCTGTCTAT  TTTGTCATCTGTCTAT-1  KMA1  \n",
       "\n",
       "[17334 rows x 5 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pool_df = cells_df[cells_df['pool'] == 'KMA1']\n",
    "pool_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "bb8228ce",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:26:49.622689Z",
     "start_time": "2023-07-16T02:26:49.610538Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "donorLB       6225\n",
       "doublet       4761\n",
       "unassigned    2980\n",
       "tumorGD       1861\n",
       "donorJS        884\n",
       "donorEL        316\n",
       "donorGD        259\n",
       "tumorJS         48\n",
       "Name: donor_id, dtype: int64"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pool_df['donor_id'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "2f593c7b",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:27:44.201003Z",
     "start_time": "2023-07-16T02:27:44.180203Z"
    },
    "hidden": true,
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACGGGTCTAACGGT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACGGGTCTAACGGT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AATCCAGGTCGCGTGT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>AATCCAGGTCGCGTGT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AATCGGTCATTAGCCA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>AATCGGTCATTAGCCA-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_ACAGCCGTCATCATTC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>ACAGCCGTCATCATTC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_ACGGGTCAGGGTCGAT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>ACGGGTCAGGGTCGAT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_ACGGGTCCAAGTCATC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>ACGGGTCCAAGTCATC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AGAGTGGTCTCAAACG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>AGAGTGGTCTCAAACG-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AGGCCGTTCCCTGACT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>AGGCCGTTCCCTGACT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AGTGTCAGTGCAGTAG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>AGTGTCAGTGCAGTAG-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_ATAAGAGGTCCGAATT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>ATAAGAGGTCCGAATT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_ATTATCCTCCCAAGAT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>ATTATCCTCCCAAGAT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_ATTGGACTCAATACCG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>ATTGGACTCAATACCG-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CACATTTAGGCGCTCT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>CACATTTAGGCGCTCT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CAGCATAAGAAACCTA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>CAGCATAAGAAACCTA-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CAGCTGGAGCCACCTG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>CAGCTGGAGCCACCTG-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CATCGAAAGATACACA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>CATCGAAAGATACACA-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CGAGCACAGCCTCGTG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>CGAGCACAGCCTCGTG-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CGCGGTAAGCGATTCT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>CGCGGTAAGCGATTCT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CGGACGTGTTTGTTTC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>CGGACGTGTTTGTTTC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CTTAGGACAATCCAAC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>CTTAGGACAATCCAAC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GACACGCGTCCCGACA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>GACACGCGTCCCGACA-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GACTACAAGTGAAGAG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>GACTACAAGTGAAGAG-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GAGGTGAAGTACGTAA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>GAGGTGAAGTACGTAA-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GATCGATGTATGCTTG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>GATCGATGTATGCTTG-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GATCGCGTCTTGCCGT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>GATCGCGTCTTGCCGT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GCATACAAGCCACGCT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>GCATACAAGCCACGCT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GCTGCAGTCAGTCCCT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>GCTGCAGTCAGTCCCT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GTCATTTCATAGAAAC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>GTCATTTCATAGAAAC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GTGCGGTCAGTCTTCC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>GTGCGGTCAGTCTTCC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GTGGGTCGTGTGGCTC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>GTGGGTCGTGTGGCTC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TACCTTACACGTCAGC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TACCTTACACGTCAGC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TACTCATTCTGGCGAC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TACTCATTCTGGCGAC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TACTCGCGTACCGTAT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TACTCGCGTACCGTAT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TAGTTGGAGAGGGCTT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TAGTTGGAGAGGGCTT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TAGTTGGAGTGACATA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TAGTTGGAGTGACATA-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TAGTTGGAGTGTGGCA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TAGTTGGAGTGTGGCA-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TCGGGACCACGCCAGT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TCGGGACCACGCCAGT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TCTTTCCAGTATCTCG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TCTTTCCAGTATCTCG-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TGTTCCGCATGACGGA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TGTTCCGCATGACGGA-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTAGTTCTCGCAAACT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTAGTTCTCGCAAACT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTGACTTAGTACGCCC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTGACTTAGTACGCCC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTGCGTCAGTGAACGC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTGCGTCAGTGAACGC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGGTTAGTTCGCAT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorJS</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGGTTAGTTCGCAT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                        ref_sample donor_id  cluster_number  \\\n",
       "KMA1_AAACGGGTCTAACGGT  not in data  tumorJS              -1   \n",
       "KMA1_AATCCAGGTCGCGTGT  not in data  tumorJS              -1   \n",
       "KMA1_AATCGGTCATTAGCCA  not in data  tumorJS              -1   \n",
       "KMA1_ACAGCCGTCATCATTC  not in data  tumorJS              -1   \n",
       "KMA1_ACGGGTCAGGGTCGAT  not in data  tumorJS              -1   \n",
       "KMA1_ACGGGTCCAAGTCATC  not in data  tumorJS              -1   \n",
       "KMA1_AGAGTGGTCTCAAACG  not in data  tumorJS              -1   \n",
       "KMA1_AGGCCGTTCCCTGACT  not in data  tumorJS              -1   \n",
       "KMA1_AGTGTCAGTGCAGTAG  not in data  tumorJS              -1   \n",
       "KMA1_ATAAGAGGTCCGAATT  not in data  tumorJS              -1   \n",
       "KMA1_ATTATCCTCCCAAGAT  not in data  tumorJS              -1   \n",
       "KMA1_ATTGGACTCAATACCG  not in data  tumorJS              -1   \n",
       "KMA1_CACATTTAGGCGCTCT  not in data  tumorJS              -1   \n",
       "KMA1_CAGCATAAGAAACCTA  not in data  tumorJS              -1   \n",
       "KMA1_CAGCTGGAGCCACCTG  not in data  tumorJS              -1   \n",
       "KMA1_CATCGAAAGATACACA  not in data  tumorJS              -1   \n",
       "KMA1_CGAGCACAGCCTCGTG  not in data  tumorJS              -1   \n",
       "KMA1_CGCGGTAAGCGATTCT  not in data  tumorJS              -1   \n",
       "KMA1_CGGACGTGTTTGTTTC  not in data  tumorJS              -1   \n",
       "KMA1_CTTAGGACAATCCAAC  not in data  tumorJS              -1   \n",
       "KMA1_GACACGCGTCCCGACA  not in data  tumorJS              -1   \n",
       "KMA1_GACTACAAGTGAAGAG  not in data  tumorJS              -1   \n",
       "KMA1_GAGGTGAAGTACGTAA  not in data  tumorJS              -1   \n",
       "KMA1_GATCGATGTATGCTTG  not in data  tumorJS              -1   \n",
       "KMA1_GATCGCGTCTTGCCGT  not in data  tumorJS              -1   \n",
       "KMA1_GCATACAAGCCACGCT  not in data  tumorJS              -1   \n",
       "KMA1_GCTGCAGTCAGTCCCT  not in data  tumorJS              -1   \n",
       "KMA1_GTCATTTCATAGAAAC  not in data  tumorJS              -1   \n",
       "KMA1_GTGCGGTCAGTCTTCC  not in data  tumorJS              -1   \n",
       "KMA1_GTGGGTCGTGTGGCTC  not in data  tumorJS              -1   \n",
       "KMA1_TACCTTACACGTCAGC  not in data  tumorJS              -1   \n",
       "KMA1_TACTCATTCTGGCGAC  not in data  tumorJS              -1   \n",
       "KMA1_TACTCGCGTACCGTAT  not in data  tumorJS              -1   \n",
       "KMA1_TAGTTGGAGAGGGCTT  not in data  tumorJS              -1   \n",
       "KMA1_TAGTTGGAGTGACATA  not in data  tumorJS              -1   \n",
       "KMA1_TAGTTGGAGTGTGGCA  not in data  tumorJS              -1   \n",
       "KMA1_TCGGGACCACGCCAGT  not in data  tumorJS              -1   \n",
       "KMA1_TCTTTCCAGTATCTCG  not in data  tumorJS              -1   \n",
       "KMA1_TGTTCCGCATGACGGA  not in data  tumorJS              -1   \n",
       "KMA1_TTAGTTCTCGCAAACT  not in data  tumorJS              -1   \n",
       "KMA1_TTGACTTAGTACGCCC  not in data  tumorJS              -1   \n",
       "KMA1_TTGCGTCAGTGAACGC  not in data  tumorJS              -1   \n",
       "KMA1_TTTGGTTAGTTCGCAT  not in data  tumorJS              -1   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA1_AAACGGGTCTAACGGT  AAACGGGTCTAACGGT-1  KMA1  \n",
       "KMA1_AATCCAGGTCGCGTGT  AATCCAGGTCGCGTGT-1  KMA1  \n",
       "KMA1_AATCGGTCATTAGCCA  AATCGGTCATTAGCCA-1  KMA1  \n",
       "KMA1_ACAGCCGTCATCATTC  ACAGCCGTCATCATTC-1  KMA1  \n",
       "KMA1_ACGGGTCAGGGTCGAT  ACGGGTCAGGGTCGAT-1  KMA1  \n",
       "KMA1_ACGGGTCCAAGTCATC  ACGGGTCCAAGTCATC-1  KMA1  \n",
       "KMA1_AGAGTGGTCTCAAACG  AGAGTGGTCTCAAACG-1  KMA1  \n",
       "KMA1_AGGCCGTTCCCTGACT  AGGCCGTTCCCTGACT-1  KMA1  \n",
       "KMA1_AGTGTCAGTGCAGTAG  AGTGTCAGTGCAGTAG-1  KMA1  \n",
       "KMA1_ATAAGAGGTCCGAATT  ATAAGAGGTCCGAATT-1  KMA1  \n",
       "KMA1_ATTATCCTCCCAAGAT  ATTATCCTCCCAAGAT-1  KMA1  \n",
       "KMA1_ATTGGACTCAATACCG  ATTGGACTCAATACCG-1  KMA1  \n",
       "KMA1_CACATTTAGGCGCTCT  CACATTTAGGCGCTCT-1  KMA1  \n",
       "KMA1_CAGCATAAGAAACCTA  CAGCATAAGAAACCTA-1  KMA1  \n",
       "KMA1_CAGCTGGAGCCACCTG  CAGCTGGAGCCACCTG-1  KMA1  \n",
       "KMA1_CATCGAAAGATACACA  CATCGAAAGATACACA-1  KMA1  \n",
       "KMA1_CGAGCACAGCCTCGTG  CGAGCACAGCCTCGTG-1  KMA1  \n",
       "KMA1_CGCGGTAAGCGATTCT  CGCGGTAAGCGATTCT-1  KMA1  \n",
       "KMA1_CGGACGTGTTTGTTTC  CGGACGTGTTTGTTTC-1  KMA1  \n",
       "KMA1_CTTAGGACAATCCAAC  CTTAGGACAATCCAAC-1  KMA1  \n",
       "KMA1_GACACGCGTCCCGACA  GACACGCGTCCCGACA-1  KMA1  \n",
       "KMA1_GACTACAAGTGAAGAG  GACTACAAGTGAAGAG-1  KMA1  \n",
       "KMA1_GAGGTGAAGTACGTAA  GAGGTGAAGTACGTAA-1  KMA1  \n",
       "KMA1_GATCGATGTATGCTTG  GATCGATGTATGCTTG-1  KMA1  \n",
       "KMA1_GATCGCGTCTTGCCGT  GATCGCGTCTTGCCGT-1  KMA1  \n",
       "KMA1_GCATACAAGCCACGCT  GCATACAAGCCACGCT-1  KMA1  \n",
       "KMA1_GCTGCAGTCAGTCCCT  GCTGCAGTCAGTCCCT-1  KMA1  \n",
       "KMA1_GTCATTTCATAGAAAC  GTCATTTCATAGAAAC-1  KMA1  \n",
       "KMA1_GTGCGGTCAGTCTTCC  GTGCGGTCAGTCTTCC-1  KMA1  \n",
       "KMA1_GTGGGTCGTGTGGCTC  GTGGGTCGTGTGGCTC-1  KMA1  \n",
       "KMA1_TACCTTACACGTCAGC  TACCTTACACGTCAGC-1  KMA1  \n",
       "KMA1_TACTCATTCTGGCGAC  TACTCATTCTGGCGAC-1  KMA1  \n",
       "KMA1_TACTCGCGTACCGTAT  TACTCGCGTACCGTAT-1  KMA1  \n",
       "KMA1_TAGTTGGAGAGGGCTT  TAGTTGGAGAGGGCTT-1  KMA1  \n",
       "KMA1_TAGTTGGAGTGACATA  TAGTTGGAGTGACATA-1  KMA1  \n",
       "KMA1_TAGTTGGAGTGTGGCA  TAGTTGGAGTGTGGCA-1  KMA1  \n",
       "KMA1_TCGGGACCACGCCAGT  TCGGGACCACGCCAGT-1  KMA1  \n",
       "KMA1_TCTTTCCAGTATCTCG  TCTTTCCAGTATCTCG-1  KMA1  \n",
       "KMA1_TGTTCCGCATGACGGA  TGTTCCGCATGACGGA-1  KMA1  \n",
       "KMA1_TTAGTTCTCGCAAACT  TTAGTTCTCGCAAACT-1  KMA1  \n",
       "KMA1_TTGACTTAGTACGCCC  TTGACTTAGTACGCCC-1  KMA1  \n",
       "KMA1_TTGCGTCAGTGAACGC  TTGCGTCAGTGAACGC-1  KMA1  \n",
       "KMA1_TTTGGTTAGTTCGCAT  TTTGGTTAGTTCGCAT-1  KMA1  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sample_df = pool_df[pool_df['donor_id'] == 'tumorJS']\n",
    "myeloid_aml_cells_df = sample_df[sample_df['cluster_number'].isin(\n",
    "                            myeloid_clusters + aml_clusters + [-1])]\n",
    "myeloid_aml_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "17e99638",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:25:10.750182Z",
     "start_time": "2023-07-16T02:25:10.741338Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(43, 5)"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "myeloid_aml_cells_df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "f4b373e1",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:29:14.226520Z",
     "start_time": "2023-07-16T02:29:14.211038Z"
    },
    "hidden": true,
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>barcode</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACGGGTCTAACGGT</th>\n",
       "      <td>AAACGGGTCTAACGGT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AATCCAGGTCGCGTGT</th>\n",
       "      <td>AATCCAGGTCGCGTGT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AATCGGTCATTAGCCA</th>\n",
       "      <td>AATCGGTCATTAGCCA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_ACAGCCGTCATCATTC</th>\n",
       "      <td>ACAGCCGTCATCATTC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_ACGGGTCAGGGTCGAT</th>\n",
       "      <td>ACGGGTCAGGGTCGAT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_ACGGGTCCAAGTCATC</th>\n",
       "      <td>ACGGGTCCAAGTCATC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AGAGTGGTCTCAAACG</th>\n",
       "      <td>AGAGTGGTCTCAAACG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AGGCCGTTCCCTGACT</th>\n",
       "      <td>AGGCCGTTCCCTGACT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AGTGTCAGTGCAGTAG</th>\n",
       "      <td>AGTGTCAGTGCAGTAG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_ATAAGAGGTCCGAATT</th>\n",
       "      <td>ATAAGAGGTCCGAATT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_ATTATCCTCCCAAGAT</th>\n",
       "      <td>ATTATCCTCCCAAGAT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_ATTGGACTCAATACCG</th>\n",
       "      <td>ATTGGACTCAATACCG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CACATTTAGGCGCTCT</th>\n",
       "      <td>CACATTTAGGCGCTCT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CAGCATAAGAAACCTA</th>\n",
       "      <td>CAGCATAAGAAACCTA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CAGCTGGAGCCACCTG</th>\n",
       "      <td>CAGCTGGAGCCACCTG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CATCGAAAGATACACA</th>\n",
       "      <td>CATCGAAAGATACACA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CGAGCACAGCCTCGTG</th>\n",
       "      <td>CGAGCACAGCCTCGTG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CGCGGTAAGCGATTCT</th>\n",
       "      <td>CGCGGTAAGCGATTCT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CGGACGTGTTTGTTTC</th>\n",
       "      <td>CGGACGTGTTTGTTTC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_CTTAGGACAATCCAAC</th>\n",
       "      <td>CTTAGGACAATCCAAC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GACACGCGTCCCGACA</th>\n",
       "      <td>GACACGCGTCCCGACA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GACTACAAGTGAAGAG</th>\n",
       "      <td>GACTACAAGTGAAGAG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GAGGTGAAGTACGTAA</th>\n",
       "      <td>GAGGTGAAGTACGTAA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GATCGATGTATGCTTG</th>\n",
       "      <td>GATCGATGTATGCTTG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GATCGCGTCTTGCCGT</th>\n",
       "      <td>GATCGCGTCTTGCCGT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GCATACAAGCCACGCT</th>\n",
       "      <td>GCATACAAGCCACGCT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GCTGCAGTCAGTCCCT</th>\n",
       "      <td>GCTGCAGTCAGTCCCT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GTCATTTCATAGAAAC</th>\n",
       "      <td>GTCATTTCATAGAAAC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GTGCGGTCAGTCTTCC</th>\n",
       "      <td>GTGCGGTCAGTCTTCC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_GTGGGTCGTGTGGCTC</th>\n",
       "      <td>GTGGGTCGTGTGGCTC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TACCTTACACGTCAGC</th>\n",
       "      <td>TACCTTACACGTCAGC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TACTCATTCTGGCGAC</th>\n",
       "      <td>TACTCATTCTGGCGAC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TACTCGCGTACCGTAT</th>\n",
       "      <td>TACTCGCGTACCGTAT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TAGTTGGAGAGGGCTT</th>\n",
       "      <td>TAGTTGGAGAGGGCTT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TAGTTGGAGTGACATA</th>\n",
       "      <td>TAGTTGGAGTGACATA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TAGTTGGAGTGTGGCA</th>\n",
       "      <td>TAGTTGGAGTGTGGCA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TCGGGACCACGCCAGT</th>\n",
       "      <td>TCGGGACCACGCCAGT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TCTTTCCAGTATCTCG</th>\n",
       "      <td>TCTTTCCAGTATCTCG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TGTTCCGCATGACGGA</th>\n",
       "      <td>TGTTCCGCATGACGGA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTAGTTCTCGCAAACT</th>\n",
       "      <td>TTAGTTCTCGCAAACT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTGACTTAGTACGCCC</th>\n",
       "      <td>TTGACTTAGTACGCCC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTGCGTCAGTGAACGC</th>\n",
       "      <td>TTGCGTCAGTGAACGC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGGTTAGTTCGCAT</th>\n",
       "      <td>TTTGGTTAGTTCGCAT-1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                  barcode\n",
       "KMA1_AAACGGGTCTAACGGT  AAACGGGTCTAACGGT-1\n",
       "KMA1_AATCCAGGTCGCGTGT  AATCCAGGTCGCGTGT-1\n",
       "KMA1_AATCGGTCATTAGCCA  AATCGGTCATTAGCCA-1\n",
       "KMA1_ACAGCCGTCATCATTC  ACAGCCGTCATCATTC-1\n",
       "KMA1_ACGGGTCAGGGTCGAT  ACGGGTCAGGGTCGAT-1\n",
       "KMA1_ACGGGTCCAAGTCATC  ACGGGTCCAAGTCATC-1\n",
       "KMA1_AGAGTGGTCTCAAACG  AGAGTGGTCTCAAACG-1\n",
       "KMA1_AGGCCGTTCCCTGACT  AGGCCGTTCCCTGACT-1\n",
       "KMA1_AGTGTCAGTGCAGTAG  AGTGTCAGTGCAGTAG-1\n",
       "KMA1_ATAAGAGGTCCGAATT  ATAAGAGGTCCGAATT-1\n",
       "KMA1_ATTATCCTCCCAAGAT  ATTATCCTCCCAAGAT-1\n",
       "KMA1_ATTGGACTCAATACCG  ATTGGACTCAATACCG-1\n",
       "KMA1_CACATTTAGGCGCTCT  CACATTTAGGCGCTCT-1\n",
       "KMA1_CAGCATAAGAAACCTA  CAGCATAAGAAACCTA-1\n",
       "KMA1_CAGCTGGAGCCACCTG  CAGCTGGAGCCACCTG-1\n",
       "KMA1_CATCGAAAGATACACA  CATCGAAAGATACACA-1\n",
       "KMA1_CGAGCACAGCCTCGTG  CGAGCACAGCCTCGTG-1\n",
       "KMA1_CGCGGTAAGCGATTCT  CGCGGTAAGCGATTCT-1\n",
       "KMA1_CGGACGTGTTTGTTTC  CGGACGTGTTTGTTTC-1\n",
       "KMA1_CTTAGGACAATCCAAC  CTTAGGACAATCCAAC-1\n",
       "KMA1_GACACGCGTCCCGACA  GACACGCGTCCCGACA-1\n",
       "KMA1_GACTACAAGTGAAGAG  GACTACAAGTGAAGAG-1\n",
       "KMA1_GAGGTGAAGTACGTAA  GAGGTGAAGTACGTAA-1\n",
       "KMA1_GATCGATGTATGCTTG  GATCGATGTATGCTTG-1\n",
       "KMA1_GATCGCGTCTTGCCGT  GATCGCGTCTTGCCGT-1\n",
       "KMA1_GCATACAAGCCACGCT  GCATACAAGCCACGCT-1\n",
       "KMA1_GCTGCAGTCAGTCCCT  GCTGCAGTCAGTCCCT-1\n",
       "KMA1_GTCATTTCATAGAAAC  GTCATTTCATAGAAAC-1\n",
       "KMA1_GTGCGGTCAGTCTTCC  GTGCGGTCAGTCTTCC-1\n",
       "KMA1_GTGGGTCGTGTGGCTC  GTGGGTCGTGTGGCTC-1\n",
       "KMA1_TACCTTACACGTCAGC  TACCTTACACGTCAGC-1\n",
       "KMA1_TACTCATTCTGGCGAC  TACTCATTCTGGCGAC-1\n",
       "KMA1_TACTCGCGTACCGTAT  TACTCGCGTACCGTAT-1\n",
       "KMA1_TAGTTGGAGAGGGCTT  TAGTTGGAGAGGGCTT-1\n",
       "KMA1_TAGTTGGAGTGACATA  TAGTTGGAGTGACATA-1\n",
       "KMA1_TAGTTGGAGTGTGGCA  TAGTTGGAGTGTGGCA-1\n",
       "KMA1_TCGGGACCACGCCAGT  TCGGGACCACGCCAGT-1\n",
       "KMA1_TCTTTCCAGTATCTCG  TCTTTCCAGTATCTCG-1\n",
       "KMA1_TGTTCCGCATGACGGA  TGTTCCGCATGACGGA-1\n",
       "KMA1_TTAGTTCTCGCAAACT  TTAGTTCTCGCAAACT-1\n",
       "KMA1_TTGACTTAGTACGCCC  TTGACTTAGTACGCCC-1\n",
       "KMA1_TTGCGTCAGTGAACGC  TTGCGTCAGTGAACGC-1\n",
       "KMA1_TTTGGTTAGTTCGCAT  TTTGGTTAGTTCGCAT-1"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "myeloid_aml_cells_barcodes = myeloid_aml_cells_df[['barcode']]\n",
    "myeloid_aml_cells_barcodes.to_csv('data/JS1/myeloid_aml_cells_barcodes.tsv', \n",
    "                                  index=False, header=False)\n",
    "myeloid_aml_cells_barcodes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "15393912",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:29:21.755199Z",
     "start_time": "2023-07-16T02:29:21.738321Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGCAAAGAATC</th>\n",
       "      <td>GD1_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>30</td>\n",
       "      <td>AAACCTGCAAAGAATC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGCAGTTCATG</th>\n",
       "      <td>LB1_</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>2</td>\n",
       "      <td>AAACCTGCAGTTCATG-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGGTTCTGAAC</th>\n",
       "      <td>LB1_</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>0</td>\n",
       "      <td>AAACCTGGTTCTGAAC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGGTTGTACAC</th>\n",
       "      <td>GD1_</td>\n",
       "      <td>tumorGD</td>\n",
       "      <td>2</td>\n",
       "      <td>AAACCTGGTTGTACAC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGTCAAACCAC</th>\n",
       "      <td>GD1_</td>\n",
       "      <td>unassigned</td>\n",
       "      <td>35</td>\n",
       "      <td>AAACCTGTCAAACCAC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCAGTACTTCTT</th>\n",
       "      <td>LB1_</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>2</td>\n",
       "      <td>TTTGTCAGTACTTCTT-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCAGTATGAATG</th>\n",
       "      <td>LB1_</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>0</td>\n",
       "      <td>TTTGTCAGTATGAATG-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCAGTCACAAGG</th>\n",
       "      <td>GD1_</td>\n",
       "      <td>tumorGD</td>\n",
       "      <td>2</td>\n",
       "      <td>TTTGTCAGTCACAAGG-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCAGTTGATTGC</th>\n",
       "      <td>LB1_</td>\n",
       "      <td>donorLB</td>\n",
       "      <td>0</td>\n",
       "      <td>TTTGTCAGTTGATTGC-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCATCTAAGCCA</th>\n",
       "      <td>GD1_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>1</td>\n",
       "      <td>TTTGTCATCTAAGCCA-1</td>\n",
       "      <td>KMA1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5757 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                      ref_sample    donor_id  cluster_number  \\\n",
       "KMA1_AAACCTGCAAAGAATC       GD1_  unassigned              30   \n",
       "KMA1_AAACCTGCAGTTCATG       LB1_     donorLB               2   \n",
       "KMA1_AAACCTGGTTCTGAAC       LB1_     donorLB               0   \n",
       "KMA1_AAACCTGGTTGTACAC       GD1_     tumorGD               2   \n",
       "KMA1_AAACCTGTCAAACCAC       GD1_  unassigned              35   \n",
       "...                          ...         ...             ...   \n",
       "KMA1_TTTGTCAGTACTTCTT       LB1_     donorLB               2   \n",
       "KMA1_TTTGTCAGTATGAATG       LB1_     donorLB               0   \n",
       "KMA1_TTTGTCAGTCACAAGG       GD1_     tumorGD               2   \n",
       "KMA1_TTTGTCAGTTGATTGC       LB1_     donorLB               0   \n",
       "KMA1_TTTGTCATCTAAGCCA       GD1_     doublet               1   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA1_AAACCTGCAAAGAATC  AAACCTGCAAAGAATC-1  KMA1  \n",
       "KMA1_AAACCTGCAGTTCATG  AAACCTGCAGTTCATG-1  KMA1  \n",
       "KMA1_AAACCTGGTTCTGAAC  AAACCTGGTTCTGAAC-1  KMA1  \n",
       "KMA1_AAACCTGGTTGTACAC  AAACCTGGTTGTACAC-1  KMA1  \n",
       "KMA1_AAACCTGTCAAACCAC  AAACCTGTCAAACCAC-1  KMA1  \n",
       "...                                   ...   ...  \n",
       "KMA1_TTTGTCAGTACTTCTT  TTTGTCAGTACTTCTT-1  KMA1  \n",
       "KMA1_TTTGTCAGTATGAATG  TTTGTCAGTATGAATG-1  KMA1  \n",
       "KMA1_TTTGTCAGTCACAAGG  TTTGTCAGTCACAAGG-1  KMA1  \n",
       "KMA1_TTTGTCAGTTGATTGC  TTTGTCAGTTGATTGC-1  KMA1  \n",
       "KMA1_TTTGTCATCTAAGCCA  TTTGTCATCTAAGCCA-1  KMA1  \n",
       "\n",
       "[5757 rows x 5 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = pool_df[pool_df['cluster_number'].\\\n",
    "                    isin(t_cell_clusters + b_cell_clusters + nk_cell_clusters)]\n",
    "normal_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "7cac6b01",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:31:38.513051Z",
     "start_time": "2023-07-16T02:31:38.499965Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "2     1897\n",
       "0     1645\n",
       "1      682\n",
       "3      630\n",
       "15     261\n",
       "7      182\n",
       "24      93\n",
       "30      80\n",
       "45      77\n",
       "11      57\n",
       "36      44\n",
       "40      42\n",
       "35      36\n",
       "25      31\n",
       "Name: cluster_number, dtype: int64"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df['cluster_number'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "8954b9f2",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:32:34.473857Z",
     "start_time": "2023-07-16T02:32:34.451267Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>cell</th>\n",
       "      <th>group</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGCAAAGAATC</th>\n",
       "      <td>AAACCTGCAAAGAATC-1</td>\n",
       "      <td>30</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGCAGTTCATG</th>\n",
       "      <td>AAACCTGCAGTTCATG-1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGGTTCTGAAC</th>\n",
       "      <td>AAACCTGGTTCTGAAC-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGGTTGTACAC</th>\n",
       "      <td>AAACCTGGTTGTACAC-1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_AAACCTGTCAAACCAC</th>\n",
       "      <td>AAACCTGTCAAACCAC-1</td>\n",
       "      <td>35</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCAGTACTTCTT</th>\n",
       "      <td>TTTGTCAGTACTTCTT-1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCAGTATGAATG</th>\n",
       "      <td>TTTGTCAGTATGAATG-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCAGTCACAAGG</th>\n",
       "      <td>TTTGTCAGTCACAAGG-1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCAGTTGATTGC</th>\n",
       "      <td>TTTGTCAGTTGATTGC-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA1_TTTGTCATCTAAGCCA</th>\n",
       "      <td>TTTGTCATCTAAGCCA-1</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5757 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                     cell  group\n",
       "KMA1_AAACCTGCAAAGAATC  AAACCTGCAAAGAATC-1     30\n",
       "KMA1_AAACCTGCAGTTCATG  AAACCTGCAGTTCATG-1      2\n",
       "KMA1_AAACCTGGTTCTGAAC  AAACCTGGTTCTGAAC-1      0\n",
       "KMA1_AAACCTGGTTGTACAC  AAACCTGGTTGTACAC-1      2\n",
       "KMA1_AAACCTGTCAAACCAC  AAACCTGTCAAACCAC-1     35\n",
       "...                                   ...    ...\n",
       "KMA1_TTTGTCAGTACTTCTT  TTTGTCAGTACTTCTT-1      2\n",
       "KMA1_TTTGTCAGTATGAATG  TTTGTCAGTATGAATG-1      0\n",
       "KMA1_TTTGTCAGTCACAAGG  TTTGTCAGTCACAAGG-1      2\n",
       "KMA1_TTTGTCAGTTGATTGC  TTTGTCAGTTGATTGC-1      0\n",
       "KMA1_TTTGTCATCTAAGCCA  TTTGTCATCTAAGCCA-1      1\n",
       "\n",
       "[5757 rows x 2 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = normal_cells_df[['barcode', 'cluster_number']]\n",
    "normal_cells_df.columns = ['cell', 'group']\n",
    "normal_cells_df.to_csv('data/JS1/normal_cells_annotations.csv', index=False)\n",
    "normal_cells_df"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "3ef71e68",
   "metadata": {
    "heading_collapsed": true
   },
   "source": [
    "### KMA7, AH3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "2475b11b",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:26:42.817143Z",
     "start_time": "2023-07-16T02:26:42.784813Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACCTGAGGATGCGT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>doublet</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGGATGCGT-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACCTGAGGGCTTGA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGGGCTTGA-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACCTGAGTCAATAG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGTCAATAG-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACCTGAGTGGTAAT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGAGTGGTAAT-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACCTGCAGATCTGT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>doublet</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAACCTGCAGATCTGT-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCATCGAGGTAG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCGAGGTAG-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCATCTTCAACT</th>\n",
       "      <td>MS4_</td>\n",
       "      <td>tumorGD</td>\n",
       "      <td>22</td>\n",
       "      <td>TTTGTCATCTTCAACT-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCATCTTCCTTC</th>\n",
       "      <td>MS4_</td>\n",
       "      <td>donorMS</td>\n",
       "      <td>28</td>\n",
       "      <td>TTTGTCATCTTCCTTC-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCATCTTCGGTC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>doublet</td>\n",
       "      <td>-1</td>\n",
       "      <td>TTTGTCATCTTCGGTC-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCATCTTGCCGT</th>\n",
       "      <td>MS4_</td>\n",
       "      <td>donorMS</td>\n",
       "      <td>4</td>\n",
       "      <td>TTTGTCATCTTGCCGT-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5974 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                        ref_sample donor_id  cluster_number  \\\n",
       "KMA7_AAACCTGAGGATGCGT  not in data  doublet              -1   \n",
       "KMA7_AAACCTGAGGGCTTGA  not in data  donorKC              -1   \n",
       "KMA7_AAACCTGAGTCAATAG  not in data  donorKC              -1   \n",
       "KMA7_AAACCTGAGTGGTAAT  not in data  donorKC              -1   \n",
       "KMA7_AAACCTGCAGATCTGT  not in data  doublet              -1   \n",
       "...                            ...      ...             ...   \n",
       "KMA7_TTTGTCATCGAGGTAG  not in data  donorKC              -1   \n",
       "KMA7_TTTGTCATCTTCAACT         MS4_  tumorGD              22   \n",
       "KMA7_TTTGTCATCTTCCTTC         MS4_  donorMS              28   \n",
       "KMA7_TTTGTCATCTTCGGTC  not in data  doublet              -1   \n",
       "KMA7_TTTGTCATCTTGCCGT         MS4_  donorMS               4   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA7_AAACCTGAGGATGCGT  AAACCTGAGGATGCGT-1  KMA7  \n",
       "KMA7_AAACCTGAGGGCTTGA  AAACCTGAGGGCTTGA-1  KMA7  \n",
       "KMA7_AAACCTGAGTCAATAG  AAACCTGAGTCAATAG-1  KMA7  \n",
       "KMA7_AAACCTGAGTGGTAAT  AAACCTGAGTGGTAAT-1  KMA7  \n",
       "KMA7_AAACCTGCAGATCTGT  AAACCTGCAGATCTGT-1  KMA7  \n",
       "...                                   ...   ...  \n",
       "KMA7_TTTGTCATCGAGGTAG  TTTGTCATCGAGGTAG-1  KMA7  \n",
       "KMA7_TTTGTCATCTTCAACT  TTTGTCATCTTCAACT-1  KMA7  \n",
       "KMA7_TTTGTCATCTTCCTTC  TTTGTCATCTTCCTTC-1  KMA7  \n",
       "KMA7_TTTGTCATCTTCGGTC  TTTGTCATCTTCGGTC-1  KMA7  \n",
       "KMA7_TTTGTCATCTTGCCGT  TTTGTCATCTTGCCGT-1  KMA7  \n",
       "\n",
       "[5974 rows x 5 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pool_df = cells_df[cells_df['pool'] == 'KMA7']\n",
    "pool_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "68595a04",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:26:49.622689Z",
     "start_time": "2023-07-16T02:26:49.610538Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "donorKC       2899\n",
       "donorMS        884\n",
       "doublet        798\n",
       "unassigned     760\n",
       "tumorGD        480\n",
       "donorAH        130\n",
       "tumorAH         23\n",
       "Name: donor_id, dtype: int64"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pool_df['donor_id'].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "8a8698a5",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:27:44.201003Z",
     "start_time": "2023-07-16T02:27:44.180203Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
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       "    }\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>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA7_AAGACCTTCCCGGATG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>AAGACCTTCCCGGATG-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_ACGGGTCTCTGTGCAA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>ACGGGTCTCTGTGCAA-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AGTAGTCTCTCAAGTG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>AGTAGTCTCTCAAGTG-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AGTGTCATCAACGCTA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>AGTGTCATCAACGCTA-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CAAGGCCTCGCGTAGC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>CAAGGCCTCGCGTAGC-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CATCAGAGTGCCTTGG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>CATCAGAGTGCCTTGG-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CATGCCTAGGCGACAT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>CATGCCTAGGCGACAT-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CCGTGGAAGAAGGGTA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>CCGTGGAAGAAGGGTA-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CCTAAAGCATAACCTG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>CCTAAAGCATAACCTG-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CCTATTAGTACCCAAT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>CCTATTAGTACCCAAT-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CGCGTTTCACGCATCG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>CGCGTTTCACGCATCG-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CTGCTGTCAGACTCGC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>CTGCTGTCAGACTCGC-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_GTACGTAGTTATGTGC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>GTACGTAGTTATGTGC-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_GTGCAGCTCCGTCAAA</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>GTGCAGCTCCGTCAAA-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TACGGATCAACGATCT</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>TACGGATCAACGATCT-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TCTTCGGCAAGAGTCG</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>TCTTCGGCAAGAGTCG-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TGACGGCAGGATGGTC</th>\n",
       "      <td>not in data</td>\n",
       "      <td>tumorAH</td>\n",
       "      <td>-1</td>\n",
       "      <td>TGACGGCAGGATGGTC-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                        ref_sample donor_id  cluster_number  \\\n",
       "KMA7_AAGACCTTCCCGGATG  not in data  tumorAH              -1   \n",
       "KMA7_ACGGGTCTCTGTGCAA  not in data  tumorAH              -1   \n",
       "KMA7_AGTAGTCTCTCAAGTG  not in data  tumorAH              -1   \n",
       "KMA7_AGTGTCATCAACGCTA  not in data  tumorAH              -1   \n",
       "KMA7_CAAGGCCTCGCGTAGC  not in data  tumorAH              -1   \n",
       "KMA7_CATCAGAGTGCCTTGG  not in data  tumorAH              -1   \n",
       "KMA7_CATGCCTAGGCGACAT  not in data  tumorAH              -1   \n",
       "KMA7_CCGTGGAAGAAGGGTA  not in data  tumorAH              -1   \n",
       "KMA7_CCTAAAGCATAACCTG  not in data  tumorAH              -1   \n",
       "KMA7_CCTATTAGTACCCAAT  not in data  tumorAH              -1   \n",
       "KMA7_CGCGTTTCACGCATCG  not in data  tumorAH              -1   \n",
       "KMA7_CTGCTGTCAGACTCGC  not in data  tumorAH              -1   \n",
       "KMA7_GTACGTAGTTATGTGC  not in data  tumorAH              -1   \n",
       "KMA7_GTGCAGCTCCGTCAAA  not in data  tumorAH              -1   \n",
       "KMA7_TACGGATCAACGATCT  not in data  tumorAH              -1   \n",
       "KMA7_TCTTCGGCAAGAGTCG  not in data  tumorAH              -1   \n",
       "KMA7_TGACGGCAGGATGGTC  not in data  tumorAH              -1   \n",
       "\n",
       "                                  barcode  pool  \n",
       "KMA7_AAGACCTTCCCGGATG  AAGACCTTCCCGGATG-1  KMA7  \n",
       "KMA7_ACGGGTCTCTGTGCAA  ACGGGTCTCTGTGCAA-1  KMA7  \n",
       "KMA7_AGTAGTCTCTCAAGTG  AGTAGTCTCTCAAGTG-1  KMA7  \n",
       "KMA7_AGTGTCATCAACGCTA  AGTGTCATCAACGCTA-1  KMA7  \n",
       "KMA7_CAAGGCCTCGCGTAGC  CAAGGCCTCGCGTAGC-1  KMA7  \n",
       "KMA7_CATCAGAGTGCCTTGG  CATCAGAGTGCCTTGG-1  KMA7  \n",
       "KMA7_CATGCCTAGGCGACAT  CATGCCTAGGCGACAT-1  KMA7  \n",
       "KMA7_CCGTGGAAGAAGGGTA  CCGTGGAAGAAGGGTA-1  KMA7  \n",
       "KMA7_CCTAAAGCATAACCTG  CCTAAAGCATAACCTG-1  KMA7  \n",
       "KMA7_CCTATTAGTACCCAAT  CCTATTAGTACCCAAT-1  KMA7  \n",
       "KMA7_CGCGTTTCACGCATCG  CGCGTTTCACGCATCG-1  KMA7  \n",
       "KMA7_CTGCTGTCAGACTCGC  CTGCTGTCAGACTCGC-1  KMA7  \n",
       "KMA7_GTACGTAGTTATGTGC  GTACGTAGTTATGTGC-1  KMA7  \n",
       "KMA7_GTGCAGCTCCGTCAAA  GTGCAGCTCCGTCAAA-1  KMA7  \n",
       "KMA7_TACGGATCAACGATCT  TACGGATCAACGATCT-1  KMA7  \n",
       "KMA7_TCTTCGGCAAGAGTCG  TCTTCGGCAAGAGTCG-1  KMA7  \n",
       "KMA7_TGACGGCAGGATGGTC  TGACGGCAGGATGGTC-1  KMA7  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sample_df = pool_df[pool_df['donor_id'] == 'tumorAH']\n",
    "myeloid_aml_cells_df = sample_df[sample_df['cluster_number'].isin(\n",
    "                            myeloid_clusters + aml_clusters + [-1])]\n",
    "myeloid_aml_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "637a376f",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:27:51.995719Z",
     "start_time": "2023-07-16T02:27:51.986383Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(17, 5)"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "myeloid_aml_cells_df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "b6bebee4",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:29:14.226520Z",
     "start_time": "2023-07-16T02:29:14.211038Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>barcode</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA7_AAGACCTTCCCGGATG</th>\n",
       "      <td>AAGACCTTCCCGGATG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_ACGGGTCTCTGTGCAA</th>\n",
       "      <td>ACGGGTCTCTGTGCAA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AGTAGTCTCTCAAGTG</th>\n",
       "      <td>AGTAGTCTCTCAAGTG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AGTGTCATCAACGCTA</th>\n",
       "      <td>AGTGTCATCAACGCTA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CAAGGCCTCGCGTAGC</th>\n",
       "      <td>CAAGGCCTCGCGTAGC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CATCAGAGTGCCTTGG</th>\n",
       "      <td>CATCAGAGTGCCTTGG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CATGCCTAGGCGACAT</th>\n",
       "      <td>CATGCCTAGGCGACAT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CCGTGGAAGAAGGGTA</th>\n",
       "      <td>CCGTGGAAGAAGGGTA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CCTAAAGCATAACCTG</th>\n",
       "      <td>CCTAAAGCATAACCTG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CCTATTAGTACCCAAT</th>\n",
       "      <td>CCTATTAGTACCCAAT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CGCGTTTCACGCATCG</th>\n",
       "      <td>CGCGTTTCACGCATCG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_CTGCTGTCAGACTCGC</th>\n",
       "      <td>CTGCTGTCAGACTCGC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_GTACGTAGTTATGTGC</th>\n",
       "      <td>GTACGTAGTTATGTGC-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_GTGCAGCTCCGTCAAA</th>\n",
       "      <td>GTGCAGCTCCGTCAAA-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TACGGATCAACGATCT</th>\n",
       "      <td>TACGGATCAACGATCT-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TCTTCGGCAAGAGTCG</th>\n",
       "      <td>TCTTCGGCAAGAGTCG-1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TGACGGCAGGATGGTC</th>\n",
       "      <td>TGACGGCAGGATGGTC-1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                                  barcode\n",
       "KMA7_AAGACCTTCCCGGATG  AAGACCTTCCCGGATG-1\n",
       "KMA7_ACGGGTCTCTGTGCAA  ACGGGTCTCTGTGCAA-1\n",
       "KMA7_AGTAGTCTCTCAAGTG  AGTAGTCTCTCAAGTG-1\n",
       "KMA7_AGTGTCATCAACGCTA  AGTGTCATCAACGCTA-1\n",
       "KMA7_CAAGGCCTCGCGTAGC  CAAGGCCTCGCGTAGC-1\n",
       "KMA7_CATCAGAGTGCCTTGG  CATCAGAGTGCCTTGG-1\n",
       "KMA7_CATGCCTAGGCGACAT  CATGCCTAGGCGACAT-1\n",
       "KMA7_CCGTGGAAGAAGGGTA  CCGTGGAAGAAGGGTA-1\n",
       "KMA7_CCTAAAGCATAACCTG  CCTAAAGCATAACCTG-1\n",
       "KMA7_CCTATTAGTACCCAAT  CCTATTAGTACCCAAT-1\n",
       "KMA7_CGCGTTTCACGCATCG  CGCGTTTCACGCATCG-1\n",
       "KMA7_CTGCTGTCAGACTCGC  CTGCTGTCAGACTCGC-1\n",
       "KMA7_GTACGTAGTTATGTGC  GTACGTAGTTATGTGC-1\n",
       "KMA7_GTGCAGCTCCGTCAAA  GTGCAGCTCCGTCAAA-1\n",
       "KMA7_TACGGATCAACGATCT  TACGGATCAACGATCT-1\n",
       "KMA7_TCTTCGGCAAGAGTCG  TCTTCGGCAAGAGTCG-1\n",
       "KMA7_TGACGGCAGGATGGTC  TGACGGCAGGATGGTC-1"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "myeloid_aml_cells_barcodes = myeloid_aml_cells_df[['barcode']]\n",
    "myeloid_aml_cells_barcodes.to_csv('data/AH3/myeloid_aml_cells_barcodes.tsv', \n",
    "                                  index=False, header=False)\n",
    "myeloid_aml_cells_barcodes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "1efe9266",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:29:21.755199Z",
     "start_time": "2023-07-16T02:29:21.738321Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>ref_sample</th>\n",
       "      <th>donor_id</th>\n",
       "      <th>cluster_number</th>\n",
       "      <th>barcode</th>\n",
       "      <th>pool</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACCTGCAGTAAGAT</th>\n",
       "      <td>AH3_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>2</td>\n",
       "      <td>AAACCTGCAGTAAGAT-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACCTGGTCCGCTGA</th>\n",
       "      <td>KC4_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>0</td>\n",
       "      <td>AAACCTGGTCCGCTGA-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACGGGGTCAACATC</th>\n",
       "      <td>KC4_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>2</td>\n",
       "      <td>AAACGGGGTCAACATC-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACGGGGTTCAACCA</th>\n",
       "      <td>KC4_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>0</td>\n",
       "      <td>AAACGGGGTTCAACCA-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACGGGTCATAAAGG</th>\n",
       "      <td>KC4_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>0</td>\n",
       "      <td>AAACGGGTCATAAAGG-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGCGCTCACAACGT</th>\n",
       "      <td>KC4_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>2</td>\n",
       "      <td>TTTGCGCTCACAACGT-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGGTTTCTTGTATC</th>\n",
       "      <td>KC4_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>0</td>\n",
       "      <td>TTTGGTTTCTTGTATC-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCAAGCCACCTG</th>\n",
       "      <td>KC4_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>0</td>\n",
       "      <td>TTTGTCAAGCCACCTG-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCAAGGCCCTCA</th>\n",
       "      <td>KC4_</td>\n",
       "      <td>donorKC</td>\n",
       "      <td>2</td>\n",
       "      <td>TTTGTCAAGGCCCTCA-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCACACGAAAGC</th>\n",
       "      <td>KC4_</td>\n",
       "      <td>doublet</td>\n",
       "      <td>0</td>\n",
       "      <td>TTTGTCACACGAAAGC-1</td>\n",
       "      <td>KMA7</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1433 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                      ref_sample donor_id  cluster_number             barcode  \\\n",
       "KMA7_AAACCTGCAGTAAGAT       AH3_  doublet               2  AAACCTGCAGTAAGAT-1   \n",
       "KMA7_AAACCTGGTCCGCTGA       KC4_  donorKC               0  AAACCTGGTCCGCTGA-1   \n",
       "KMA7_AAACGGGGTCAACATC       KC4_  donorKC               2  AAACGGGGTCAACATC-1   \n",
       "KMA7_AAACGGGGTTCAACCA       KC4_  donorKC               0  AAACGGGGTTCAACCA-1   \n",
       "KMA7_AAACGGGTCATAAAGG       KC4_  donorKC               0  AAACGGGTCATAAAGG-1   \n",
       "...                          ...      ...             ...                 ...   \n",
       "KMA7_TTTGCGCTCACAACGT       KC4_  donorKC               2  TTTGCGCTCACAACGT-1   \n",
       "KMA7_TTTGGTTTCTTGTATC       KC4_  donorKC               0  TTTGGTTTCTTGTATC-1   \n",
       "KMA7_TTTGTCAAGCCACCTG       KC4_  donorKC               0  TTTGTCAAGCCACCTG-1   \n",
       "KMA7_TTTGTCAAGGCCCTCA       KC4_  donorKC               2  TTTGTCAAGGCCCTCA-1   \n",
       "KMA7_TTTGTCACACGAAAGC       KC4_  doublet               0  TTTGTCACACGAAAGC-1   \n",
       "\n",
       "                       pool  \n",
       "KMA7_AAACCTGCAGTAAGAT  KMA7  \n",
       "KMA7_AAACCTGGTCCGCTGA  KMA7  \n",
       "KMA7_AAACGGGGTCAACATC  KMA7  \n",
       "KMA7_AAACGGGGTTCAACCA  KMA7  \n",
       "KMA7_AAACGGGTCATAAAGG  KMA7  \n",
       "...                     ...  \n",
       "KMA7_TTTGCGCTCACAACGT  KMA7  \n",
       "KMA7_TTTGGTTTCTTGTATC  KMA7  \n",
       "KMA7_TTTGTCAAGCCACCTG  KMA7  \n",
       "KMA7_TTTGTCAAGGCCCTCA  KMA7  \n",
       "KMA7_TTTGTCACACGAAAGC  KMA7  \n",
       "\n",
       "[1433 rows x 5 columns]"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = pool_df[pool_df['cluster_number'].\\\n",
    "                    isin(t_cell_clusters + b_cell_clusters + nk_cell_clusters)]\n",
    "normal_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "3b5acdb1",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:31:38.513051Z",
     "start_time": "2023-07-16T02:31:38.499965Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0     648\n",
       "2     293\n",
       "35    202\n",
       "1     141\n",
       "7      43\n",
       "3      37\n",
       "45     26\n",
       "15     16\n",
       "40      9\n",
       "36      8\n",
       "24      5\n",
       "30      4\n",
       "25      1\n",
       "Name: cluster_number, dtype: int64"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cluster_counts = normal_cells_df['cluster_number'].value_counts()\n",
    "cluster_counts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "9bd24c94",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:32:19.542433Z",
     "start_time": "2023-07-16T02:32:19.527432Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0     648\n",
       "2     293\n",
       "35    202\n",
       "1     141\n",
       "7      43\n",
       "3      37\n",
       "45     26\n",
       "15     16\n",
       "40      9\n",
       "36      8\n",
       "24      5\n",
       "30      4\n",
       "Name: cluster_number, dtype: int64"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = normal_cells_df[normal_cells_df['cluster_number'].isin(\n",
    "                    cluster_counts[cluster_counts > 1].index)]\n",
    "\n",
    "cluster_counts = normal_cells_df['cluster_number'].value_counts()\n",
    "cluster_counts"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "45c70d0f",
   "metadata": {
    "ExecuteTime": {
     "end_time": "2023-07-16T02:32:34.473857Z",
     "start_time": "2023-07-16T02:32:34.451267Z"
    },
    "hidden": true
   },
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>cell</th>\n",
       "      <th>group</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACCTGCAGTAAGAT</th>\n",
       "      <td>AAACCTGCAGTAAGAT-1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACCTGGTCCGCTGA</th>\n",
       "      <td>AAACCTGGTCCGCTGA-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACGGGGTCAACATC</th>\n",
       "      <td>AAACGGGGTCAACATC-1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACGGGGTTCAACCA</th>\n",
       "      <td>AAACGGGGTTCAACCA-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_AAACGGGTCATAAAGG</th>\n",
       "      <td>AAACGGGTCATAAAGG-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGCGCTCACAACGT</th>\n",
       "      <td>TTTGCGCTCACAACGT-1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGGTTTCTTGTATC</th>\n",
       "      <td>TTTGGTTTCTTGTATC-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCAAGCCACCTG</th>\n",
       "      <td>TTTGTCAAGCCACCTG-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCAAGGCCCTCA</th>\n",
       "      <td>TTTGTCAAGGCCCTCA-1</td>\n",
       "      <td>2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>KMA7_TTTGTCACACGAAAGC</th>\n",
       "      <td>TTTGTCACACGAAAGC-1</td>\n",
       "      <td>0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1432 rows × 2 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                     cell  group\n",
       "KMA7_AAACCTGCAGTAAGAT  AAACCTGCAGTAAGAT-1      2\n",
       "KMA7_AAACCTGGTCCGCTGA  AAACCTGGTCCGCTGA-1      0\n",
       "KMA7_AAACGGGGTCAACATC  AAACGGGGTCAACATC-1      2\n",
       "KMA7_AAACGGGGTTCAACCA  AAACGGGGTTCAACCA-1      0\n",
       "KMA7_AAACGGGTCATAAAGG  AAACGGGTCATAAAGG-1      0\n",
       "...                                   ...    ...\n",
       "KMA7_TTTGCGCTCACAACGT  TTTGCGCTCACAACGT-1      2\n",
       "KMA7_TTTGGTTTCTTGTATC  TTTGGTTTCTTGTATC-1      0\n",
       "KMA7_TTTGTCAAGCCACCTG  TTTGTCAAGCCACCTG-1      0\n",
       "KMA7_TTTGTCAAGGCCCTCA  TTTGTCAAGGCCCTCA-1      2\n",
       "KMA7_TTTGTCACACGAAAGC  TTTGTCACACGAAAGC-1      0\n",
       "\n",
       "[1432 rows x 2 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "normal_cells_df = normal_cells_df[['barcode', 'cluster_number']]\n",
    "normal_cells_df.columns = ['cell', 'group']\n",
    "normal_cells_df.to_csv('data/AH3/normal_cells_annotations.csv', index=False)\n",
    "normal_cells_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "f3862039",
   "metadata": {
    "hidden": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "ea7ba335",
   "metadata": {
    "hidden": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "b3acedfc",
   "metadata": {
    "hidden": true
   },
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "0ea5ed74",
   "metadata": {
    "hidden": true
   },
   "outputs": [],
   "source": []
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