formated_integrated_data.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 105,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import os"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# expression matrix\n",
    "exp_path = 'TcellDev/Data/T_cell_development/integrated/t_data.txt'\n",
    "\n",
    "# cluster ids and cell type ids\n",
    "id_path = 'TcellDev/Data/T_cell_development/integrated/cluster_pseudotime.txt'"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp = pd.read_csv(exp_path, sep = \"\\t\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp = exp.rename(columns = {'Unnamed: 0':'gene_id'})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</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>TACGGTATCAGTTAGC_1</th>\n",
       "      <th>CGTTCTGGTAGAAAGG_1</th>\n",
       "      <th>TGAGAGGGTACGAAAT_1</th>\n",
       "      <th>GCTCCTATCAGAAATG_2</th>\n",
       "      <th>GCGCGATCAGCCTTTC_2</th>\n",
       "      <th>CTAATGGGTGTTTGTG_1</th>\n",
       "      <th>GTCACAAAGATCGATA_1</th>\n",
       "      <th>GTATTCTGTTGTTTGG_1</th>\n",
       "      <th>AGTCTTTTCACCTTAT_2</th>\n",
       "      <th>...</th>\n",
       "      <th>ATTGGACGTCATATCG_2</th>\n",
       "      <th>ACGGGTCAGCTAGTCT_1</th>\n",
       "      <th>AACTCTTGTATGAATG_1</th>\n",
       "      <th>CCCAATCCATTAACCG_1</th>\n",
       "      <th>CCAGCGACATCTATGG_1</th>\n",
       "      <th>CCCAGTTCACAAGTAA_1</th>\n",
       "      <th>TTGGAACCATGCGCAC_1</th>\n",
       "      <th>CTGTGCTAGCTTCGCG_2</th>\n",
       "      <th>TGCGCAGGTGCGCTTG_2</th>\n",
       "      <th>GTGGGTCCAGCCTTTC_1</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>Mrpl15</td>\n",
       "      <td>0.850588</td>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.888734</td>\n",
       "      <td>1.324457</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.9919</td>\n",
       "      <td>0.915991</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.901838</td>\n",
       "      <td>1.096749</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.645935</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.00000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>Lypla1</td>\n",
       "      <td>0.850588</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.9919</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.095158</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.358346</td>\n",
       "      <td>0.90859</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>Tcea1</td>\n",
       "      <td>0.850588</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.9919</td>\n",
       "      <td>0.915991</td>\n",
       "      <td>1.095158</td>\n",
       "      <td>...</td>\n",
       "      <td>0.799977</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.901838</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.645935</td>\n",
       "      <td>0.712599</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.90859</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>Atp6v1h</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.00000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.450139</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.095158</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.358346</td>\n",
       "      <td>0.00000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>Rb1cc1</td>\n",
       "      <td>0.850588</td>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.78639</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.652350</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0000</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.605291</td>\n",
       "      <td>...</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>1.096749</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.035154</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>0.893995</td>\n",
       "      <td>0.00000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 3186 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   gene_id  TACGGTATCAGTTAGC_1  CGTTCTGGTAGAAAGG_1  TGAGAGGGTACGAAAT_1  \\\n",
       "0   Mrpl15            0.850588            1.068103             0.00000   \n",
       "1   Lypla1            0.850588            0.000000             0.00000   \n",
       "2    Tcea1            0.850588            0.000000             0.00000   \n",
       "3  Atp6v1h            0.000000            0.000000             0.00000   \n",
       "4   Rb1cc1            0.850588            1.068103             0.78639   \n",
       "\n",
       "   GCTCCTATCAGAAATG_2  GCGCGATCAGCCTTTC_2  CTAATGGGTGTTTGTG_1  \\\n",
       "0            0.888734            1.324457            0.000000   \n",
       "1            0.000000            0.000000            0.000000   \n",
       "2            0.000000            0.000000            0.000000   \n",
       "3            0.000000            0.000000            1.450139   \n",
       "4            0.000000            0.652350            0.000000   \n",
       "\n",
       "   GTCACAAAGATCGATA_1  GTATTCTGTTGTTTGG_1  AGTCTTTTCACCTTAT_2  ...  \\\n",
       "0              0.9919            0.915991            0.000000  ...   \n",
       "1              0.9919            0.000000            1.095158  ...   \n",
       "2              0.9919            0.915991            1.095158  ...   \n",
       "3              0.0000            0.000000            1.095158  ...   \n",
       "4              0.0000            0.000000            1.605291  ...   \n",
       "\n",
       "   ATTGGACGTCATATCG_2  ACGGGTCAGCTAGTCT_1  AACTCTTGTATGAATG_1  \\\n",
       "0            0.000000                 0.0                 0.0   \n",
       "1            0.000000                 0.0                 0.0   \n",
       "2            0.799977                 0.0                 0.0   \n",
       "3            0.000000                 0.0                 0.0   \n",
       "4            0.000000                 0.0                 0.0   \n",
       "\n",
       "   CCCAATCCATTAACCG_1  CCAGCGACATCTATGG_1  CCCAGTTCACAAGTAA_1  \\\n",
       "0            0.901838            1.096749                 0.0   \n",
       "1            0.000000            0.000000                 0.0   \n",
       "2            0.901838            0.000000                 0.0   \n",
       "3            0.000000            0.000000                 0.0   \n",
       "4            0.000000            1.096749                 0.0   \n",
       "\n",
       "   TTGGAACCATGCGCAC_1  CTGTGCTAGCTTCGCG_2  TGCGCAGGTGCGCTTG_2  \\\n",
       "0            0.645935            0.000000            0.000000   \n",
       "1            0.000000            0.000000            1.358346   \n",
       "2            0.645935            0.712599            0.000000   \n",
       "3            0.000000            0.000000            1.358346   \n",
       "4            1.035154            0.000000            0.893995   \n",
       "\n",
       "   GTGGGTCCAGCCTTTC_1  \n",
       "0             0.00000  \n",
       "1             0.90859  \n",
       "2             0.90859  \n",
       "3             0.00000  \n",
       "4             0.00000  \n",
       "\n",
       "[5 rows x 3186 columns]"
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(14414, 3186)"
      ]
     },
     "execution_count": 28,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "id_info = pd.read_csv(id_path, sep = \"\\t\")\n",
    "id_info = id_info.rename(columns = {'Unnamed: 0':'barcode'})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>barcode</th>\n",
       "      <th>orig.ident</th>\n",
       "      <th>nCount_RNA</th>\n",
       "      <th>nFeature_RNA</th>\n",
       "      <th>percent.mt</th>\n",
       "      <th>stim</th>\n",
       "      <th>seurat_clusters</th>\n",
       "      <th>RNA_snn_res.1</th>\n",
       "      <th>stage</th>\n",
       "      <th>bigstage</th>\n",
       "      <th>color</th>\n",
       "      <th>PBA_order</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TACGGTATCAGTTAGC_1</td>\n",
       "      <td>Self</td>\n",
       "      <td>7457</td>\n",
       "      <td>2156</td>\n",
       "      <td>3.728041</td>\n",
       "      <td>Self</td>\n",
       "      <td>12</td>\n",
       "      <td>12</td>\n",
       "      <td>DN</td>\n",
       "      <td>DN</td>\n",
       "      <td>darkcyan</td>\n",
       "      <td>0.211898</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CGTTCTGGTAGAAAGG_1</td>\n",
       "      <td>Self</td>\n",
       "      <td>5236</td>\n",
       "      <td>1991</td>\n",
       "      <td>3.781513</td>\n",
       "      <td>Self</td>\n",
       "      <td>12</td>\n",
       "      <td>12</td>\n",
       "      <td>DN</td>\n",
       "      <td>DN</td>\n",
       "      <td>darkcyan</td>\n",
       "      <td>0.239283</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TGAGAGGGTACGAAAT_1</td>\n",
       "      <td>Self</td>\n",
       "      <td>8365</td>\n",
       "      <td>2529</td>\n",
       "      <td>3.371189</td>\n",
       "      <td>Self</td>\n",
       "      <td>12</td>\n",
       "      <td>12</td>\n",
       "      <td>DN</td>\n",
       "      <td>DN</td>\n",
       "      <td>darkcyan</td>\n",
       "      <td>0.218463</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GCTCCTATCAGAAATG_2</td>\n",
       "      <td>Tabula</td>\n",
       "      <td>6983</td>\n",
       "      <td>2507</td>\n",
       "      <td>2.420163</td>\n",
       "      <td>Tabula</td>\n",
       "      <td>12</td>\n",
       "      <td>12</td>\n",
       "      <td>DN</td>\n",
       "      <td>DN</td>\n",
       "      <td>darkcyan</td>\n",
       "      <td>0.227197</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GCGCGATCAGCCTTTC_2</td>\n",
       "      <td>Tabula</td>\n",
       "      <td>10869</td>\n",
       "      <td>3112</td>\n",
       "      <td>2.474929</td>\n",
       "      <td>Tabula</td>\n",
       "      <td>12</td>\n",
       "      <td>12</td>\n",
       "      <td>DN</td>\n",
       "      <td>DN</td>\n",
       "      <td>darkcyan</td>\n",
       "      <td>0.251930</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3180</th>\n",
       "      <td>CCCAGTTCACAAGTAA_1</td>\n",
       "      <td>Self</td>\n",
       "      <td>4297</td>\n",
       "      <td>1539</td>\n",
       "      <td>2.885734</td>\n",
       "      <td>Self</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>CD8</td>\n",
       "      <td>CD8</td>\n",
       "      <td>#BB4A94</td>\n",
       "      <td>1.535600</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3181</th>\n",
       "      <td>TTGGAACCATGCGCAC_1</td>\n",
       "      <td>Self</td>\n",
       "      <td>11016</td>\n",
       "      <td>2793</td>\n",
       "      <td>2.995643</td>\n",
       "      <td>Self</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>CD8</td>\n",
       "      <td>CD8</td>\n",
       "      <td>#BB4A94</td>\n",
       "      <td>1.301503</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3182</th>\n",
       "      <td>CTGTGCTAGCTTCGCG_2</td>\n",
       "      <td>Tabula</td>\n",
       "      <td>9622</td>\n",
       "      <td>2334</td>\n",
       "      <td>2.525462</td>\n",
       "      <td>Tabula</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>CD8</td>\n",
       "      <td>CD8</td>\n",
       "      <td>#BB4A94</td>\n",
       "      <td>1.524193</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3183</th>\n",
       "      <td>TGCGCAGGTGCGCTTG_2</td>\n",
       "      <td>Tabula</td>\n",
       "      <td>6921</td>\n",
       "      <td>2322</td>\n",
       "      <td>2.225112</td>\n",
       "      <td>Tabula</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>CD8</td>\n",
       "      <td>CD8</td>\n",
       "      <td>#BB4A94</td>\n",
       "      <td>1.501979</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3184</th>\n",
       "      <td>GTGGGTCCAGCCTTTC_1</td>\n",
       "      <td>Self</td>\n",
       "      <td>6753</td>\n",
       "      <td>1770</td>\n",
       "      <td>2.532208</td>\n",
       "      <td>Self</td>\n",
       "      <td>8</td>\n",
       "      <td>8</td>\n",
       "      <td>CD8</td>\n",
       "      <td>CD8</td>\n",
       "      <td>#BB4A94</td>\n",
       "      <td>1.524600</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3185 rows × 12 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                 barcode orig.ident  nCount_RNA  nFeature_RNA  percent.mt  \\\n",
       "0     TACGGTATCAGTTAGC_1       Self        7457          2156    3.728041   \n",
       "1     CGTTCTGGTAGAAAGG_1       Self        5236          1991    3.781513   \n",
       "2     TGAGAGGGTACGAAAT_1       Self        8365          2529    3.371189   \n",
       "3     GCTCCTATCAGAAATG_2     Tabula        6983          2507    2.420163   \n",
       "4     GCGCGATCAGCCTTTC_2     Tabula       10869          3112    2.474929   \n",
       "...                  ...        ...         ...           ...         ...   \n",
       "3180  CCCAGTTCACAAGTAA_1       Self        4297          1539    2.885734   \n",
       "3181  TTGGAACCATGCGCAC_1       Self       11016          2793    2.995643   \n",
       "3182  CTGTGCTAGCTTCGCG_2     Tabula        9622          2334    2.525462   \n",
       "3183  TGCGCAGGTGCGCTTG_2     Tabula        6921          2322    2.225112   \n",
       "3184  GTGGGTCCAGCCTTTC_1       Self        6753          1770    2.532208   \n",
       "\n",
       "        stim  seurat_clusters  RNA_snn_res.1 stage bigstage     color  \\\n",
       "0       Self               12             12    DN       DN  darkcyan   \n",
       "1       Self               12             12    DN       DN  darkcyan   \n",
       "2       Self               12             12    DN       DN  darkcyan   \n",
       "3     Tabula               12             12    DN       DN  darkcyan   \n",
       "4     Tabula               12             12    DN       DN  darkcyan   \n",
       "...      ...              ...            ...   ...      ...       ...   \n",
       "3180    Self                8              8   CD8      CD8   #BB4A94   \n",
       "3181    Self                8              8   CD8      CD8   #BB4A94   \n",
       "3182  Tabula                8              8   CD8      CD8   #BB4A94   \n",
       "3183  Tabula                8              8   CD8      CD8   #BB4A94   \n",
       "3184    Self                8              8   CD8      CD8   #BB4A94   \n",
       "\n",
       "      PBA_order  \n",
       "0      0.211898  \n",
       "1      0.239283  \n",
       "2      0.218463  \n",
       "3      0.227197  \n",
       "4      0.251930  \n",
       "...         ...  \n",
       "3180   1.535600  \n",
       "3181   1.301503  \n",
       "3182   1.524193  \n",
       "3183   1.501979  \n",
       "3184   1.524600  \n",
       "\n",
       "[3185 rows x 12 columns]"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "id_info"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "metadata": {},
   "outputs": [],
   "source": [
    "# transpose \n",
    "exp_alt = exp.transpose()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "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": 76,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp_alt['barcode'] = exp_alt.index"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp_alt = exp_alt.reset_index(drop = True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 81,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th>gene_id</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>Gm26901</th>\n",
       "      <th>Rrs1</th>\n",
       "      <th>Mybl1</th>\n",
       "      <th>...</th>\n",
       "      <th>Rbp4</th>\n",
       "      <th>Plce1</th>\n",
       "      <th>Gm16244</th>\n",
       "      <th>Gpam</th>\n",
       "      <th>Gm9529</th>\n",
       "      <th>Gm7102</th>\n",
       "      <th>AC133103.1</th>\n",
       "      <th>AC132444.1</th>\n",
       "      <th>AC125149.2</th>\n",
       "      <th>barcode</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0.850588</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>TACGGTATCAGTTAGC_1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.068103</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>CGTTCTGGTAGAAAGG_1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.78639</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.523089</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.78639</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>0.0</td>\n",
       "      <td>TGAGAGGGTACGAAAT_1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.888734</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>1.351728</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>GCTCCTATCAGAAATG_2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1.324457</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.65235</td>\n",
       "      <td>0.65235</td>\n",
       "      <td>1.043838</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.043838</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>0.0</td>\n",
       "      <td>GCGCGATCAGCCTTTC_2</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",
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       "    <tr>\n",
       "      <th>3180</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
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       "      <td>0.0</td>\n",
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       "      <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>CCCAGTTCACAAGTAA_1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3181</th>\n",
       "      <td>0.645935</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.645935</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.035154</td>\n",
       "      <td>0.645935</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",
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       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
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       "      <td>TTGGAACCATGCGCAC_1</td>\n",
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       "    <tr>\n",
       "      <th>3182</th>\n",
       "      <td>0.0</td>\n",
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       "      <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>CTGTGCTAGCTTCGCG_2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3183</th>\n",
       "      <td>0.0</td>\n",
       "      <td>1.358346</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.358346</td>\n",
       "      <td>0.893995</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",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>TGCGCAGGTGCGCTTG_2</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3184</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.90859</td>\n",
       "      <td>0.90859</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>1.37666</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>0.0</td>\n",
       "      <td>GTGGGTCCAGCCTTTC_1</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3185 rows × 14415 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "gene_id    Mrpl15    Lypla1     Tcea1   Atp6v1h    Rb1cc1 4732440D04Rik  \\\n",
       "0        0.850588  0.850588  0.850588       0.0  0.850588           0.0   \n",
       "1        1.068103       0.0       0.0       0.0  1.068103           0.0   \n",
       "2             0.0       0.0       0.0       0.0   0.78639           0.0   \n",
       "3        0.888734       0.0       0.0       0.0       0.0           0.0   \n",
       "4        1.324457       0.0       0.0       0.0   0.65235       0.65235   \n",
       "...           ...       ...       ...       ...       ...           ...   \n",
       "3180          0.0       0.0       0.0       0.0       0.0           0.0   \n",
       "3181     0.645935       0.0  0.645935       0.0  1.035154      0.645935   \n",
       "3182          0.0       0.0  0.712599       0.0       0.0           0.0   \n",
       "3183          0.0  1.358346       0.0  1.358346  0.893995           0.0   \n",
       "3184          0.0   0.90859   0.90859       0.0       0.0           0.0   \n",
       "\n",
       "gene_id    Pcmtd1 Gm26901      Rrs1 Mybl1  ... Rbp4 Plce1 Gm16244 Gpam Gm9529  \\\n",
       "0             0.0     0.0       0.0   0.0  ...  0.0   0.0     0.0  0.0    0.0   \n",
       "1        1.068103     0.0  1.068103   0.0  ...  0.0   0.0     0.0  0.0    0.0   \n",
       "2        1.523089     0.0   0.78639   0.0  ...  0.0   0.0     0.0  0.0    0.0   \n",
       "3             0.0     0.0  1.351728   0.0  ...  0.0   0.0     0.0  0.0    0.0   \n",
       "4        1.043838     0.0  1.043838   0.0  ...  0.0   0.0     0.0  0.0    0.0   \n",
       "...           ...     ...       ...   ...  ...  ...   ...     ...  ...    ...   \n",
       "3180          0.0     0.0       0.0   0.0  ...  0.0   0.0     0.0  0.0    0.0   \n",
       "3181          0.0     0.0       0.0   0.0  ...  0.0   0.0     0.0  0.0    0.0   \n",
       "3182          0.0     0.0       0.0   0.0  ...  0.0   0.0     0.0  0.0    0.0   \n",
       "3183          0.0     0.0       0.0   0.0  ...  0.0   0.0     0.0  0.0    0.0   \n",
       "3184          0.0     0.0   1.37666   0.0  ...  0.0   0.0     0.0  0.0    0.0   \n",
       "\n",
       "gene_id Gm7102 AC133103.1 AC132444.1 AC125149.2             barcode  \n",
       "0          0.0        0.0        0.0        0.0  TACGGTATCAGTTAGC_1  \n",
       "1          0.0        0.0        0.0        0.0  CGTTCTGGTAGAAAGG_1  \n",
       "2          0.0        0.0        0.0        0.0  TGAGAGGGTACGAAAT_1  \n",
       "3          0.0        0.0        0.0        0.0  GCTCCTATCAGAAATG_2  \n",
       "4          0.0        0.0        0.0        0.0  GCGCGATCAGCCTTTC_2  \n",
       "...        ...        ...        ...        ...                 ...  \n",
       "3180       0.0        0.0        0.0        0.0  CCCAGTTCACAAGTAA_1  \n",
       "3181       0.0        0.0        0.0        0.0  TTGGAACCATGCGCAC_1  \n",
       "3182       0.0        0.0        0.0        0.0  CTGTGCTAGCTTCGCG_2  \n",
       "3183       0.0        0.0        0.0        0.0  TGCGCAGGTGCGCTTG_2  \n",
       "3184       0.0        0.0        0.0        0.0  GTGGGTCCAGCCTTTC_1  \n",
       "\n",
       "[3185 rows x 14415 columns]"
      ]
     },
     "execution_count": 81,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp_alt"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 82,
   "metadata": {},
   "outputs": [],
   "source": [
    "# left join to get IDs for barcodes\n",
    "exp_df_join = exp_alt.merge(id_info[['barcode', 'bigstage']], left_on = 'barcode',\n",
    "                          right_on = 'barcode')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Mrpl15</th>\n",
       "      <th>Lypla1</th>\n",
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       "      <th>barcode</th>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>TACGGTATCAGTTAGC_1</td>\n",
       "      <td>1DN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>CGTTCTGGTAGAAAGG_1</td>\n",
       "      <td>1DN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.78639</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.523089</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.78639</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>TGAGAGGGTACGAAAT_1</td>\n",
       "      <td>1DN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.888734</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>1.351728</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>GCTCCTATCAGAAATG_2</td>\n",
       "      <td>1DN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1.324457</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.65235</td>\n",
       "      <td>0.65235</td>\n",
       "      <td>1.043838</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.043838</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>GCGCGATCAGCCTTTC_2</td>\n",
       "      <td>1DN</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>3180</th>\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>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>CCCAGTTCACAAGTAA_1</td>\n",
       "      <td>7CD8sp</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3181</th>\n",
       "      <td>0.645935</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.645935</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.035154</td>\n",
       "      <td>0.645935</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>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>TTGGAACCATGCGCAC_1</td>\n",
       "      <td>7CD8sp</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3182</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.712599</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>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>CTGTGCTAGCTTCGCG_2</td>\n",
       "      <td>7CD8sp</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3183</th>\n",
       "      <td>0.0</td>\n",
       "      <td>1.358346</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.358346</td>\n",
       "      <td>0.893995</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>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>TGCGCAGGTGCGCTTG_2</td>\n",
       "      <td>7CD8sp</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3184</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.90859</td>\n",
       "      <td>0.90859</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>1.37666</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>GTGGGTCCAGCCTTTC_1</td>\n",
       "      <td>7CD8sp</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3185 rows × 14416 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Mrpl15    Lypla1     Tcea1   Atp6v1h    Rb1cc1 4732440D04Rik  \\\n",
       "0     0.850588  0.850588  0.850588       0.0  0.850588           0.0   \n",
       "1     1.068103       0.0       0.0       0.0  1.068103           0.0   \n",
       "2          0.0       0.0       0.0       0.0   0.78639           0.0   \n",
       "3     0.888734       0.0       0.0       0.0       0.0           0.0   \n",
       "4     1.324457       0.0       0.0       0.0   0.65235       0.65235   \n",
       "...        ...       ...       ...       ...       ...           ...   \n",
       "3180       0.0       0.0       0.0       0.0       0.0           0.0   \n",
       "3181  0.645935       0.0  0.645935       0.0  1.035154      0.645935   \n",
       "3182       0.0       0.0  0.712599       0.0       0.0           0.0   \n",
       "3183       0.0  1.358346       0.0  1.358346  0.893995           0.0   \n",
       "3184       0.0   0.90859   0.90859       0.0       0.0           0.0   \n",
       "\n",
       "        Pcmtd1 Gm26901      Rrs1 Mybl1  ... Plce1 Gm16244 Gpam Gm9529 Gm7102  \\\n",
       "0          0.0     0.0       0.0   0.0  ...   0.0     0.0  0.0    0.0    0.0   \n",
       "1     1.068103     0.0  1.068103   0.0  ...   0.0     0.0  0.0    0.0    0.0   \n",
       "2     1.523089     0.0   0.78639   0.0  ...   0.0     0.0  0.0    0.0    0.0   \n",
       "3          0.0     0.0  1.351728   0.0  ...   0.0     0.0  0.0    0.0    0.0   \n",
       "4     1.043838     0.0  1.043838   0.0  ...   0.0     0.0  0.0    0.0    0.0   \n",
       "...        ...     ...       ...   ...  ...   ...     ...  ...    ...    ...   \n",
       "3180       0.0     0.0       0.0   0.0  ...   0.0     0.0  0.0    0.0    0.0   \n",
       "3181       0.0     0.0       0.0   0.0  ...   0.0     0.0  0.0    0.0    0.0   \n",
       "3182       0.0     0.0       0.0   0.0  ...   0.0     0.0  0.0    0.0    0.0   \n",
       "3183       0.0     0.0       0.0   0.0  ...   0.0     0.0  0.0    0.0    0.0   \n",
       "3184       0.0     0.0   1.37666   0.0  ...   0.0     0.0  0.0    0.0    0.0   \n",
       "\n",
       "     AC133103.1 AC132444.1 AC125149.2             barcode bigstage  \n",
       "0           0.0        0.0        0.0  TACGGTATCAGTTAGC_1      1DN  \n",
       "1           0.0        0.0        0.0  CGTTCTGGTAGAAAGG_1      1DN  \n",
       "2           0.0        0.0        0.0  TGAGAGGGTACGAAAT_1      1DN  \n",
       "3           0.0        0.0        0.0  GCTCCTATCAGAAATG_2      1DN  \n",
       "4           0.0        0.0        0.0  GCGCGATCAGCCTTTC_2      1DN  \n",
       "...         ...        ...        ...                 ...      ...  \n",
       "3180        0.0        0.0        0.0  CCCAGTTCACAAGTAA_1   7CD8sp  \n",
       "3181        0.0        0.0        0.0  TTGGAACCATGCGCAC_1   7CD8sp  \n",
       "3182        0.0        0.0        0.0  CTGTGCTAGCTTCGCG_2   7CD8sp  \n",
       "3183        0.0        0.0        0.0  TGCGCAGGTGCGCTTG_2   7CD8sp  \n",
       "3184        0.0        0.0        0.0  GTGGGTCCAGCCTTTC_1   7CD8sp  \n",
       "\n",
       "[3185 rows x 14416 columns]"
      ]
     },
     "execution_count": 87,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp_df_join"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "metadata": {},
   "outputs": [],
   "source": [
    "# rename these to match\n",
    "exp_df_join['bigstage'] = exp_df_join['bigstage'].replace({'DN': '1DN', 'ISP': '2preDP', 'DPbla':'3DPbla',\n",
    "                                        'DPre': '4DPre', 'DPsel': '5DPsel', 'CD4': '6CD4sp',\n",
    "                                        'CD8': '7CD8sp'})\n",
    "\n",
    "\n",
    "# array(['6CD4sp', '10APC', '5DPsel', '4DPre', '2preDP', '3DPbla', '1DN',\n",
    "#        '7CD8sp', '9NCL']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 89,
   "metadata": {},
   "outputs": [],
   "source": [
    "# add time column\n",
    "exp_df_join['time'] = exp_df_join['bigstage'].replace({'1DN':1, '2preDP':2, '3DPbla':3, '4DPre':4,\n",
    "                                          '5DPsel':5, '6CD4sp':6, '7CD8sp':6})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>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>Gm26901</th>\n",
       "      <th>Rrs1</th>\n",
       "      <th>Mybl1</th>\n",
       "      <th>...</th>\n",
       "      <th>Gm16244</th>\n",
       "      <th>Gpam</th>\n",
       "      <th>Gm9529</th>\n",
       "      <th>Gm7102</th>\n",
       "      <th>AC133103.1</th>\n",
       "      <th>AC132444.1</th>\n",
       "      <th>AC125149.2</th>\n",
       "      <th>barcode</th>\n",
       "      <th>bigstage</th>\n",
       "      <th>time</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0.850588</td>\n",
       "      <td>0.850588</td>\n",
       "      <td>0.850588</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.850588</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>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>TACGGTATCAGTTAGC_1</td>\n",
       "      <td>1DN</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>CGTTCTGGTAGAAAGG_1</td>\n",
       "      <td>1DN</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.78639</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.523089</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.78639</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>TGAGAGGGTACGAAAT_1</td>\n",
       "      <td>1DN</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>0.888734</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>1.351728</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>GCTCCTATCAGAAATG_2</td>\n",
       "      <td>1DN</td>\n",
       "      <td>1</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>1.324457</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.65235</td>\n",
       "      <td>0.65235</td>\n",
       "      <td>1.043838</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.043838</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>GCGCGATCAGCCTTTC_2</td>\n",
       "      <td>1DN</td>\n",
       "      <td>1</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>3180</th>\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>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>CCCAGTTCACAAGTAA_1</td>\n",
       "      <td>7CD8sp</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3181</th>\n",
       "      <td>0.645935</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.645935</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.035154</td>\n",
       "      <td>0.645935</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>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>TTGGAACCATGCGCAC_1</td>\n",
       "      <td>7CD8sp</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3182</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.712599</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>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>CTGTGCTAGCTTCGCG_2</td>\n",
       "      <td>7CD8sp</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3183</th>\n",
       "      <td>0.0</td>\n",
       "      <td>1.358346</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.358346</td>\n",
       "      <td>0.893995</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>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>TGCGCAGGTGCGCTTG_2</td>\n",
       "      <td>7CD8sp</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3184</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.90859</td>\n",
       "      <td>0.90859</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>1.37666</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>GTGGGTCCAGCCTTTC_1</td>\n",
       "      <td>7CD8sp</td>\n",
       "      <td>6</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3185 rows × 14417 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "        Mrpl15    Lypla1     Tcea1   Atp6v1h    Rb1cc1 4732440D04Rik  \\\n",
       "0     0.850588  0.850588  0.850588       0.0  0.850588           0.0   \n",
       "1     1.068103       0.0       0.0       0.0  1.068103           0.0   \n",
       "2          0.0       0.0       0.0       0.0   0.78639           0.0   \n",
       "3     0.888734       0.0       0.0       0.0       0.0           0.0   \n",
       "4     1.324457       0.0       0.0       0.0   0.65235       0.65235   \n",
       "...        ...       ...       ...       ...       ...           ...   \n",
       "3180       0.0       0.0       0.0       0.0       0.0           0.0   \n",
       "3181  0.645935       0.0  0.645935       0.0  1.035154      0.645935   \n",
       "3182       0.0       0.0  0.712599       0.0       0.0           0.0   \n",
       "3183       0.0  1.358346       0.0  1.358346  0.893995           0.0   \n",
       "3184       0.0   0.90859   0.90859       0.0       0.0           0.0   \n",
       "\n",
       "        Pcmtd1 Gm26901      Rrs1 Mybl1  ... Gm16244 Gpam Gm9529 Gm7102  \\\n",
       "0          0.0     0.0       0.0   0.0  ...     0.0  0.0    0.0    0.0   \n",
       "1     1.068103     0.0  1.068103   0.0  ...     0.0  0.0    0.0    0.0   \n",
       "2     1.523089     0.0   0.78639   0.0  ...     0.0  0.0    0.0    0.0   \n",
       "3          0.0     0.0  1.351728   0.0  ...     0.0  0.0    0.0    0.0   \n",
       "4     1.043838     0.0  1.043838   0.0  ...     0.0  0.0    0.0    0.0   \n",
       "...        ...     ...       ...   ...  ...     ...  ...    ...    ...   \n",
       "3180       0.0     0.0       0.0   0.0  ...     0.0  0.0    0.0    0.0   \n",
       "3181       0.0     0.0       0.0   0.0  ...     0.0  0.0    0.0    0.0   \n",
       "3182       0.0     0.0       0.0   0.0  ...     0.0  0.0    0.0    0.0   \n",
       "3183       0.0     0.0       0.0   0.0  ...     0.0  0.0    0.0    0.0   \n",
       "3184       0.0     0.0   1.37666   0.0  ...     0.0  0.0    0.0    0.0   \n",
       "\n",
       "     AC133103.1 AC132444.1 AC125149.2             barcode bigstage time  \n",
       "0           0.0        0.0        0.0  TACGGTATCAGTTAGC_1      1DN    1  \n",
       "1           0.0        0.0        0.0  CGTTCTGGTAGAAAGG_1      1DN    1  \n",
       "2           0.0        0.0        0.0  TGAGAGGGTACGAAAT_1      1DN    1  \n",
       "3           0.0        0.0        0.0  GCTCCTATCAGAAATG_2      1DN    1  \n",
       "4           0.0        0.0        0.0  GCGCGATCAGCCTTTC_2      1DN    1  \n",
       "...         ...        ...        ...                 ...      ...  ...  \n",
       "3180        0.0        0.0        0.0  CCCAGTTCACAAGTAA_1   7CD8sp    6  \n",
       "3181        0.0        0.0        0.0  TTGGAACCATGCGCAC_1   7CD8sp    6  \n",
       "3182        0.0        0.0        0.0  CTGTGCTAGCTTCGCG_2   7CD8sp    6  \n",
       "3183        0.0        0.0        0.0  TGCGCAGGTGCGCTTG_2   7CD8sp    6  \n",
       "3184        0.0        0.0        0.0  GTGGGTCCAGCCTTTC_1   7CD8sp    6  \n",
       "\n",
       "[3185 rows x 14417 columns]"
      ]
     },
     "execution_count": 90,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp_df_join"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 91,
   "metadata": {},
   "outputs": [],
   "source": [
    "dfcols = exp_df_join.columns.tolist()\n",
    "reorder_cols = dfcols[-3:] + dfcols[:-3]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 92,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp_df2 = exp_df_join[reorder_cols]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 99,
   "metadata": {},
   "outputs": [],
   "source": [
    "# put time before bistage\n",
    "dfcols = exp_df2.columns.tolist()\n",
    "reorder_cols = [dfcols[0], dfcols[2], dfcols[1]] +  dfcols[3:]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 100,
   "metadata": {},
   "outputs": [],
   "source": [
    "exp_df2 = exp_df2[reorder_cols]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 102,
   "metadata": {},
   "outputs": [],
   "source": [
    "# drop cols with all zeros\n",
    "exp_df3 = exp_df2.loc[:, (exp_df2 != 0).any(axis = 0)]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 103,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>barcode</th>\n",
       "      <th>time</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>...</th>\n",
       "      <th>Ifit1bl2</th>\n",
       "      <th>Rbp4</th>\n",
       "      <th>Plce1</th>\n",
       "      <th>Gm16244</th>\n",
       "      <th>Gpam</th>\n",
       "      <th>Gm9529</th>\n",
       "      <th>Gm7102</th>\n",
       "      <th>AC133103.1</th>\n",
       "      <th>AC132444.1</th>\n",
       "      <th>AC125149.2</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>TACGGTATCAGTTAGC_1</td>\n",
       "      <td>1</td>\n",
       "      <td>1DN</td>\n",
       "      <td>0.850588</td>\n",
       "      <td>0.850588</td>\n",
       "      <td>0.850588</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.850588</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>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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>CGTTCTGGTAGAAAGG_1</td>\n",
       "      <td>1</td>\n",
       "      <td>1DN</td>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.068103</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.068103</td>\n",
       "      <td>...</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>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>TGAGAGGGTACGAAAT_1</td>\n",
       "      <td>1</td>\n",
       "      <td>1DN</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.78639</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.523089</td>\n",
       "      <td>...</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>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>GCTCCTATCAGAAATG_2</td>\n",
       "      <td>1</td>\n",
       "      <td>1DN</td>\n",
       "      <td>0.888734</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>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>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>GCGCGATCAGCCTTTC_2</td>\n",
       "      <td>1</td>\n",
       "      <td>1DN</td>\n",
       "      <td>1.324457</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.65235</td>\n",
       "      <td>0.65235</td>\n",
       "      <td>1.043838</td>\n",
       "      <td>...</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>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "    <tr>\n",
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       "      <td>...</td>\n",
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       "      <td>...</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3180</th>\n",
       "      <td>CCCAGTTCACAAGTAA_1</td>\n",
       "      <td>6</td>\n",
       "      <td>7CD8sp</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>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>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3181</th>\n",
       "      <td>TTGGAACCATGCGCAC_1</td>\n",
       "      <td>6</td>\n",
       "      <td>7CD8sp</td>\n",
       "      <td>0.645935</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.645935</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.035154</td>\n",
       "      <td>0.645935</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</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>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3182</th>\n",
       "      <td>CTGTGCTAGCTTCGCG_2</td>\n",
       "      <td>6</td>\n",
       "      <td>7CD8sp</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.712599</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>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>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3183</th>\n",
       "      <td>TGCGCAGGTGCGCTTG_2</td>\n",
       "      <td>6</td>\n",
       "      <td>7CD8sp</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.358346</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.358346</td>\n",
       "      <td>0.893995</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>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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3184</th>\n",
       "      <td>GTGGGTCCAGCCTTTC_1</td>\n",
       "      <td>6</td>\n",
       "      <td>7CD8sp</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.90859</td>\n",
       "      <td>0.90859</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>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>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>3185 rows × 14369 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                 barcode  time bigstage    Mrpl15    Lypla1     Tcea1  \\\n",
       "0     TACGGTATCAGTTAGC_1     1      1DN  0.850588  0.850588  0.850588   \n",
       "1     CGTTCTGGTAGAAAGG_1     1      1DN  1.068103       0.0       0.0   \n",
       "2     TGAGAGGGTACGAAAT_1     1      1DN       0.0       0.0       0.0   \n",
       "3     GCTCCTATCAGAAATG_2     1      1DN  0.888734       0.0       0.0   \n",
       "4     GCGCGATCAGCCTTTC_2     1      1DN  1.324457       0.0       0.0   \n",
       "...                  ...   ...      ...       ...       ...       ...   \n",
       "3180  CCCAGTTCACAAGTAA_1     6   7CD8sp       0.0       0.0       0.0   \n",
       "3181  TTGGAACCATGCGCAC_1     6   7CD8sp  0.645935       0.0  0.645935   \n",
       "3182  CTGTGCTAGCTTCGCG_2     6   7CD8sp       0.0       0.0  0.712599   \n",
       "3183  TGCGCAGGTGCGCTTG_2     6   7CD8sp       0.0  1.358346       0.0   \n",
       "3184  GTGGGTCCAGCCTTTC_1     6   7CD8sp       0.0   0.90859   0.90859   \n",
       "\n",
       "       Atp6v1h    Rb1cc1 4732440D04Rik    Pcmtd1  ... Ifit1bl2 Rbp4 Plce1  \\\n",
       "0          0.0  0.850588           0.0       0.0  ...      0.0  0.0   0.0   \n",
       "1          0.0  1.068103           0.0  1.068103  ...      0.0  0.0   0.0   \n",
       "2          0.0   0.78639           0.0  1.523089  ...      0.0  0.0   0.0   \n",
       "3          0.0       0.0           0.0       0.0  ...      0.0  0.0   0.0   \n",
       "4          0.0   0.65235       0.65235  1.043838  ...      0.0  0.0   0.0   \n",
       "...        ...       ...           ...       ...  ...      ...  ...   ...   \n",
       "3180       0.0       0.0           0.0       0.0  ...      0.0  0.0   0.0   \n",
       "3181       0.0  1.035154      0.645935       0.0  ...      0.0  0.0   0.0   \n",
       "3182       0.0       0.0           0.0       0.0  ...      0.0  0.0   0.0   \n",
       "3183  1.358346  0.893995           0.0       0.0  ...      0.0  0.0   0.0   \n",
       "3184       0.0       0.0           0.0       0.0  ...      0.0  0.0   0.0   \n",
       "\n",
       "     Gm16244 Gpam Gm9529 Gm7102 AC133103.1 AC132444.1 AC125149.2  \n",
       "0        0.0  0.0    0.0    0.0        0.0        0.0        0.0  \n",
       "1        0.0  0.0    0.0    0.0        0.0        0.0        0.0  \n",
       "2        0.0  0.0    0.0    0.0        0.0        0.0        0.0  \n",
       "3        0.0  0.0    0.0    0.0        0.0        0.0        0.0  \n",
       "4        0.0  0.0    0.0    0.0        0.0        0.0        0.0  \n",
       "...      ...  ...    ...    ...        ...        ...        ...  \n",
       "3180     0.0  0.0    0.0    0.0        0.0        0.0        0.0  \n",
       "3181     0.0  0.0    0.0    0.0        0.0        0.0        0.0  \n",
       "3182     0.0  0.0    0.0    0.0        0.0        0.0        0.0  \n",
       "3183     0.0  0.0    0.0    0.0        0.0        0.0        0.0  \n",
       "3184     0.0  0.0    0.0    0.0        0.0        0.0        0.0  \n",
       "\n",
       "[3185 rows x 14369 columns]"
      ]
     },
     "execution_count": 103,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "exp_df3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 104,
   "metadata": {},
   "outputs": [],
   "source": [
    "# save\n",
    "exp_df3.to_csv('integrated_data.E', sep = \"\\t\", index = 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",
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       "      <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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