format_data.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import os"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "# expression matrix\n",
    "exp_path = 'TcellDev/Data/T_cell_development/10x_1993_log2_q_norm.txt'\n",
    "\n",
    "# cluster ids and cell type ids\n",
    "id_path = 'TcellDev/Data/T_cell_development/cell_cluster15_self_modcell.txt'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp = pd.read_csv(exp_path, sep = \"\\t\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "        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>gene_id</th>\n",
       "      <th>AAACCTGGTCGACTGC-1</th>\n",
       "      <th>AAACGGGAGCTAACAA-1</th>\n",
       "      <th>AAACGGGCACATGGGA-1</th>\n",
       "      <th>AAACGGGGTAGCGTGA-1</th>\n",
       "      <th>AAACGGGGTATCGCAT-1</th>\n",
       "      <th>AAAGATGAGGACCACA-1</th>\n",
       "      <th>AAAGATGCAATCTGCA-1</th>\n",
       "      <th>AAAGATGGTGCAGGTA-1</th>\n",
       "      <th>AAAGATGGTTTGTTTC-1</th>\n",
       "      <th>...</th>\n",
       "      <th>TTTGCGCTCGTAGATC-1</th>\n",
       "      <th>TTTGGTTAGAGGACGG-1</th>\n",
       "      <th>TTTGGTTCAATGGAGC-1</th>\n",
       "      <th>TTTGGTTGTGTTTGTG-1</th>\n",
       "      <th>TTTGGTTTCTACCAGA-1</th>\n",
       "      <th>TTTGTCACAAGTCATC-1</th>\n",
       "      <th>TTTGTCACACCACCAG-1</th>\n",
       "      <th>TTTGTCACACTTGGAT-1</th>\n",
       "      <th>TTTGTCACAGACGCAA-1</th>\n",
       "      <th>TTTGTCAGTTAGATGA-1</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Mrpl15</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.033627</td>\n",
       "      <td>0.350455</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.185843</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.705498</td>\n",
       "      <td>0.550533</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.32352</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.192193</td>\n",
       "      <td>1.706164</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Lypla1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.269895</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.705498</td>\n",
       "      <td>0.005779</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.957765</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Tcea1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.111742</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.227245</td>\n",
       "      <td>0.350455</td>\n",
       "      <td>0.210451</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.005779</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>1.875916</td>\n",
       "      <td>0.192193</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Atp6v1h</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.044197</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.692119</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.705498</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.800410</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Rb1cc1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.111742</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.692119</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.208573</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 1994 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   gene_id  AAACCTGGTCGACTGC-1  AAACGGGAGCTAACAA-1  AAACGGGCACATGGGA-1  \\\n",
       "0   Mrpl15                 0.0            0.000000                 0.0   \n",
       "1   Lypla1                 0.0            0.000000                 0.0   \n",
       "2    Tcea1                 0.0            1.111742                 0.0   \n",
       "3  Atp6v1h                 0.0            0.000000                 0.0   \n",
       "4   Rb1cc1                 0.0            1.111742                 0.0   \n",
       "\n",
       "   AAACGGGGTAGCGTGA-1  AAACGGGGTATCGCAT-1  AAAGATGAGGACCACA-1  \\\n",
       "0            0.000000            1.033627            0.350455   \n",
       "1            0.000000            0.269895            0.000000   \n",
       "2            0.000000            1.227245            0.350455   \n",
       "3            1.044197            0.000000            0.000000   \n",
       "4            0.000000            0.000000            0.000000   \n",
       "\n",
       "   AAAGATGCAATCTGCA-1  AAAGATGGTGCAGGTA-1  AAAGATGGTTTGTTTC-1  ...  \\\n",
       "0            0.000000            0.185843                 0.0  ...   \n",
       "1            0.000000            0.000000                 0.0  ...   \n",
       "2            0.210451            0.000000                 0.0  ...   \n",
       "3            0.000000            0.000000                 0.0  ...   \n",
       "4            0.000000            0.000000                 0.0  ...   \n",
       "\n",
       "   TTTGCGCTCGTAGATC-1  TTTGGTTAGAGGACGG-1  TTTGGTTCAATGGAGC-1  \\\n",
       "0            0.000000                 0.0            0.705498   \n",
       "1            0.000000                 0.0            0.705498   \n",
       "2            0.000000                 0.0            0.000000   \n",
       "3            0.692119                 0.0            0.705498   \n",
       "4            0.692119                 0.0            0.000000   \n",
       "\n",
       "   TTTGGTTGTGTTTGTG-1  TTTGGTTTCTACCAGA-1  TTTGTCACAAGTCATC-1  \\\n",
       "0            0.550533                 0.0             0.32352   \n",
       "1            0.005779                 0.0             0.00000   \n",
       "2            0.005779                 0.0             0.00000   \n",
       "3            0.000000                 0.0             0.00000   \n",
       "4            0.208573                 0.0             0.00000   \n",
       "\n",
       "   TTTGTCACACCACCAG-1  TTTGTCACACTTGGAT-1  TTTGTCACAGACGCAA-1  \\\n",
       "0            0.000000            0.192193            1.706164   \n",
       "1            0.000000            0.000000            0.000000   \n",
       "2            1.875916            0.192193            0.000000   \n",
       "3            0.000000            0.000000            0.800410   \n",
       "4            0.000000            0.000000            0.000000   \n",
       "\n",
       "   TTTGTCAGTTAGATGA-1  \n",
       "0            0.000000  \n",
       "1            0.957765  \n",
       "2            0.000000  \n",
       "3            0.000000  \n",
       "4            0.000000  \n",
       "\n",
       "[5 rows x 1994 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(8846, 1994)"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "id_info = pd.read_csv(id_path, sep = \"\\t\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "\n",
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       "        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>nGene</th>\n",
       "      <th>nUMI</th>\n",
       "      <th>orig.ident</th>\n",
       "      <th>percent.mito</th>\n",
       "      <th>res.2</th>\n",
       "      <th>stage</th>\n",
       "      <th>bigstage</th>\n",
       "      <th>color</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>CAAGGCCGTATATGAG-1</td>\n",
       "      <td>1652</td>\n",
       "      <td>1616.439338</td>\n",
       "      <td>T cell development</td>\n",
       "      <td>0.026182</td>\n",
       "      <td>12</td>\n",
       "      <td>1DN</td>\n",
       "      <td>1DN</td>\n",
       "      <td>darkcyan</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>GTCACAAAGATCGATA-1</td>\n",
       "      <td>1783</td>\n",
       "      <td>1705.195521</td>\n",
       "      <td>T cell development</td>\n",
       "      <td>0.025659</td>\n",
       "      <td>12</td>\n",
       "      <td>1DN</td>\n",
       "      <td>1DN</td>\n",
       "      <td>darkcyan</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TGCCCATAGGTACTCT-1</td>\n",
       "      <td>2245</td>\n",
       "      <td>1833.787767</td>\n",
       "      <td>T cell development</td>\n",
       "      <td>0.022659</td>\n",
       "      <td>12</td>\n",
       "      <td>1DN</td>\n",
       "      <td>1DN</td>\n",
       "      <td>darkcyan</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GACGGCTCACGGTGTC-1</td>\n",
       "      <td>2304</td>\n",
       "      <td>1868.152040</td>\n",
       "      <td>T cell development</td>\n",
       "      <td>0.020664</td>\n",
       "      <td>12</td>\n",
       "      <td>1DN</td>\n",
       "      <td>1DN</td>\n",
       "      <td>darkcyan</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>TAGGCATTCTTTACGT-1</td>\n",
       "      <td>3399</td>\n",
       "      <td>2079.426036</td>\n",
       "      <td>T cell development</td>\n",
       "      <td>0.018608</td>\n",
       "      <td>12</td>\n",
       "      <td>1DN</td>\n",
       "      <td>1DN</td>\n",
       "      <td>darkcyan</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1981</th>\n",
       "      <td>CGCGGTATCGCTTAGA-1</td>\n",
       "      <td>1173</td>\n",
       "      <td>1557.990006</td>\n",
       "      <td>T cell development</td>\n",
       "      <td>0.025489</td>\n",
       "      <td>13</td>\n",
       "      <td>10APC</td>\n",
       "      <td>10APC</td>\n",
       "      <td>cadetblue</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1982</th>\n",
       "      <td>AAACGGGAGCTAACAA-1</td>\n",
       "      <td>1051</td>\n",
       "      <td>1555.424337</td>\n",
       "      <td>T cell development</td>\n",
       "      <td>0.011485</td>\n",
       "      <td>13</td>\n",
       "      <td>10APC</td>\n",
       "      <td>10APC</td>\n",
       "      <td>cadetblue</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1983</th>\n",
       "      <td>CGTTCTGAGGAGTCTG-1</td>\n",
       "      <td>1331</td>\n",
       "      <td>1593.063887</td>\n",
       "      <td>T cell development</td>\n",
       "      <td>0.027733</td>\n",
       "      <td>13</td>\n",
       "      <td>10APC</td>\n",
       "      <td>10APC</td>\n",
       "      <td>cadetblue</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1984</th>\n",
       "      <td>TGAGGGAGTTGTGGAG-1</td>\n",
       "      <td>1077</td>\n",
       "      <td>1545.898994</td>\n",
       "      <td>T cell development</td>\n",
       "      <td>0.027595</td>\n",
       "      <td>13</td>\n",
       "      <td>10APC</td>\n",
       "      <td>10APC</td>\n",
       "      <td>cadetblue</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1985</th>\n",
       "      <td>TTTATGCTCACTTACT-1</td>\n",
       "      <td>1188</td>\n",
       "      <td>1559.547061</td>\n",
       "      <td>T cell development</td>\n",
       "      <td>0.020869</td>\n",
       "      <td>13</td>\n",
       "      <td>10APC</td>\n",
       "      <td>10APC</td>\n",
       "      <td>cadetblue</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1986 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    cell  nGene         nUMI          orig.ident  \\\n",
       "0     CAAGGCCGTATATGAG-1   1652  1616.439338  T cell development   \n",
       "1     GTCACAAAGATCGATA-1   1783  1705.195521  T cell development   \n",
       "2     TGCCCATAGGTACTCT-1   2245  1833.787767  T cell development   \n",
       "3     GACGGCTCACGGTGTC-1   2304  1868.152040  T cell development   \n",
       "4     TAGGCATTCTTTACGT-1   3399  2079.426036  T cell development   \n",
       "...                  ...    ...          ...                 ...   \n",
       "1981  CGCGGTATCGCTTAGA-1   1173  1557.990006  T cell development   \n",
       "1982  AAACGGGAGCTAACAA-1   1051  1555.424337  T cell development   \n",
       "1983  CGTTCTGAGGAGTCTG-1   1331  1593.063887  T cell development   \n",
       "1984  TGAGGGAGTTGTGGAG-1   1077  1545.898994  T cell development   \n",
       "1985  TTTATGCTCACTTACT-1   1188  1559.547061  T cell development   \n",
       "\n",
       "      percent.mito  res.2  stage bigstage      color  \n",
       "0         0.026182     12    1DN      1DN   darkcyan  \n",
       "1         0.025659     12    1DN      1DN   darkcyan  \n",
       "2         0.022659     12    1DN      1DN   darkcyan  \n",
       "3         0.020664     12    1DN      1DN   darkcyan  \n",
       "4         0.018608     12    1DN      1DN   darkcyan  \n",
       "...            ...    ...    ...      ...        ...  \n",
       "1981      0.025489     13  10APC    10APC  cadetblue  \n",
       "1982      0.011485     13  10APC    10APC  cadetblue  \n",
       "1983      0.027733     13  10APC    10APC  cadetblue  \n",
       "1984      0.027595     13  10APC    10APC  cadetblue  \n",
       "1985      0.020869     13  10APC    10APC  cadetblue  \n",
       "\n",
       "[1986 rows x 9 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "id_info"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "# pivot column names into a row\n",
    "barcodes_exp = exp.columns[1:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['AAACCTGGTCGACTGC-1', 'AAACGGGAGCTAACAA-1', 'AAACGGGCACATGGGA-1',\n",
       "       'AAACGGGGTAGCGTGA-1', 'AAACGGGGTATCGCAT-1', 'AAAGATGAGGACCACA-1',\n",
       "       'AAAGATGCAATCTGCA-1', 'AAAGATGGTGCAGGTA-1', 'AAAGATGGTTTGTTTC-1',\n",
       "       'AAAGATGTCCAAATGC-1',\n",
       "       ...\n",
       "       'TTTGCGCTCGTAGATC-1', 'TTTGGTTAGAGGACGG-1', 'TTTGGTTCAATGGAGC-1',\n",
       "       'TTTGGTTGTGTTTGTG-1', 'TTTGGTTTCTACCAGA-1', 'TTTGTCACAAGTCATC-1',\n",
       "       'TTTGTCACACCACCAG-1', 'TTTGTCACACTTGGAT-1', 'TTTGTCACAGACGCAA-1',\n",
       "       'TTTGTCAGTTAGATGA-1'],\n",
       "      dtype='object', length=1993)"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "barcodes_exp"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "# pivot to get column names (barcodes) into rows in list\n",
    "exp_df = exp.melt(id_vars = ['gene_id'],value_vars = barcodes_exp,\n",
    "                 var_name = 'barcode', value_name = 'count')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>gene_id</th>\n",
       "      <th>barcode</th>\n",
       "      <th>count</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
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       "      <td>Mrpl15</td>\n",
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       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Lypla1</td>\n",
       "      <td>AAACCTGGTCGACTGC-1</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Tcea1</td>\n",
       "      <td>AAACCTGGTCGACTGC-1</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Atp6v1h</td>\n",
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       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Rb1cc1</td>\n",
       "      <td>AAACCTGGTCGACTGC-1</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
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       "      <th>17630073</th>\n",
       "      <td>mt-Cytb</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>5.273960</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17630074</th>\n",
       "      <td>Vamp7</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>0.957765</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17630075</th>\n",
       "      <td>AC125149.3</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17630076</th>\n",
       "      <td>AC149090.1</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>1.908289</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17630077</th>\n",
       "      <td>DHRSX</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>0.957765</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>17630078 rows × 3 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "             gene_id             barcode     count\n",
       "0             Mrpl15  AAACCTGGTCGACTGC-1  0.000000\n",
       "1             Lypla1  AAACCTGGTCGACTGC-1  0.000000\n",
       "2              Tcea1  AAACCTGGTCGACTGC-1  0.000000\n",
       "3            Atp6v1h  AAACCTGGTCGACTGC-1  0.000000\n",
       "4             Rb1cc1  AAACCTGGTCGACTGC-1  0.000000\n",
       "...              ...                 ...       ...\n",
       "17630073     mt-Cytb  TTTGTCAGTTAGATGA-1  5.273960\n",
       "17630074       Vamp7  TTTGTCAGTTAGATGA-1  0.957765\n",
       "17630075  AC125149.3  TTTGTCAGTTAGATGA-1  0.000000\n",
       "17630076  AC149090.1  TTTGTCAGTTAGATGA-1  1.908289\n",
       "17630077       DHRSX  TTTGTCAGTTAGATGA-1  0.957765\n",
       "\n",
       "[17630078 rows x 3 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp_df"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "# left join to get IDs for barcodes\n",
    "exp_df_join = exp_df.merge(id_info[['cell', 'bigstage']], left_on = 'barcode',\n",
    "                          right_on = 'cell')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
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       "      <th></th>\n",
       "      <th>gene_id</th>\n",
       "      <th>barcode</th>\n",
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       "      <th>bigstage</th>\n",
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       "      <th>1</th>\n",
       "      <td>Lypla1</td>\n",
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       "      <td>0.000000</td>\n",
       "      <td>AAACCTGGTCGACTGC-1</td>\n",
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       "      <td>Tcea1</td>\n",
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       "      <td>6CD4sp</td>\n",
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       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Rb1cc1</td>\n",
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       "      <td>0.000000</td>\n",
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       "      <td>mt-Cytb</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>5.273960</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>4DPre</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17568152</th>\n",
       "      <td>Vamp7</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>0.957765</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>4DPre</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17568153</th>\n",
       "      <td>AC125149.3</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>4DPre</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17568154</th>\n",
       "      <td>AC149090.1</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>1.908289</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>4DPre</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>17568155</th>\n",
       "      <td>DHRSX</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>0.957765</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>4DPre</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>17568156 rows × 5 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "             gene_id             barcode     count                cell  \\\n",
       "0             Mrpl15  AAACCTGGTCGACTGC-1  0.000000  AAACCTGGTCGACTGC-1   \n",
       "1             Lypla1  AAACCTGGTCGACTGC-1  0.000000  AAACCTGGTCGACTGC-1   \n",
       "2              Tcea1  AAACCTGGTCGACTGC-1  0.000000  AAACCTGGTCGACTGC-1   \n",
       "3            Atp6v1h  AAACCTGGTCGACTGC-1  0.000000  AAACCTGGTCGACTGC-1   \n",
       "4             Rb1cc1  AAACCTGGTCGACTGC-1  0.000000  AAACCTGGTCGACTGC-1   \n",
       "...              ...                 ...       ...                 ...   \n",
       "17568151     mt-Cytb  TTTGTCAGTTAGATGA-1  5.273960  TTTGTCAGTTAGATGA-1   \n",
       "17568152       Vamp7  TTTGTCAGTTAGATGA-1  0.957765  TTTGTCAGTTAGATGA-1   \n",
       "17568153  AC125149.3  TTTGTCAGTTAGATGA-1  0.000000  TTTGTCAGTTAGATGA-1   \n",
       "17568154  AC149090.1  TTTGTCAGTTAGATGA-1  1.908289  TTTGTCAGTTAGATGA-1   \n",
       "17568155       DHRSX  TTTGTCAGTTAGATGA-1  0.957765  TTTGTCAGTTAGATGA-1   \n",
       "\n",
       "         bigstage  \n",
       "0          6CD4sp  \n",
       "1          6CD4sp  \n",
       "2          6CD4sp  \n",
       "3          6CD4sp  \n",
       "4          6CD4sp  \n",
       "...           ...  \n",
       "17568151    4DPre  \n",
       "17568152    4DPre  \n",
       "17568153    4DPre  \n",
       "17568154    4DPre  \n",
       "17568155    4DPre  \n",
       "\n",
       "[17568156 rows x 5 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp_df_join"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "# slightly easier way to make this df\n",
    "exp_alt = exp.transpose()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp_alt.columns = exp_alt.loc['gene_id']\n",
    "\n",
    "exp_alt = exp_alt.drop(labels = 'gene_id', axis = 0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "# make column for barcode\n",
    "gene_names= exp_alt.columns[1:]\n",
    "\n",
    "exp_alt['barcode'] = exp_alt.index\n",
    "\n",
    "# exp_alt = exp_alt.reset_index()\n",
    "\n",
    "exp_df2 = exp_alt.merge(id_info[['cell', 'bigstage']], left_on = 'barcode',\n",
    "                          right_on = 'cell')\n",
    "# exp_join = exp_alt.merge(id_info[['cell', 'bigstage']], left_on = 'barcode',\n",
    "#                           right_on = 'cell')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
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       "      <td>0.0</td>\n",
       "      <td>0.32352</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1.230642</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.218717</td>\n",
       "      <td>0.32352</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>TTTGTCACAAGTCATC-1</td>\n",
       "      <td>3DPbla</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1982</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.875916</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>2.527867</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.318413</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>TTTGTCACACCACCAG-1</td>\n",
       "      <td>4DPre</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1983</th>\n",
       "      <td>0.192193</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.192193</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>3.305255</td>\n",
       "      <td>0.192193</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.044241</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>TTTGTCACACTTGGAT-1</td>\n",
       "      <td>3DPbla</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1984</th>\n",
       "      <td>1.706164</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.80041</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.80041</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>3.069424</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.758743</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>TTTGTCACAGACGCAA-1</td>\n",
       "      <td>6CD4sp</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1985</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.957765</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.957765</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>4.449692</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5.27396</td>\n",
       "      <td>0.957765</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.908289</td>\n",
       "      <td>0.957765</td>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>4DPre</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1986 rows × 8848 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Mrpl15    Lypla1     Tcea1   Atp6v1h    Rb1cc1 4732440D04Rik  \\\n",
       "0          0.0       0.0       0.0       0.0       0.0           0.0   \n",
       "1          0.0       0.0  1.111742       0.0  1.111742           0.0   \n",
       "2          0.0       0.0       0.0       0.0       0.0           0.0   \n",
       "3          0.0       0.0       0.0  1.044197       0.0           0.0   \n",
       "4     1.033627  0.269895  1.227245       0.0       0.0           0.0   \n",
       "...        ...       ...       ...       ...       ...           ...   \n",
       "1981   0.32352       0.0       0.0       0.0       0.0           0.0   \n",
       "1982       0.0       0.0  1.875916       0.0       0.0           0.0   \n",
       "1983  0.192193       0.0  0.192193       0.0       0.0           0.0   \n",
       "1984  1.706164       0.0       0.0   0.80041       0.0           0.0   \n",
       "1985       0.0  0.957765       0.0       0.0       0.0           0.0   \n",
       "\n",
       "        Pcmtd1      Rrs1   Vcpip1     Sgk3  ...    mt-Nd4    mt-Nd5    mt-Nd6  \\\n",
       "0          0.0       0.0   1.0512      0.0  ...  3.828043    1.0512       0.0   \n",
       "1          0.0       0.0      0.0      0.0  ...  1.903654       0.0       0.0   \n",
       "2          0.0  1.078193      0.0      0.0  ...  3.755879  1.078193  1.078193   \n",
       "3          0.0       0.0      0.0      0.0  ...  3.448532  1.963344       0.0   \n",
       "4     0.269895  0.269895  0.00938  0.00938  ...   3.16904  1.577705       0.0   \n",
       "...        ...       ...      ...      ...  ...       ...       ...       ...   \n",
       "1981   0.32352       0.0      0.0      0.0  ...  1.230642       0.0       0.0   \n",
       "1982       0.0       0.0      0.0      0.0  ...  2.527867       0.0       0.0   \n",
       "1983       0.0       0.0      0.0      0.0  ...  3.305255  0.192193       0.0   \n",
       "1984       0.0       0.0  0.80041      0.0  ...  3.069424       0.0       0.0   \n",
       "1985  0.957765       0.0      0.0      0.0  ...  4.449692       0.0       0.0   \n",
       "\n",
       "       mt-Cytb     Vamp7 AC125149.3 AC149090.1     DHRSX             barcode  \\\n",
       "0      4.52142    1.0512        0.0        0.0       0.0  AAACCTGGTCGACTGC-1   \n",
       "1     2.527867       0.0        0.0        0.0       0.0  AAACGGGAGCTAACAA-1   \n",
       "2      4.25708  1.935039        0.0        0.0       0.0  AAACGGGCACATGGGA-1   \n",
       "3     4.940801  1.044197        0.0        0.0       0.0  AAACGGGGTAGCGTGA-1   \n",
       "4     4.201823   0.00938        0.0        0.0   0.00938  AAACGGGGTATCGCAT-1   \n",
       "...        ...       ...        ...        ...       ...                 ...   \n",
       "1981  3.218717   0.32352        0.0        0.0       0.0  TTTGTCACAAGTCATC-1   \n",
       "1982  4.318413       0.0        0.0        0.0       0.0  TTTGTCACACCACCAG-1   \n",
       "1983  4.044241       0.0        0.0        0.0       0.0  TTTGTCACACTTGGAT-1   \n",
       "1984  4.758743       0.0        0.0        0.0       0.0  TTTGTCACAGACGCAA-1   \n",
       "1985   5.27396  0.957765        0.0   1.908289  0.957765  TTTGTCAGTTAGATGA-1   \n",
       "\n",
       "     bigstage  \n",
       "0      6CD4sp  \n",
       "1       10APC  \n",
       "2      5DPsel  \n",
       "3       4DPre  \n",
       "4      2preDP  \n",
       "...       ...  \n",
       "1981   3DPbla  \n",
       "1982    4DPre  \n",
       "1983   3DPbla  \n",
       "1984   6CD4sp  \n",
       "1985    4DPre  \n",
       "\n",
       "[1986 rows x 8848 columns]"
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp_df2 = exp_df2.drop(labels = 'cell', axis = 1)\n",
    "exp_df2\n",
    "\n",
    "# exp_df2 = exp_df2[['barcode', 'bigstage', gene_names]]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "dfcols = exp_df2.columns.tolist()\n",
    "reorder_cols = dfcols[-2:] + dfcols[:-2]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp_df3 = exp_df2[reorder_cols]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "# exp_df3.to_csv('pivoted_exp.csv', sep = \"\\t\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\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>barcode</th>\n",
       "      <th>bigstage</th>\n",
       "      <th>Mrpl15</th>\n",
       "      <th>Lypla1</th>\n",
       "      <th>Tcea1</th>\n",
       "      <th>Atp6v1h</th>\n",
       "      <th>Rb1cc1</th>\n",
       "      <th>4732440D04Rik</th>\n",
       "      <th>Pcmtd1</th>\n",
       "      <th>Rrs1</th>\n",
       "      <th>...</th>\n",
       "      <th>mt-Nd3</th>\n",
       "      <th>mt-Nd4l</th>\n",
       "      <th>mt-Nd4</th>\n",
       "      <th>mt-Nd5</th>\n",
       "      <th>mt-Nd6</th>\n",
       "      <th>mt-Cytb</th>\n",
       "      <th>Vamp7</th>\n",
       "      <th>AC125149.3</th>\n",
       "      <th>AC149090.1</th>\n",
       "      <th>DHRSX</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AAACCTGGTCGACTGC-1</td>\n",
       "      <td>6CD4sp</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>3.026627</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.828043</td>\n",
       "      <td>1.0512</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.52142</td>\n",
       "      <td>1.0512</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AAACGGGAGCTAACAA-1</td>\n",
       "      <td>10APC</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.111742</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.111742</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.903654</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.527867</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AAACGGGCACATGGGA-1</td>\n",
       "      <td>5DPsel</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.078193</td>\n",
       "      <td>...</td>\n",
       "      <td>2.632782</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.755879</td>\n",
       "      <td>1.078193</td>\n",
       "      <td>1.078193</td>\n",
       "      <td>4.25708</td>\n",
       "      <td>1.935039</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AAACGGGGTAGCGTGA-1</td>\n",
       "      <td>4DPre</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.044197</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1.963344</td>\n",
       "      <td>1.963344</td>\n",
       "      <td>3.448532</td>\n",
       "      <td>1.963344</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.940801</td>\n",
       "      <td>1.044197</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AAACGGGGTATCGCAT-1</td>\n",
       "      <td>2preDP</td>\n",
       "      <td>1.033627</td>\n",
       "      <td>0.269895</td>\n",
       "      <td>1.227245</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.269895</td>\n",
       "      <td>0.269895</td>\n",
       "      <td>...</td>\n",
       "      <td>2.333177</td>\n",
       "      <td>0.269895</td>\n",
       "      <td>3.16904</td>\n",
       "      <td>1.577705</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.201823</td>\n",
       "      <td>0.00938</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.00938</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1981</th>\n",
       "      <td>TTTGTCACAAGTCATC-1</td>\n",
       "      <td>3DPbla</td>\n",
       "      <td>0.32352</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.32352</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.230642</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.218717</td>\n",
       "      <td>0.32352</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1982</th>\n",
       "      <td>TTTGTCACACCACCAG-1</td>\n",
       "      <td>4DPre</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.875916</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1.875916</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.527867</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.318413</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1983</th>\n",
       "      <td>TTTGTCACACTTGGAT-1</td>\n",
       "      <td>3DPbla</td>\n",
       "      <td>0.192193</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.192193</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1.624941</td>\n",
       "      <td>0.192193</td>\n",
       "      <td>3.305255</td>\n",
       "      <td>0.192193</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.044241</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1984</th>\n",
       "      <td>TTTGTCACAGACGCAA-1</td>\n",
       "      <td>6CD4sp</td>\n",
       "      <td>1.706164</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.80041</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>2.770593</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.069424</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.758743</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1985</th>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>4DPre</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.957765</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.957765</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>2.577827</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.449692</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5.27396</td>\n",
       "      <td>0.957765</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.908289</td>\n",
       "      <td>0.957765</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1986 rows × 8848 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                 barcode bigstage    Mrpl15    Lypla1     Tcea1   Atp6v1h  \\\n",
       "0     AAACCTGGTCGACTGC-1   6CD4sp       0.0       0.0       0.0       0.0   \n",
       "1     AAACGGGAGCTAACAA-1    10APC       0.0       0.0  1.111742       0.0   \n",
       "2     AAACGGGCACATGGGA-1   5DPsel       0.0       0.0       0.0       0.0   \n",
       "3     AAACGGGGTAGCGTGA-1    4DPre       0.0       0.0       0.0  1.044197   \n",
       "4     AAACGGGGTATCGCAT-1   2preDP  1.033627  0.269895  1.227245       0.0   \n",
       "...                  ...      ...       ...       ...       ...       ...   \n",
       "1981  TTTGTCACAAGTCATC-1   3DPbla   0.32352       0.0       0.0       0.0   \n",
       "1982  TTTGTCACACCACCAG-1    4DPre       0.0       0.0  1.875916       0.0   \n",
       "1983  TTTGTCACACTTGGAT-1   3DPbla  0.192193       0.0  0.192193       0.0   \n",
       "1984  TTTGTCACAGACGCAA-1   6CD4sp  1.706164       0.0       0.0   0.80041   \n",
       "1985  TTTGTCAGTTAGATGA-1    4DPre       0.0  0.957765       0.0       0.0   \n",
       "\n",
       "        Rb1cc1 4732440D04Rik    Pcmtd1      Rrs1  ...    mt-Nd3   mt-Nd4l  \\\n",
       "0          0.0           0.0       0.0       0.0  ...  3.026627       0.0   \n",
       "1     1.111742           0.0       0.0       0.0  ...       0.0       0.0   \n",
       "2          0.0           0.0       0.0  1.078193  ...  2.632782       0.0   \n",
       "3          0.0           0.0       0.0       0.0  ...  1.963344  1.963344   \n",
       "4          0.0           0.0  0.269895  0.269895  ...  2.333177  0.269895   \n",
       "...        ...           ...       ...       ...  ...       ...       ...   \n",
       "1981       0.0           0.0   0.32352       0.0  ...       0.0       0.0   \n",
       "1982       0.0           0.0       0.0       0.0  ...  1.875916       0.0   \n",
       "1983       0.0           0.0       0.0       0.0  ...  1.624941  0.192193   \n",
       "1984       0.0           0.0       0.0       0.0  ...  2.770593       0.0   \n",
       "1985       0.0           0.0  0.957765       0.0  ...  2.577827       0.0   \n",
       "\n",
       "        mt-Nd4    mt-Nd5    mt-Nd6   mt-Cytb     Vamp7 AC125149.3 AC149090.1  \\\n",
       "0     3.828043    1.0512       0.0   4.52142    1.0512        0.0        0.0   \n",
       "1     1.903654       0.0       0.0  2.527867       0.0        0.0        0.0   \n",
       "2     3.755879  1.078193  1.078193   4.25708  1.935039        0.0        0.0   \n",
       "3     3.448532  1.963344       0.0  4.940801  1.044197        0.0        0.0   \n",
       "4      3.16904  1.577705       0.0  4.201823   0.00938        0.0        0.0   \n",
       "...        ...       ...       ...       ...       ...        ...        ...   \n",
       "1981  1.230642       0.0       0.0  3.218717   0.32352        0.0        0.0   \n",
       "1982  2.527867       0.0       0.0  4.318413       0.0        0.0        0.0   \n",
       "1983  3.305255  0.192193       0.0  4.044241       0.0        0.0        0.0   \n",
       "1984  3.069424       0.0       0.0  4.758743       0.0        0.0        0.0   \n",
       "1985  4.449692       0.0       0.0   5.27396  0.957765        0.0   1.908289   \n",
       "\n",
       "         DHRSX  \n",
       "0          0.0  \n",
       "1          0.0  \n",
       "2          0.0  \n",
       "3          0.0  \n",
       "4      0.00938  \n",
       "...        ...  \n",
       "1981       0.0  \n",
       "1982       0.0  \n",
       "1983       0.0  \n",
       "1984       0.0  \n",
       "1985  0.957765  \n",
       "\n",
       "[1986 rows x 8848 columns]"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp_df3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['6CD4sp', '10APC', '5DPsel', '4DPre', '2preDP', '3DPbla', '1DN',\n",
       "       '7CD8sp', '9NCL'], dtype=object)"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# unique values\n",
    "exp_df3['bigstage'].unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "tcell_stages = id_info['bigstage'].unique()[:-2]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp_df4 = exp_df3.loc[exp_df3['bigstage'].isin(tcell_stages)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['6CD4sp', '5DPsel', '4DPre', '2preDP', '3DPbla', '1DN', '7CD8sp'],\n",
       "      dtype=object)"
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp_df4['bigstage'].unique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [],
   "source": [
    "#rename\n",
    "exp_df5 = exp_df4.copy()\n",
    "# exp_df5 = exp_df4.rename(columns = {\"barcode\": \"index\", \"bigstage\": \"time\", \"\"})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp_df5['time'] = exp_df5['bigstage']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp_df5['time'] = exp_df5['time'].replace({'1DN':1, '2preDP':2, '3DPbla':3, '4DPre':4,\n",
    "                                          '5DPsel':5, '6CD4sp':6, '7CD8sp':6})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "metadata": {},
   "outputs": [],
   "source": [
    "cols_rename = exp_df5.columns.tolist()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "cols_reorder = [cols_rename[0]] + [cols_rename[-1]] + cols_rename[1:-1]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp_df5 = exp_df5[cols_reorder]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>cell_name</th>\n",
       "      <th>time_point</th>\n",
       "      <th>assignment</th>\n",
       "      <th>Mrpl15</th>\n",
       "      <th>Lypla1</th>\n",
       "      <th>Tcea1</th>\n",
       "      <th>Atp6v1h</th>\n",
       "      <th>Rb1cc1</th>\n",
       "      <th>4732440D04Rik</th>\n",
       "      <th>Pcmtd1</th>\n",
       "      <th>...</th>\n",
       "      <th>mt-Nd3</th>\n",
       "      <th>mt-Nd4l</th>\n",
       "      <th>mt-Nd4</th>\n",
       "      <th>mt-Nd5</th>\n",
       "      <th>mt-Nd6</th>\n",
       "      <th>mt-Cytb</th>\n",
       "      <th>Vamp7</th>\n",
       "      <th>AC125149.3</th>\n",
       "      <th>AC149090.1</th>\n",
       "      <th>DHRSX</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>AAACCTGGTCGACTGC-1</td>\n",
       "      <td>6</td>\n",
       "      <td>6CD4sp</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>3.026627</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.828043</td>\n",
       "      <td>1.0512</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.52142</td>\n",
       "      <td>1.0512</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>AAACGGGCACATGGGA-1</td>\n",
       "      <td>5</td>\n",
       "      <td>5DPsel</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>2.632782</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.755879</td>\n",
       "      <td>1.078193</td>\n",
       "      <td>1.078193</td>\n",
       "      <td>4.25708</td>\n",
       "      <td>1.935039</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>AAACGGGGTAGCGTGA-1</td>\n",
       "      <td>4</td>\n",
       "      <td>4DPre</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.044197</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1.963344</td>\n",
       "      <td>1.963344</td>\n",
       "      <td>3.448532</td>\n",
       "      <td>1.963344</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.940801</td>\n",
       "      <td>1.044197</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>AAACGGGGTATCGCAT-1</td>\n",
       "      <td>2</td>\n",
       "      <td>2preDP</td>\n",
       "      <td>1.033627</td>\n",
       "      <td>0.269895</td>\n",
       "      <td>1.227245</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.269895</td>\n",
       "      <td>...</td>\n",
       "      <td>2.333177</td>\n",
       "      <td>0.269895</td>\n",
       "      <td>3.16904</td>\n",
       "      <td>1.577705</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.201823</td>\n",
       "      <td>0.00938</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.00938</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>AAAGATGAGGACCACA-1</td>\n",
       "      <td>3</td>\n",
       "      <td>3DPbla</td>\n",
       "      <td>0.350455</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.350455</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1.599129</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.26997</td>\n",
       "      <td>1.248423</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.659723</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.350455</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1917</th>\n",
       "      <td>TTTGTCACAAGTCATC-1</td>\n",
       "      <td>3</td>\n",
       "      <td>3DPbla</td>\n",
       "      <td>0.32352</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.32352</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.230642</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.218717</td>\n",
       "      <td>0.32352</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1918</th>\n",
       "      <td>TTTGTCACACCACCAG-1</td>\n",
       "      <td>4</td>\n",
       "      <td>4DPre</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.875916</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1.875916</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.527867</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.318413</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1919</th>\n",
       "      <td>TTTGTCACACTTGGAT-1</td>\n",
       "      <td>3</td>\n",
       "      <td>3DPbla</td>\n",
       "      <td>0.192193</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.192193</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>1.624941</td>\n",
       "      <td>0.192193</td>\n",
       "      <td>3.305255</td>\n",
       "      <td>0.192193</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.044241</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1920</th>\n",
       "      <td>TTTGTCACAGACGCAA-1</td>\n",
       "      <td>6</td>\n",
       "      <td>6CD4sp</td>\n",
       "      <td>1.706164</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.80041</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>2.770593</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.069424</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.758743</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1921</th>\n",
       "      <td>TTTGTCAGTTAGATGA-1</td>\n",
       "      <td>4</td>\n",
       "      <td>4DPre</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.957765</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.957765</td>\n",
       "      <td>...</td>\n",
       "      <td>2.577827</td>\n",
       "      <td>0.0</td>\n",
       "      <td>4.449692</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>5.27396</td>\n",
       "      <td>0.957765</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.908289</td>\n",
       "      <td>0.957765</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>1922 rows × 8849 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               cell_name  time_point assignment    Mrpl15    Lypla1     Tcea1  \\\n",
       "0     AAACCTGGTCGACTGC-1           6     6CD4sp       0.0       0.0       0.0   \n",
       "1     AAACGGGCACATGGGA-1           5     5DPsel       0.0       0.0       0.0   \n",
       "2     AAACGGGGTAGCGTGA-1           4      4DPre       0.0       0.0       0.0   \n",
       "3     AAACGGGGTATCGCAT-1           2     2preDP  1.033627  0.269895  1.227245   \n",
       "4     AAAGATGAGGACCACA-1           3     3DPbla  0.350455       0.0  0.350455   \n",
       "...                  ...         ...        ...       ...       ...       ...   \n",
       "1917  TTTGTCACAAGTCATC-1           3     3DPbla   0.32352       0.0       0.0   \n",
       "1918  TTTGTCACACCACCAG-1           4      4DPre       0.0       0.0  1.875916   \n",
       "1919  TTTGTCACACTTGGAT-1           3     3DPbla  0.192193       0.0  0.192193   \n",
       "1920  TTTGTCACAGACGCAA-1           6     6CD4sp  1.706164       0.0       0.0   \n",
       "1921  TTTGTCAGTTAGATGA-1           4      4DPre       0.0  0.957765       0.0   \n",
       "\n",
       "       Atp6v1h Rb1cc1 4732440D04Rik    Pcmtd1  ...    mt-Nd3   mt-Nd4l  \\\n",
       "0          0.0    0.0           0.0       0.0  ...  3.026627       0.0   \n",
       "1          0.0    0.0           0.0       0.0  ...  2.632782       0.0   \n",
       "2     1.044197    0.0           0.0       0.0  ...  1.963344  1.963344   \n",
       "3          0.0    0.0           0.0  0.269895  ...  2.333177  0.269895   \n",
       "4          0.0    0.0           0.0       0.0  ...  1.599129       0.0   \n",
       "...        ...    ...           ...       ...  ...       ...       ...   \n",
       "1917       0.0    0.0           0.0   0.32352  ...       0.0       0.0   \n",
       "1918       0.0    0.0           0.0       0.0  ...  1.875916       0.0   \n",
       "1919       0.0    0.0           0.0       0.0  ...  1.624941  0.192193   \n",
       "1920   0.80041    0.0           0.0       0.0  ...  2.770593       0.0   \n",
       "1921       0.0    0.0           0.0  0.957765  ...  2.577827       0.0   \n",
       "\n",
       "        mt-Nd4    mt-Nd5    mt-Nd6   mt-Cytb     Vamp7 AC125149.3 AC149090.1  \\\n",
       "0     3.828043    1.0512       0.0   4.52142    1.0512        0.0        0.0   \n",
       "1     3.755879  1.078193  1.078193   4.25708  1.935039        0.0        0.0   \n",
       "2     3.448532  1.963344       0.0  4.940801  1.044197        0.0        0.0   \n",
       "3      3.16904  1.577705       0.0  4.201823   0.00938        0.0        0.0   \n",
       "4      3.26997  1.248423       0.0  3.659723       0.0        0.0   0.350455   \n",
       "...        ...       ...       ...       ...       ...        ...        ...   \n",
       "1917  1.230642       0.0       0.0  3.218717   0.32352        0.0        0.0   \n",
       "1918  2.527867       0.0       0.0  4.318413       0.0        0.0        0.0   \n",
       "1919  3.305255  0.192193       0.0  4.044241       0.0        0.0        0.0   \n",
       "1920  3.069424       0.0       0.0  4.758743       0.0        0.0        0.0   \n",
       "1921  4.449692       0.0       0.0   5.27396  0.957765        0.0   1.908289   \n",
       "\n",
       "         DHRSX  \n",
       "0          0.0  \n",
       "1          0.0  \n",
       "2          0.0  \n",
       "3      0.00938  \n",
       "4          0.0  \n",
       "...        ...  \n",
       "1917       0.0  \n",
       "1918       0.0  \n",
       "1919       0.0  \n",
       "1920       0.0  \n",
       "1921  0.957765  \n",
       "\n",
       "[1922 rows x 8849 columns]"
      ]
     },
     "execution_count": 32,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp_df5 = exp_df5.rename(columns = {'barcode':'cell_name', 'time': 'time_point', 'bigstage':'assignment'})\n",
    "exp_df5 = exp_df5.reset_index(drop = True)\n",
    "exp_df5"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [],
   "source": [
    "# exp_df5.to_csv('data/tcell_data.E', sep = \"\\t\", index = False, index_label = False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# example from repo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 149,
   "metadata": {},
   "outputs": [],
   "source": [
    "# from the example repo\n",
    "exdf = pd.read_csv('/net/dali/home/mscbio/aar126/genomics/scdiff2/example/example.E', sep = \"\\t\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 150,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>cell_name</th>\n",
       "      <th>time_point</th>\n",
       "      <th>assignment</th>\n",
       "      <th>0610007C21Rik</th>\n",
       "      <th>0610007L01Rik</th>\n",
       "      <th>0610007N19Rik</th>\n",
       "      <th>0610007P08Rik</th>\n",
       "      <th>0610007P14Rik</th>\n",
       "      <th>0610007P22Rik</th>\n",
       "      <th>0610009B22Rik</th>\n",
       "      <th>...</th>\n",
       "      <th>Zwint</th>\n",
       "      <th>Zxda</th>\n",
       "      <th>Zxdb</th>\n",
       "      <th>Zxdc</th>\n",
       "      <th>Zyg11b</th>\n",
       "      <th>Zyx</th>\n",
       "      <th>Zzef1</th>\n",
       "      <th>Zzz3</th>\n",
       "      <th>l7Rn6</th>\n",
       "      <th>rtTA</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>1_iN2_C02</td>\n",
       "      <td>0</td>\n",
       "      <td>MEF</td>\n",
       "      <td>6.341676</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>5.690383</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>2.556539</td>\n",
       "      <td>...</td>\n",
       "      <td>4.829228</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>2.895336</td>\n",
       "      <td>1.682171</td>\n",
       "      <td>1.139292</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>2.065228</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1_iN2_C05</td>\n",
       "      <td>0</td>\n",
       "      <td>MEF</td>\n",
       "      <td>4.959945</td>\n",
       "      <td>6.231432</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>6.055019</td>\n",
       "      <td>4.024706</td>\n",
       "      <td>4.957429</td>\n",
       "      <td>...</td>\n",
       "      <td>5.320143</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.010157</td>\n",
       "      <td>1.912734</td>\n",
       "      <td>5.838476</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>3.642170</td>\n",
       "      <td>5.092430</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>1_iN2_C07</td>\n",
       "      <td>0</td>\n",
       "      <td>MEF</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>3.888991</td>\n",
       "      <td>0.041368</td>\n",
       "      <td>5.530216</td>\n",
       "      <td>1.793932</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>5.096867</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>2.614466</td>\n",
       "      <td>2.145846</td>\n",
       "      <td>3.864990</td>\n",
       "      <td>1.989720</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>1_iN2_C08</td>\n",
       "      <td>0</td>\n",
       "      <td>MEF</td>\n",
       "      <td>4.697531</td>\n",
       "      <td>3.062912</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.693764</td>\n",
       "      <td>4.297325</td>\n",
       "      <td>4.853152</td>\n",
       "      <td>...</td>\n",
       "      <td>6.068946</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>7.464196</td>\n",
       "      <td>3.407588</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>3.995451</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1_iN2_C09</td>\n",
       "      <td>0</td>\n",
       "      <td>MEF</td>\n",
       "      <td>6.609152</td>\n",
       "      <td>6.627976</td>\n",
       "      <td>5.559868</td>\n",
       "      <td>3.247370</td>\n",
       "      <td>6.673742</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>5.390071</td>\n",
       "      <td>...</td>\n",
       "      <td>6.639057</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>7.933592</td>\n",
       "      <td>1.933924</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>3.627951</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>247</th>\n",
       "      <td>1ggS_iN4_C67</td>\n",
       "      <td>22</td>\n",
       "      <td>Neuron</td>\n",
       "      <td>2.415375</td>\n",
       "      <td>6.725156</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>2.295439</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>4.324884</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>5.542317</td>\n",
       "      <td>0.539820</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>5.958162</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>248</th>\n",
       "      <td>1gL_iN4_C02</td>\n",
       "      <td>22</td>\n",
       "      <td>Fibroblast</td>\n",
       "      <td>6.489037</td>\n",
       "      <td>4.404424</td>\n",
       "      <td>4.184277</td>\n",
       "      <td>2.311201</td>\n",
       "      <td>4.459130</td>\n",
       "      <td>3.554364</td>\n",
       "      <td>6.509553</td>\n",
       "      <td>...</td>\n",
       "      <td>3.597637</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.402421</td>\n",
       "      <td>0.924023</td>\n",
       "      <td>0.571557</td>\n",
       "      <td>4.965917</td>\n",
       "      <td>0.019243</td>\n",
       "      <td>0.975106</td>\n",
       "      <td>4.752770</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>249</th>\n",
       "      <td>1gL_iN4_C31</td>\n",
       "      <td>22</td>\n",
       "      <td>Fibroblast</td>\n",
       "      <td>7.409229</td>\n",
       "      <td>5.107711</td>\n",
       "      <td>4.009006</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>3.430740</td>\n",
       "      <td>2.524009</td>\n",
       "      <td>1.500461</td>\n",
       "      <td>...</td>\n",
       "      <td>5.825282</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>2.183213</td>\n",
       "      <td>1.254021</td>\n",
       "      <td>7.190141</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>5.681482</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>250</th>\n",
       "      <td>1gL_iN4_C39</td>\n",
       "      <td>22</td>\n",
       "      <td>Myocyte</td>\n",
       "      <td>4.128706</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>4.580872</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>6.351578</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.862890</td>\n",
       "      <td>6.099715</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.623088</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>5.621044</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>251</th>\n",
       "      <td>1gM_iN4_C42</td>\n",
       "      <td>22</td>\n",
       "      <td>Fibroblast</td>\n",
       "      <td>6.616127</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>4.209771</td>\n",
       "      <td>5.131456</td>\n",
       "      <td>7.495259</td>\n",
       "      <td>1.837260</td>\n",
       "      <td>5.385572</td>\n",
       "      <td>...</td>\n",
       "      <td>1.604785</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>3.468716</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>6.061304</td>\n",
       "      <td>3.275710</td>\n",
       "      <td>4.260047</td>\n",
       "      <td>4.541520</td>\n",
       "      <td>0.000000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>252 rows × 11838 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        cell_name  time_point  assignment  0610007C21Rik  0610007L01Rik  \\\n",
       "0       1_iN2_C02           0         MEF       6.341676       0.000000   \n",
       "1       1_iN2_C05           0         MEF       4.959945       6.231432   \n",
       "2       1_iN2_C07           0         MEF       0.000000       0.000000   \n",
       "3       1_iN2_C08           0         MEF       4.697531       3.062912   \n",
       "4       1_iN2_C09           0         MEF       6.609152       6.627976   \n",
       "..            ...         ...         ...            ...            ...   \n",
       "247  1ggS_iN4_C67          22      Neuron       2.415375       6.725156   \n",
       "248   1gL_iN4_C02          22  Fibroblast       6.489037       4.404424   \n",
       "249   1gL_iN4_C31          22  Fibroblast       7.409229       5.107711   \n",
       "250   1gL_iN4_C39          22     Myocyte       4.128706       0.000000   \n",
       "251   1gM_iN4_C42          22  Fibroblast       6.616127       0.000000   \n",
       "\n",
       "     0610007N19Rik  0610007P08Rik  0610007P14Rik  0610007P22Rik  \\\n",
       "0         0.000000       0.000000       5.690383       0.000000   \n",
       "1         0.000000       0.000000       6.055019       4.024706   \n",
       "2         3.888991       0.041368       5.530216       1.793932   \n",
       "3         0.000000       0.000000       0.693764       4.297325   \n",
       "4         5.559868       3.247370       6.673742       0.000000   \n",
       "..             ...            ...            ...            ...   \n",
       "247       0.000000       0.000000       0.000000       2.295439   \n",
       "248       4.184277       2.311201       4.459130       3.554364   \n",
       "249       4.009006       0.000000       3.430740       2.524009   \n",
       "250       0.000000       0.000000       4.580872       0.000000   \n",
       "251       4.209771       5.131456       7.495259       1.837260   \n",
       "\n",
       "     0610009B22Rik  ...     Zwint  Zxda      Zxdb      Zxdc    Zyg11b  \\\n",
       "0         2.556539  ...  4.829228   0.0  0.000000  0.000000  2.895336   \n",
       "1         4.957429  ...  5.320143   0.0  0.000000  0.010157  1.912734   \n",
       "2         0.000000  ...  5.096867   0.0  0.000000  0.000000  0.000000   \n",
       "3         4.853152  ...  6.068946   0.0  0.000000  0.000000  0.000000   \n",
       "4         5.390071  ...  6.639057   0.0  0.000000  0.000000  0.000000   \n",
       "..             ...  ...       ...   ...       ...       ...       ...   \n",
       "247       0.000000  ...  4.324884   0.0  0.000000  0.000000  5.542317   \n",
       "248       6.509553  ...  3.597637   0.0  2.402421  0.924023  0.571557   \n",
       "249       1.500461  ...  5.825282   0.0  0.000000  2.183213  1.254021   \n",
       "250       6.351578  ...  0.000000   0.0  0.000000  0.000000  1.862890   \n",
       "251       5.385572  ...  1.604785   0.0  0.000000  3.468716  0.000000   \n",
       "\n",
       "          Zyx     Zzef1      Zzz3     l7Rn6      rtTA  \n",
       "0    1.682171  1.139292  0.000000  2.065228  0.000000  \n",
       "1    5.838476  0.000000  3.642170  5.092430  0.000000  \n",
       "2    2.614466  2.145846  3.864990  1.989720  0.000000  \n",
       "3    7.464196  3.407588  0.000000  3.995451  0.000000  \n",
       "4    7.933592  1.933924  0.000000  3.627951  0.000000  \n",
       "..        ...       ...       ...       ...       ...  \n",
       "247  0.539820  0.000000  0.000000  0.000000  5.958162  \n",
       "248  4.965917  0.019243  0.975106  4.752770  0.000000  \n",
       "249  7.190141  0.000000  0.000000  5.681482  0.000000  \n",
       "250  6.099715  0.000000  1.623088  0.000000  5.621044  \n",
       "251  6.061304  3.275710  4.260047  4.541520  0.000000  \n",
       "\n",
       "[252 rows x 11838 columns]"
      ]
     },
     "execution_count": 150,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exdf"
   ]
  }
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