logistic regression for prediction from cell population.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Let us try to make a basic prediction using just fit and no pipeline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 150,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 151,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = pd.read_csv('/home/srivastava/Documents/sklearn_work/NK_Cells.csv')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 152,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(40, 58)"
      ]
     },
     "execution_count": 152,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 153,
   "metadata": {},
   "outputs": [],
   "source": [
    "df = df.drop('Donor', axis='columns')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 154,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['Status', '         NK Cells ', '           CD16plus CD56int NK Cells ',\n",
       "       '           CD16plus CD56int CD69plus NK Cells ',\n",
       "       '           CD16plus CD56int NKp44plus NK Cells ',\n",
       "       '           CD16plus CD56int CXCR2hi NK Cells ',\n",
       "       '           CD16plus CD56int CD127plus NK Cells ',\n",
       "       '           CD16plus CD56int NKp46plus NK Cells  ',\n",
       "       '          CD16plus CD56int CD107a NK Cells ',\n",
       "       '           CD16plus CD56int CD2plus NK Cells ',\n",
       "       '           CD16plus CD56int CD56Dim CD62Lplus  NK Cells ',\n",
       "       '          CD16plus CD56int CD244plus  NK Cells ',\n",
       "       '           CD16plus CD56int NK Cells .1',\n",
       "       '           CD16plus CD56int NK Cells .2',\n",
       "       '           CD16plus CD56int NKp30plus  NK Cells ',\n",
       "       '           CD16plus CD56int CD158eplus NK Cells ',\n",
       "       '           CD16plus CD56int CRTH2plus NK Cells ',\n",
       "       '           CD16plus CD56int CD161plus NK Cells ',\n",
       "       '          CD16plus CD56int KIR2DS4plus NK Cells ',\n",
       "       '           CD16plus CD56int CD56 int NKG2D  NK Cells ',\n",
       "       '           CD16plus CD56int NKG2Cplus NK Cells ',\n",
       "       '           CD16plus CD56int CD94plus NK Cells ',\n",
       "       '           CD16plus CD56int CD25plus NK Cells ',\n",
       "       '           CD16plus CD56int CD226plus NK Cells ',\n",
       "       '           CD16plus CD56int CD57plus  NK Cells ',\n",
       "       '           CD16plus CD56int CD57-  NK Cells ',\n",
       "       '           CD16plus CD56int KLRG1plus NK Cells ',\n",
       "       '           CD16plus CD56int HLADRplus NK Cells ',\n",
       "       '           CD16plus CD56int ILRAplus NK Cells ',\n",
       "       '           CD16- CD56hi NK Cells ',\n",
       "       '            CD16- CD56hi CD69plus NK Cells ',\n",
       "       '            CD16- CD56hi NKp44plus NK Cells ',\n",
       "       '            CD16- CD56hi CXCR2hi NK Cells ',\n",
       "       '            CD16- CD56hi CD127plus NK Cells ',\n",
       "       '            CD16- CD56hi NKp46plus NK Cells  ',\n",
       "       '           CD16- CD56hi CD107a NK Cells ',\n",
       "       '            CD16- CD56hi  CD2plus NK Cells ',\n",
       "       '            CD16- CD56hi CD62Lplus  NK Cells ',\n",
       "       '           CD16- CD56hi CD244plus  NK Cells ',\n",
       "       '             CD16- CD56hi CD158aplus NK Cells ',\n",
       "       '            CD16- CD56hi CD158bplus NK Cells ',\n",
       "       '            CD16- CD56hi NKp30plus  NK Cells ',\n",
       "       '            CD16- CD56hi CD158eplus NK Cells ',\n",
       "       '            CD16- CD56hi CRTH2plus NK Cells ',\n",
       "       '            CD16- CD56hi CD161plus NK Cells ',\n",
       "       '            CD16- CD56hi KIR2DS4plus NK Cells ',\n",
       "       '            CD16- CD56hi CD56 int NKG2D  NK Cells ',\n",
       "       '            CD16- CD56hi NKG2Cplus NK Cells ',\n",
       "       '            CD16- CD56hi CD94plus NK Cells ',\n",
       "       '            CD16- CD56hi CD25plus NK Cells ',\n",
       "       '            CD16- CD56hi CD226plus NK Cells ',\n",
       "       '            CD16- CD56hi CD57plus  NK Cells ',\n",
       "       '            CD16- CD56hi CD57-  NK Cells ',\n",
       "       '            CD16- CD56hi KLRG1plus NK Cells ',\n",
       "       '            CD16- CD56hi HLADRplus NK Cells ',\n",
       "       '            CD16- CD56hi  ILRAplus NK Cells ',\n",
       "       '        NKT Population  '],\n",
       "      dtype='object')"
      ]
     },
     "execution_count": 154,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 155,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Status                                                      0\n",
       "         NK Cells                                           0\n",
       "           CD16plus CD56int NK Cells                        0\n",
       "           CD16plus CD56int CD69plus NK Cells               0\n",
       "           CD16plus CD56int NKp44plus NK Cells              0\n",
       "           CD16plus CD56int CXCR2hi NK Cells                0\n",
       "           CD16plus CD56int CD127plus NK Cells              0\n",
       "           CD16plus CD56int NKp46plus NK Cells              0\n",
       "          CD16plus CD56int CD107a NK Cells                  0\n",
       "           CD16plus CD56int CD2plus NK Cells                0\n",
       "           CD16plus CD56int CD56Dim CD62Lplus  NK Cells     0\n",
       "          CD16plus CD56int CD244plus  NK Cells              0\n",
       "           CD16plus CD56int NK Cells .1                     0\n",
       "           CD16plus CD56int NK Cells .2                     0\n",
       "           CD16plus CD56int NKp30plus  NK Cells             0\n",
       "           CD16plus CD56int CD158eplus NK Cells             0\n",
       "           CD16plus CD56int CRTH2plus NK Cells              0\n",
       "           CD16plus CD56int CD161plus NK Cells              0\n",
       "          CD16plus CD56int KIR2DS4plus NK Cells             0\n",
       "           CD16plus CD56int CD56 int NKG2D  NK Cells        0\n",
       "           CD16plus CD56int NKG2Cplus NK Cells              0\n",
       "           CD16plus CD56int CD94plus NK Cells               0\n",
       "           CD16plus CD56int CD25plus NK Cells               0\n",
       "           CD16plus CD56int CD226plus NK Cells              0\n",
       "           CD16plus CD56int CD57plus  NK Cells              0\n",
       "           CD16plus CD56int CD57-  NK Cells                 0\n",
       "           CD16plus CD56int KLRG1plus NK Cells              0\n",
       "           CD16plus CD56int HLADRplus NK Cells              0\n",
       "           CD16plus CD56int ILRAplus NK Cells               0\n",
       "           CD16- CD56hi NK Cells                            0\n",
       "            CD16- CD56hi CD69plus NK Cells                  0\n",
       "            CD16- CD56hi NKp44plus NK Cells                 0\n",
       "            CD16- CD56hi CXCR2hi NK Cells                   0\n",
       "            CD16- CD56hi CD127plus NK Cells                 0\n",
       "            CD16- CD56hi NKp46plus NK Cells                 0\n",
       "           CD16- CD56hi CD107a NK Cells                     0\n",
       "            CD16- CD56hi  CD2plus NK Cells                  0\n",
       "            CD16- CD56hi CD62Lplus  NK Cells                0\n",
       "           CD16- CD56hi CD244plus  NK Cells                 0\n",
       "             CD16- CD56hi CD158aplus NK Cells               0\n",
       "            CD16- CD56hi CD158bplus NK Cells                0\n",
       "            CD16- CD56hi NKp30plus  NK Cells                0\n",
       "            CD16- CD56hi CD158eplus NK Cells                0\n",
       "            CD16- CD56hi CRTH2plus NK Cells                 0\n",
       "            CD16- CD56hi CD161plus NK Cells                 0\n",
       "            CD16- CD56hi KIR2DS4plus NK Cells               0\n",
       "            CD16- CD56hi CD56 int NKG2D  NK Cells           0\n",
       "            CD16- CD56hi NKG2Cplus NK Cells                 0\n",
       "            CD16- CD56hi CD94plus NK Cells                  0\n",
       "            CD16- CD56hi CD25plus NK Cells                  0\n",
       "            CD16- CD56hi CD226plus NK Cells                 0\n",
       "            CD16- CD56hi CD57plus  NK Cells                 0\n",
       "            CD16- CD56hi CD57-  NK Cells                    0\n",
       "            CD16- CD56hi KLRG1plus NK Cells                 0\n",
       "            CD16- CD56hi HLADRplus NK Cells                 0\n",
       "            CD16- CD56hi  ILRAplus NK Cells                 0\n",
       "        NKT Population                                      0\n",
       "dtype: int64"
      ]
     },
     "execution_count": 155,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.isna().sum()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 157,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(40, 57)"
      ]
     },
     "execution_count": 157,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 158,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Status</th>\n",
       "      <th>NK Cells</th>\n",
       "      <th>CD16plus CD56int NK Cells</th>\n",
       "      <th>CD16plus CD56int CD69plus NK Cells</th>\n",
       "      <th>CD16plus CD56int NKp44plus NK Cells</th>\n",
       "      <th>CD16plus CD56int CXCR2hi NK Cells</th>\n",
       "      <th>CD16plus CD56int CD127plus NK Cells</th>\n",
       "      <th>CD16plus CD56int NKp46plus NK Cells</th>\n",
       "      <th>CD16plus CD56int CD107a NK Cells</th>\n",
       "      <th>CD16plus CD56int CD2plus NK Cells</th>\n",
       "      <th>...</th>\n",
       "      <th>CD16- CD56hi NKG2Cplus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD94plus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD25plus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD226plus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD57plus  NK Cells</th>\n",
       "      <th>CD16- CD56hi CD57-  NK Cells</th>\n",
       "      <th>CD16- CD56hi KLRG1plus NK Cells</th>\n",
       "      <th>CD16- CD56hi HLADRplus NK Cells</th>\n",
       "      <th>CD16- CD56hi  ILRAplus NK Cells</th>\n",
       "      <th>NKT Population</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>ND</td>\n",
       "      <td>168029</td>\n",
       "      <td>164316</td>\n",
       "      <td>16669</td>\n",
       "      <td>164</td>\n",
       "      <td>1505</td>\n",
       "      <td>0</td>\n",
       "      <td>245</td>\n",
       "      <td>474</td>\n",
       "      <td>149757</td>\n",
       "      <td>...</td>\n",
       "      <td>752</td>\n",
       "      <td>1129</td>\n",
       "      <td>180</td>\n",
       "      <td>1031</td>\n",
       "      <td>33</td>\n",
       "      <td>1145</td>\n",
       "      <td>409</td>\n",
       "      <td>33</td>\n",
       "      <td>0</td>\n",
       "      <td>59870</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>ND</td>\n",
       "      <td>319110</td>\n",
       "      <td>309188</td>\n",
       "      <td>102196</td>\n",
       "      <td>53</td>\n",
       "      <td>28706</td>\n",
       "      <td>0</td>\n",
       "      <td>1220</td>\n",
       "      <td>2122</td>\n",
       "      <td>263608</td>\n",
       "      <td>...</td>\n",
       "      <td>3201</td>\n",
       "      <td>4882</td>\n",
       "      <td>460</td>\n",
       "      <td>3502</td>\n",
       "      <td>1539</td>\n",
       "      <td>3431</td>\n",
       "      <td>2069</td>\n",
       "      <td>778</td>\n",
       "      <td>0</td>\n",
       "      <td>32898</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>ND</td>\n",
       "      <td>76104</td>\n",
       "      <td>74531</td>\n",
       "      <td>9693</td>\n",
       "      <td>96</td>\n",
       "      <td>2696</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>128</td>\n",
       "      <td>50586</td>\n",
       "      <td>...</td>\n",
       "      <td>96</td>\n",
       "      <td>706</td>\n",
       "      <td>160</td>\n",
       "      <td>481</td>\n",
       "      <td>0</td>\n",
       "      <td>770</td>\n",
       "      <td>96</td>\n",
       "      <td>64</td>\n",
       "      <td>0</td>\n",
       "      <td>234859</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>ND</td>\n",
       "      <td>12498</td>\n",
       "      <td>12330</td>\n",
       "      <td>5360</td>\n",
       "      <td>24</td>\n",
       "      <td>769</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>8941</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>168</td>\n",
       "      <td>0</td>\n",
       "      <td>144</td>\n",
       "      <td>0</td>\n",
       "      <td>168</td>\n",
       "      <td>48</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>16248</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>ND</td>\n",
       "      <td>46378</td>\n",
       "      <td>45235</td>\n",
       "      <td>7148</td>\n",
       "      <td>0</td>\n",
       "      <td>50</td>\n",
       "      <td>0</td>\n",
       "      <td>25</td>\n",
       "      <td>163</td>\n",
       "      <td>25827</td>\n",
       "      <td>...</td>\n",
       "      <td>176</td>\n",
       "      <td>1030</td>\n",
       "      <td>38</td>\n",
       "      <td>892</td>\n",
       "      <td>0</td>\n",
       "      <td>1043</td>\n",
       "      <td>13</td>\n",
       "      <td>25</td>\n",
       "      <td>0</td>\n",
       "      <td>4258</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 57 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "  Status           NK Cells              CD16plus CD56int NK Cells   \\\n",
       "0     ND              168029                                 164316   \n",
       "1     ND              319110                                 309188   \n",
       "2     ND               76104                                  74531   \n",
       "3     ND               12498                                  12330   \n",
       "4     ND               46378                                  45235   \n",
       "\n",
       "              CD16plus CD56int CD69plus NK Cells   \\\n",
       "0                                           16669   \n",
       "1                                          102196   \n",
       "2                                            9693   \n",
       "3                                            5360   \n",
       "4                                            7148   \n",
       "\n",
       "              CD16plus CD56int NKp44plus NK Cells   \\\n",
       "0                                              164   \n",
       "1                                               53   \n",
       "2                                               96   \n",
       "3                                               24   \n",
       "4                                                0   \n",
       "\n",
       "              CD16plus CD56int CXCR2hi NK Cells   \\\n",
       "0                                           1505   \n",
       "1                                          28706   \n",
       "2                                           2696   \n",
       "3                                            769   \n",
       "4                                             50   \n",
       "\n",
       "              CD16plus CD56int CD127plus NK Cells   \\\n",
       "0                                                0   \n",
       "1                                                0   \n",
       "2                                                0   \n",
       "3                                                0   \n",
       "4                                                0   \n",
       "\n",
       "              CD16plus CD56int NKp46plus NK Cells    \\\n",
       "0                                               245   \n",
       "1                                              1220   \n",
       "2                                                 0   \n",
       "3                                                 0   \n",
       "4                                                25   \n",
       "\n",
       "             CD16plus CD56int CD107a NK Cells   \\\n",
       "0                                          474   \n",
       "1                                         2122   \n",
       "2                                          128   \n",
       "3                                            0   \n",
       "4                                          163   \n",
       "\n",
       "              CD16plus CD56int CD2plus NK Cells   ...  \\\n",
       "0                                         149757  ...   \n",
       "1                                         263608  ...   \n",
       "2                                          50586  ...   \n",
       "3                                           8941  ...   \n",
       "4                                          25827  ...   \n",
       "\n",
       "               CD16- CD56hi NKG2Cplus NK Cells   \\\n",
       "0                                           752   \n",
       "1                                          3201   \n",
       "2                                            96   \n",
       "3                                             0   \n",
       "4                                           176   \n",
       "\n",
       "               CD16- CD56hi CD94plus NK Cells   \\\n",
       "0                                         1129   \n",
       "1                                         4882   \n",
       "2                                          706   \n",
       "3                                          168   \n",
       "4                                         1030   \n",
       "\n",
       "               CD16- CD56hi CD25plus NK Cells   \\\n",
       "0                                          180   \n",
       "1                                          460   \n",
       "2                                          160   \n",
       "3                                            0   \n",
       "4                                           38   \n",
       "\n",
       "               CD16- CD56hi CD226plus NK Cells   \\\n",
       "0                                          1031   \n",
       "1                                          3502   \n",
       "2                                           481   \n",
       "3                                           144   \n",
       "4                                           892   \n",
       "\n",
       "               CD16- CD56hi CD57plus  NK Cells   \\\n",
       "0                                            33   \n",
       "1                                          1539   \n",
       "2                                             0   \n",
       "3                                             0   \n",
       "4                                             0   \n",
       "\n",
       "               CD16- CD56hi CD57-  NK Cells   \\\n",
       "0                                       1145   \n",
       "1                                       3431   \n",
       "2                                        770   \n",
       "3                                        168   \n",
       "4                                       1043   \n",
       "\n",
       "               CD16- CD56hi KLRG1plus NK Cells   \\\n",
       "0                                           409   \n",
       "1                                          2069   \n",
       "2                                            96   \n",
       "3                                            48   \n",
       "4                                            13   \n",
       "\n",
       "               CD16- CD56hi HLADRplus NK Cells   \\\n",
       "0                                            33   \n",
       "1                                           778   \n",
       "2                                            64   \n",
       "3                                             0   \n",
       "4                                            25   \n",
       "\n",
       "               CD16- CD56hi  ILRAplus NK Cells           NKT Population    \n",
       "0                                             0                     59870  \n",
       "1                                             0                     32898  \n",
       "2                                             0                    234859  \n",
       "3                                             0                     16248  \n",
       "4                                             0                      4258  \n",
       "\n",
       "[5 rows x 57 columns]"
      ]
     },
     "execution_count": 158,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 159,
   "metadata": {},
   "outputs": [],
   "source": [
    "X = df.drop('Status', axis='columns')\n",
    "y=df.Status"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 160,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>NK Cells</th>\n",
       "      <th>CD16plus CD56int NK Cells</th>\n",
       "      <th>CD16plus CD56int CD69plus NK Cells</th>\n",
       "      <th>CD16plus CD56int NKp44plus NK Cells</th>\n",
       "      <th>CD16plus CD56int CXCR2hi NK Cells</th>\n",
       "      <th>CD16plus CD56int CD127plus NK Cells</th>\n",
       "      <th>CD16plus CD56int NKp46plus NK Cells</th>\n",
       "      <th>CD16plus CD56int CD107a NK Cells</th>\n",
       "      <th>CD16plus CD56int CD2plus NK Cells</th>\n",
       "      <th>CD16plus CD56int CD56Dim CD62Lplus  NK Cells</th>\n",
       "      <th>...</th>\n",
       "      <th>CD16- CD56hi NKG2Cplus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD94plus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD25plus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD226plus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD57plus  NK Cells</th>\n",
       "      <th>CD16- CD56hi CD57-  NK Cells</th>\n",
       "      <th>CD16- CD56hi KLRG1plus NK Cells</th>\n",
       "      <th>CD16- CD56hi HLADRplus NK Cells</th>\n",
       "      <th>CD16- CD56hi  ILRAplus NK Cells</th>\n",
       "      <th>NKT Population</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>168029</td>\n",
       "      <td>164316</td>\n",
       "      <td>16669</td>\n",
       "      <td>164</td>\n",
       "      <td>1505</td>\n",
       "      <td>0</td>\n",
       "      <td>245</td>\n",
       "      <td>474</td>\n",
       "      <td>149757</td>\n",
       "      <td>36167</td>\n",
       "      <td>...</td>\n",
       "      <td>752</td>\n",
       "      <td>1129</td>\n",
       "      <td>180</td>\n",
       "      <td>1031</td>\n",
       "      <td>33</td>\n",
       "      <td>1145</td>\n",
       "      <td>409</td>\n",
       "      <td>33</td>\n",
       "      <td>0</td>\n",
       "      <td>59870</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>319110</td>\n",
       "      <td>309188</td>\n",
       "      <td>102196</td>\n",
       "      <td>53</td>\n",
       "      <td>28706</td>\n",
       "      <td>0</td>\n",
       "      <td>1220</td>\n",
       "      <td>2122</td>\n",
       "      <td>263608</td>\n",
       "      <td>79539</td>\n",
       "      <td>...</td>\n",
       "      <td>3201</td>\n",
       "      <td>4882</td>\n",
       "      <td>460</td>\n",
       "      <td>3502</td>\n",
       "      <td>1539</td>\n",
       "      <td>3431</td>\n",
       "      <td>2069</td>\n",
       "      <td>778</td>\n",
       "      <td>0</td>\n",
       "      <td>32898</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>76104</td>\n",
       "      <td>74531</td>\n",
       "      <td>9693</td>\n",
       "      <td>96</td>\n",
       "      <td>2696</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>128</td>\n",
       "      <td>50586</td>\n",
       "      <td>33542</td>\n",
       "      <td>...</td>\n",
       "      <td>96</td>\n",
       "      <td>706</td>\n",
       "      <td>160</td>\n",
       "      <td>481</td>\n",
       "      <td>0</td>\n",
       "      <td>770</td>\n",
       "      <td>96</td>\n",
       "      <td>64</td>\n",
       "      <td>0</td>\n",
       "      <td>234859</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>12498</td>\n",
       "      <td>12330</td>\n",
       "      <td>5360</td>\n",
       "      <td>24</td>\n",
       "      <td>769</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>8941</td>\n",
       "      <td>4543</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>168</td>\n",
       "      <td>0</td>\n",
       "      <td>144</td>\n",
       "      <td>0</td>\n",
       "      <td>168</td>\n",
       "      <td>48</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>16248</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>46378</td>\n",
       "      <td>45235</td>\n",
       "      <td>7148</td>\n",
       "      <td>0</td>\n",
       "      <td>50</td>\n",
       "      <td>0</td>\n",
       "      <td>25</td>\n",
       "      <td>163</td>\n",
       "      <td>25827</td>\n",
       "      <td>23780</td>\n",
       "      <td>...</td>\n",
       "      <td>176</td>\n",
       "      <td>1030</td>\n",
       "      <td>38</td>\n",
       "      <td>892</td>\n",
       "      <td>0</td>\n",
       "      <td>1043</td>\n",
       "      <td>13</td>\n",
       "      <td>25</td>\n",
       "      <td>0</td>\n",
       "      <td>4258</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 56 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            NK Cells              CD16plus CD56int NK Cells   \\\n",
       "0              168029                                 164316   \n",
       "1              319110                                 309188   \n",
       "2               76104                                  74531   \n",
       "3               12498                                  12330   \n",
       "4               46378                                  45235   \n",
       "\n",
       "              CD16plus CD56int CD69plus NK Cells   \\\n",
       "0                                           16669   \n",
       "1                                          102196   \n",
       "2                                            9693   \n",
       "3                                            5360   \n",
       "4                                            7148   \n",
       "\n",
       "              CD16plus CD56int NKp44plus NK Cells   \\\n",
       "0                                              164   \n",
       "1                                               53   \n",
       "2                                               96   \n",
       "3                                               24   \n",
       "4                                                0   \n",
       "\n",
       "              CD16plus CD56int CXCR2hi NK Cells   \\\n",
       "0                                           1505   \n",
       "1                                          28706   \n",
       "2                                           2696   \n",
       "3                                            769   \n",
       "4                                             50   \n",
       "\n",
       "              CD16plus CD56int CD127plus NK Cells   \\\n",
       "0                                                0   \n",
       "1                                                0   \n",
       "2                                                0   \n",
       "3                                                0   \n",
       "4                                                0   \n",
       "\n",
       "              CD16plus CD56int NKp46plus NK Cells    \\\n",
       "0                                               245   \n",
       "1                                              1220   \n",
       "2                                                 0   \n",
       "3                                                 0   \n",
       "4                                                25   \n",
       "\n",
       "             CD16plus CD56int CD107a NK Cells   \\\n",
       "0                                          474   \n",
       "1                                         2122   \n",
       "2                                          128   \n",
       "3                                            0   \n",
       "4                                          163   \n",
       "\n",
       "              CD16plus CD56int CD2plus NK Cells   \\\n",
       "0                                         149757   \n",
       "1                                         263608   \n",
       "2                                          50586   \n",
       "3                                           8941   \n",
       "4                                          25827   \n",
       "\n",
       "              CD16plus CD56int CD56Dim CD62Lplus  NK Cells   ...  \\\n",
       "0                                              36167         ...   \n",
       "1                                              79539         ...   \n",
       "2                                              33542         ...   \n",
       "3                                               4543         ...   \n",
       "4                                              23780         ...   \n",
       "\n",
       "               CD16- CD56hi NKG2Cplus NK Cells   \\\n",
       "0                                           752   \n",
       "1                                          3201   \n",
       "2                                            96   \n",
       "3                                             0   \n",
       "4                                           176   \n",
       "\n",
       "               CD16- CD56hi CD94plus NK Cells   \\\n",
       "0                                         1129   \n",
       "1                                         4882   \n",
       "2                                          706   \n",
       "3                                          168   \n",
       "4                                         1030   \n",
       "\n",
       "               CD16- CD56hi CD25plus NK Cells   \\\n",
       "0                                          180   \n",
       "1                                          460   \n",
       "2                                          160   \n",
       "3                                            0   \n",
       "4                                           38   \n",
       "\n",
       "               CD16- CD56hi CD226plus NK Cells   \\\n",
       "0                                          1031   \n",
       "1                                          3502   \n",
       "2                                           481   \n",
       "3                                           144   \n",
       "4                                           892   \n",
       "\n",
       "               CD16- CD56hi CD57plus  NK Cells   \\\n",
       "0                                            33   \n",
       "1                                          1539   \n",
       "2                                             0   \n",
       "3                                             0   \n",
       "4                                             0   \n",
       "\n",
       "               CD16- CD56hi CD57-  NK Cells   \\\n",
       "0                                       1145   \n",
       "1                                       3431   \n",
       "2                                        770   \n",
       "3                                        168   \n",
       "4                                       1043   \n",
       "\n",
       "               CD16- CD56hi KLRG1plus NK Cells   \\\n",
       "0                                           409   \n",
       "1                                          2069   \n",
       "2                                            96   \n",
       "3                                            48   \n",
       "4                                            13   \n",
       "\n",
       "               CD16- CD56hi HLADRplus NK Cells   \\\n",
       "0                                            33   \n",
       "1                                           778   \n",
       "2                                            64   \n",
       "3                                             0   \n",
       "4                                            25   \n",
       "\n",
       "               CD16- CD56hi  ILRAplus NK Cells           NKT Population    \n",
       "0                                             0                     59870  \n",
       "1                                             0                     32898  \n",
       "2                                             0                    234859  \n",
       "3                                             0                     16248  \n",
       "4                                             0                      4258  \n",
       "\n",
       "[5 rows x 56 columns]"
      ]
     },
     "execution_count": 160,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "X.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 161,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(40,)"
      ]
     },
     "execution_count": 161,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "X.shape\n",
    "y.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 162,
   "metadata": {},
   "outputs": [],
   "source": [
    "from sklearn.linear_model import LogisticRegression"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 163,
   "metadata": {},
   "outputs": [],
   "source": [
    "logreg = LogisticRegression(solver='lbfgs')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 164,
   "metadata": {},
   "outputs": [],
   "source": [
    "from sklearn.model_selection import cross_val_score"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 114,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n",
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n",
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n",
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0.7"
      ]
     },
     "execution_count": 114,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cross_val_score(logreg, X, y, cv=5, scoring = 'accuracy').mean()\n",
    "#cross_val_score(logreg, X, y, scoring = 'accuracy').mean()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "ND      0.65\n",
       "CVID    0.35\n",
       "Name: Status, dtype: float64"
      ]
     },
     "execution_count": 84,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "y.value_counts(normalize=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 85,
   "metadata": {},
   "outputs": [],
   "source": [
    "#Now doing one hot encoding\n",
    "from sklearn.preprocessing import OneHotEncoder\n",
    "ohe = OneHotEncoder(sparse = False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Let us try to improve the model with pipeline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 86,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [0., 1.],\n",
       "       [1., 0.],\n",
       "       [1., 0.],\n",
       "       [1., 0.],\n",
       "       [1., 0.],\n",
       "       [1., 0.],\n",
       "       [1., 0.],\n",
       "       [1., 0.],\n",
       "       [1., 0.],\n",
       "       [1., 0.],\n",
       "       [1., 0.],\n",
       "       [1., 0.],\n",
       "       [1., 0.],\n",
       "       [1., 0.],\n",
       "       [1., 0.]])"
      ]
     },
     "execution_count": 86,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ohe.fit_transform(df[['Status']])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 134,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "[array(['CVID', 'ND'], dtype=object)]"
      ]
     },
     "execution_count": 134,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ohe.categories_"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 136,
   "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>NK Cells</th>\n",
       "      <th>CD16plus CD56int NK Cells</th>\n",
       "      <th>CD16plus CD56int CD69plus NK Cells</th>\n",
       "      <th>CD16plus CD56int NKp44plus NK Cells</th>\n",
       "      <th>CD16plus CD56int CXCR2hi NK Cells</th>\n",
       "      <th>CD16plus CD56int CD127plus NK Cells</th>\n",
       "      <th>CD16plus CD56int NKp46plus NK Cells</th>\n",
       "      <th>CD16plus CD56int CD107a NK Cells</th>\n",
       "      <th>CD16plus CD56int CD2plus NK Cells</th>\n",
       "      <th>CD16plus CD56int CD56Dim CD62Lplus  NK Cells</th>\n",
       "      <th>...</th>\n",
       "      <th>CD16- CD56hi NKG2Cplus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD94plus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD25plus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD226plus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD57plus  NK Cells</th>\n",
       "      <th>CD16- CD56hi CD57-  NK Cells</th>\n",
       "      <th>CD16- CD56hi KLRG1plus NK Cells</th>\n",
       "      <th>CD16- CD56hi HLADRplus NK Cells</th>\n",
       "      <th>CD16- CD56hi  ILRAplus NK Cells</th>\n",
       "      <th>NKT Population</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>168029</td>\n",
       "      <td>164316</td>\n",
       "      <td>16669</td>\n",
       "      <td>164</td>\n",
       "      <td>1505</td>\n",
       "      <td>0</td>\n",
       "      <td>245</td>\n",
       "      <td>474</td>\n",
       "      <td>149757</td>\n",
       "      <td>36167</td>\n",
       "      <td>...</td>\n",
       "      <td>752</td>\n",
       "      <td>1129</td>\n",
       "      <td>180</td>\n",
       "      <td>1031</td>\n",
       "      <td>33</td>\n",
       "      <td>1145</td>\n",
       "      <td>409</td>\n",
       "      <td>33</td>\n",
       "      <td>0</td>\n",
       "      <td>59870</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>319110</td>\n",
       "      <td>309188</td>\n",
       "      <td>102196</td>\n",
       "      <td>53</td>\n",
       "      <td>28706</td>\n",
       "      <td>0</td>\n",
       "      <td>1220</td>\n",
       "      <td>2122</td>\n",
       "      <td>263608</td>\n",
       "      <td>79539</td>\n",
       "      <td>...</td>\n",
       "      <td>3201</td>\n",
       "      <td>4882</td>\n",
       "      <td>460</td>\n",
       "      <td>3502</td>\n",
       "      <td>1539</td>\n",
       "      <td>3431</td>\n",
       "      <td>2069</td>\n",
       "      <td>778</td>\n",
       "      <td>0</td>\n",
       "      <td>32898</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>76104</td>\n",
       "      <td>74531</td>\n",
       "      <td>9693</td>\n",
       "      <td>96</td>\n",
       "      <td>2696</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>128</td>\n",
       "      <td>50586</td>\n",
       "      <td>33542</td>\n",
       "      <td>...</td>\n",
       "      <td>96</td>\n",
       "      <td>706</td>\n",
       "      <td>160</td>\n",
       "      <td>481</td>\n",
       "      <td>0</td>\n",
       "      <td>770</td>\n",
       "      <td>96</td>\n",
       "      <td>64</td>\n",
       "      <td>0</td>\n",
       "      <td>234859</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>12498</td>\n",
       "      <td>12330</td>\n",
       "      <td>5360</td>\n",
       "      <td>24</td>\n",
       "      <td>769</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>8941</td>\n",
       "      <td>4543</td>\n",
       "      <td>...</td>\n",
       "      <td>0</td>\n",
       "      <td>168</td>\n",
       "      <td>0</td>\n",
       "      <td>144</td>\n",
       "      <td>0</td>\n",
       "      <td>168</td>\n",
       "      <td>48</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>16248</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>46378</td>\n",
       "      <td>45235</td>\n",
       "      <td>7148</td>\n",
       "      <td>0</td>\n",
       "      <td>50</td>\n",
       "      <td>0</td>\n",
       "      <td>25</td>\n",
       "      <td>163</td>\n",
       "      <td>25827</td>\n",
       "      <td>23780</td>\n",
       "      <td>...</td>\n",
       "      <td>176</td>\n",
       "      <td>1030</td>\n",
       "      <td>38</td>\n",
       "      <td>892</td>\n",
       "      <td>0</td>\n",
       "      <td>1043</td>\n",
       "      <td>13</td>\n",
       "      <td>25</td>\n",
       "      <td>0</td>\n",
       "      <td>4258</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 56 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            NK Cells              CD16plus CD56int NK Cells   \\\n",
       "0              168029                                 164316   \n",
       "1              319110                                 309188   \n",
       "2               76104                                  74531   \n",
       "3               12498                                  12330   \n",
       "4               46378                                  45235   \n",
       "\n",
       "              CD16plus CD56int CD69plus NK Cells   \\\n",
       "0                                           16669   \n",
       "1                                          102196   \n",
       "2                                            9693   \n",
       "3                                            5360   \n",
       "4                                            7148   \n",
       "\n",
       "              CD16plus CD56int NKp44plus NK Cells   \\\n",
       "0                                              164   \n",
       "1                                               53   \n",
       "2                                               96   \n",
       "3                                               24   \n",
       "4                                                0   \n",
       "\n",
       "              CD16plus CD56int CXCR2hi NK Cells   \\\n",
       "0                                           1505   \n",
       "1                                          28706   \n",
       "2                                           2696   \n",
       "3                                            769   \n",
       "4                                             50   \n",
       "\n",
       "              CD16plus CD56int CD127plus NK Cells   \\\n",
       "0                                                0   \n",
       "1                                                0   \n",
       "2                                                0   \n",
       "3                                                0   \n",
       "4                                                0   \n",
       "\n",
       "              CD16plus CD56int NKp46plus NK Cells    \\\n",
       "0                                               245   \n",
       "1                                              1220   \n",
       "2                                                 0   \n",
       "3                                                 0   \n",
       "4                                                25   \n",
       "\n",
       "             CD16plus CD56int CD107a NK Cells   \\\n",
       "0                                          474   \n",
       "1                                         2122   \n",
       "2                                          128   \n",
       "3                                            0   \n",
       "4                                          163   \n",
       "\n",
       "              CD16plus CD56int CD2plus NK Cells   \\\n",
       "0                                         149757   \n",
       "1                                         263608   \n",
       "2                                          50586   \n",
       "3                                           8941   \n",
       "4                                          25827   \n",
       "\n",
       "              CD16plus CD56int CD56Dim CD62Lplus  NK Cells   ...  \\\n",
       "0                                              36167         ...   \n",
       "1                                              79539         ...   \n",
       "2                                              33542         ...   \n",
       "3                                               4543         ...   \n",
       "4                                              23780         ...   \n",
       "\n",
       "               CD16- CD56hi NKG2Cplus NK Cells   \\\n",
       "0                                           752   \n",
       "1                                          3201   \n",
       "2                                            96   \n",
       "3                                             0   \n",
       "4                                           176   \n",
       "\n",
       "               CD16- CD56hi CD94plus NK Cells   \\\n",
       "0                                         1129   \n",
       "1                                         4882   \n",
       "2                                          706   \n",
       "3                                          168   \n",
       "4                                         1030   \n",
       "\n",
       "               CD16- CD56hi CD25plus NK Cells   \\\n",
       "0                                          180   \n",
       "1                                          460   \n",
       "2                                          160   \n",
       "3                                            0   \n",
       "4                                           38   \n",
       "\n",
       "               CD16- CD56hi CD226plus NK Cells   \\\n",
       "0                                          1031   \n",
       "1                                          3502   \n",
       "2                                           481   \n",
       "3                                           144   \n",
       "4                                           892   \n",
       "\n",
       "               CD16- CD56hi CD57plus  NK Cells   \\\n",
       "0                                            33   \n",
       "1                                          1539   \n",
       "2                                             0   \n",
       "3                                             0   \n",
       "4                                             0   \n",
       "\n",
       "               CD16- CD56hi CD57-  NK Cells   \\\n",
       "0                                       1145   \n",
       "1                                       3431   \n",
       "2                                        770   \n",
       "3                                        168   \n",
       "4                                       1043   \n",
       "\n",
       "               CD16- CD56hi KLRG1plus NK Cells   \\\n",
       "0                                           409   \n",
       "1                                          2069   \n",
       "2                                            96   \n",
       "3                                            48   \n",
       "4                                            13   \n",
       "\n",
       "               CD16- CD56hi HLADRplus NK Cells   \\\n",
       "0                                            33   \n",
       "1                                           778   \n",
       "2                                            64   \n",
       "3                                             0   \n",
       "4                                            25   \n",
       "\n",
       "               CD16- CD56hi  ILRAplus NK Cells           NKT Population    \n",
       "0                                             0                     59870  \n",
       "1                                             0                     32898  \n",
       "2                                             0                    234859  \n",
       "3                                             0                     16248  \n",
       "4                                             0                      4258  \n",
       "\n",
       "[5 rows x 56 columns]"
      ]
     },
     "execution_count": 136,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "X.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 138,
   "metadata": {},
   "outputs": [],
   "source": [
    "from sklearn.compose import make_column_transformer"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 168,
   "metadata": {},
   "outputs": [],
   "source": [
    "column_trans =  make_column_transformer(\n",
    "    (OneHotEncoder(), ['Status']),\n",
    "    remainder = 'passthrough')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 170,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([[0.00000e+00, 1.00000e+00, 1.68029e+05, ..., 3.30000e+01,\n",
       "        0.00000e+00, 5.98700e+04],\n",
       "       [0.00000e+00, 1.00000e+00, 3.19110e+05, ..., 7.78000e+02,\n",
       "        0.00000e+00, 3.28980e+04],\n",
       "       [0.00000e+00, 1.00000e+00, 7.61040e+04, ..., 6.40000e+01,\n",
       "        0.00000e+00, 2.34859e+05],\n",
       "       ...,\n",
       "       [1.00000e+00, 0.00000e+00, 1.01039e+05, ..., 3.90000e+02,\n",
       "        0.00000e+00, 1.79039e+05],\n",
       "       [1.00000e+00, 0.00000e+00, 1.04790e+05, ..., 1.16000e+02,\n",
       "        0.00000e+00, 1.62780e+05],\n",
       "       [1.00000e+00, 0.00000e+00, 6.12561e+05, ..., 2.68000e+02,\n",
       "        0.00000e+00, 1.65600e+05]])"
      ]
     },
     "execution_count": 170,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "column_trans.fit_transform(df)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 171,
   "metadata": {},
   "outputs": [],
   "source": [
    "from sklearn.pipeline import make_pipeline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 172,
   "metadata": {},
   "outputs": [],
   "source": [
    "pipe = make_pipeline(column_trans, logreg)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 185,
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n",
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n",
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n",
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n",
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n",
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n",
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n",
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n",
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n",
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "0.65"
      ]
     },
     "execution_count": 185,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "cross_val_score(pipe, df, y, cv =10, scoring='accuracy').mean()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 186,
   "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>Status</th>\n",
       "      <th>NK Cells</th>\n",
       "      <th>CD16plus CD56int NK Cells</th>\n",
       "      <th>CD16plus CD56int CD69plus NK Cells</th>\n",
       "      <th>CD16plus CD56int NKp44plus NK Cells</th>\n",
       "      <th>CD16plus CD56int CXCR2hi NK Cells</th>\n",
       "      <th>CD16plus CD56int CD127plus NK Cells</th>\n",
       "      <th>CD16plus CD56int NKp46plus NK Cells</th>\n",
       "      <th>CD16plus CD56int CD107a NK Cells</th>\n",
       "      <th>CD16plus CD56int CD2plus NK Cells</th>\n",
       "      <th>...</th>\n",
       "      <th>CD16- CD56hi NKG2Cplus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD94plus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD25plus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD226plus NK Cells</th>\n",
       "      <th>CD16- CD56hi CD57plus  NK Cells</th>\n",
       "      <th>CD16- CD56hi CD57-  NK Cells</th>\n",
       "      <th>CD16- CD56hi KLRG1plus NK Cells</th>\n",
       "      <th>CD16- CD56hi HLADRplus NK Cells</th>\n",
       "      <th>CD16- CD56hi  ILRAplus NK Cells</th>\n",
       "      <th>NKT Population</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>25</th>\n",
       "      <td>ND</td>\n",
       "      <td>255761</td>\n",
       "      <td>242948</td>\n",
       "      <td>41520</td>\n",
       "      <td>86</td>\n",
       "      <td>1712</td>\n",
       "      <td>0</td>\n",
       "      <td>648</td>\n",
       "      <td>1125</td>\n",
       "      <td>174127</td>\n",
       "      <td>...</td>\n",
       "      <td>1100</td>\n",
       "      <td>2335</td>\n",
       "      <td>245</td>\n",
       "      <td>1406</td>\n",
       "      <td>37</td>\n",
       "      <td>2311</td>\n",
       "      <td>330</td>\n",
       "      <td>61</td>\n",
       "      <td>0</td>\n",
       "      <td>55556</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>36</th>\n",
       "      <td>CVID</td>\n",
       "      <td>93290</td>\n",
       "      <td>88737</td>\n",
       "      <td>33870</td>\n",
       "      <td>1107</td>\n",
       "      <td>14628</td>\n",
       "      <td>0</td>\n",
       "      <td>5498</td>\n",
       "      <td>9901</td>\n",
       "      <td>71796</td>\n",
       "      <td>...</td>\n",
       "      <td>721</td>\n",
       "      <td>1406</td>\n",
       "      <td>199</td>\n",
       "      <td>1717</td>\n",
       "      <td>473</td>\n",
       "      <td>1269</td>\n",
       "      <td>622</td>\n",
       "      <td>112</td>\n",
       "      <td>0</td>\n",
       "      <td>10921</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>29</th>\n",
       "      <td>CVID</td>\n",
       "      <td>70864</td>\n",
       "      <td>70219</td>\n",
       "      <td>31644</td>\n",
       "      <td>228</td>\n",
       "      <td>1151</td>\n",
       "      <td>0</td>\n",
       "      <td>455</td>\n",
       "      <td>228</td>\n",
       "      <td>58002</td>\n",
       "      <td>...</td>\n",
       "      <td>253</td>\n",
       "      <td>468</td>\n",
       "      <td>38</td>\n",
       "      <td>341</td>\n",
       "      <td>25</td>\n",
       "      <td>481</td>\n",
       "      <td>38</td>\n",
       "      <td>76</td>\n",
       "      <td>0</td>\n",
       "      <td>5388</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>22</th>\n",
       "      <td>ND</td>\n",
       "      <td>185191</td>\n",
       "      <td>178578</td>\n",
       "      <td>38642</td>\n",
       "      <td>283</td>\n",
       "      <td>7707</td>\n",
       "      <td>0</td>\n",
       "      <td>1107</td>\n",
       "      <td>1026</td>\n",
       "      <td>88688</td>\n",
       "      <td>...</td>\n",
       "      <td>202</td>\n",
       "      <td>945</td>\n",
       "      <td>54</td>\n",
       "      <td>580</td>\n",
       "      <td>27</td>\n",
       "      <td>958</td>\n",
       "      <td>40</td>\n",
       "      <td>27</td>\n",
       "      <td>0</td>\n",
       "      <td>19233</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>CVID</td>\n",
       "      <td>377645</td>\n",
       "      <td>375808</td>\n",
       "      <td>202995</td>\n",
       "      <td>890</td>\n",
       "      <td>12781</td>\n",
       "      <td>0</td>\n",
       "      <td>8066</td>\n",
       "      <td>1799</td>\n",
       "      <td>365982</td>\n",
       "      <td>...</td>\n",
       "      <td>114</td>\n",
       "      <td>133</td>\n",
       "      <td>19</td>\n",
       "      <td>133</td>\n",
       "      <td>0</td>\n",
       "      <td>133</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>14239</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>5 rows × 57 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "   Status           NK Cells              CD16plus CD56int NK Cells   \\\n",
       "25     ND              255761                                 242948   \n",
       "36   CVID               93290                                  88737   \n",
       "29   CVID               70864                                  70219   \n",
       "22     ND              185191                                 178578   \n",
       "28   CVID              377645                                 375808   \n",
       "\n",
       "               CD16plus CD56int CD69plus NK Cells   \\\n",
       "25                                           41520   \n",
       "36                                           33870   \n",
       "29                                           31644   \n",
       "22                                           38642   \n",
       "28                                          202995   \n",
       "\n",
       "               CD16plus CD56int NKp44plus NK Cells   \\\n",
       "25                                               86   \n",
       "36                                             1107   \n",
       "29                                              228   \n",
       "22                                              283   \n",
       "28                                              890   \n",
       "\n",
       "               CD16plus CD56int CXCR2hi NK Cells   \\\n",
       "25                                           1712   \n",
       "36                                          14628   \n",
       "29                                           1151   \n",
       "22                                           7707   \n",
       "28                                          12781   \n",
       "\n",
       "               CD16plus CD56int CD127plus NK Cells   \\\n",
       "25                                                0   \n",
       "36                                                0   \n",
       "29                                                0   \n",
       "22                                                0   \n",
       "28                                                0   \n",
       "\n",
       "               CD16plus CD56int NKp46plus NK Cells    \\\n",
       "25                                               648   \n",
       "36                                              5498   \n",
       "29                                               455   \n",
       "22                                              1107   \n",
       "28                                              8066   \n",
       "\n",
       "              CD16plus CD56int CD107a NK Cells   \\\n",
       "25                                         1125   \n",
       "36                                         9901   \n",
       "29                                          228   \n",
       "22                                         1026   \n",
       "28                                         1799   \n",
       "\n",
       "               CD16plus CD56int CD2plus NK Cells   ...  \\\n",
       "25                                         174127  ...   \n",
       "36                                          71796  ...   \n",
       "29                                          58002  ...   \n",
       "22                                          88688  ...   \n",
       "28                                         365982  ...   \n",
       "\n",
       "                CD16- CD56hi NKG2Cplus NK Cells   \\\n",
       "25                                          1100   \n",
       "36                                           721   \n",
       "29                                           253   \n",
       "22                                           202   \n",
       "28                                           114   \n",
       "\n",
       "                CD16- CD56hi CD94plus NK Cells   \\\n",
       "25                                         2335   \n",
       "36                                         1406   \n",
       "29                                          468   \n",
       "22                                          945   \n",
       "28                                          133   \n",
       "\n",
       "                CD16- CD56hi CD25plus NK Cells   \\\n",
       "25                                          245   \n",
       "36                                          199   \n",
       "29                                           38   \n",
       "22                                           54   \n",
       "28                                           19   \n",
       "\n",
       "                CD16- CD56hi CD226plus NK Cells   \\\n",
       "25                                          1406   \n",
       "36                                          1717   \n",
       "29                                           341   \n",
       "22                                           580   \n",
       "28                                           133   \n",
       "\n",
       "                CD16- CD56hi CD57plus  NK Cells   \\\n",
       "25                                            37   \n",
       "36                                           473   \n",
       "29                                            25   \n",
       "22                                            27   \n",
       "28                                             0   \n",
       "\n",
       "                CD16- CD56hi CD57-  NK Cells   \\\n",
       "25                                       2311   \n",
       "36                                       1269   \n",
       "29                                        481   \n",
       "22                                        958   \n",
       "28                                        133   \n",
       "\n",
       "                CD16- CD56hi KLRG1plus NK Cells   \\\n",
       "25                                           330   \n",
       "36                                           622   \n",
       "29                                            38   \n",
       "22                                            40   \n",
       "28                                             0   \n",
       "\n",
       "                CD16- CD56hi HLADRplus NK Cells   \\\n",
       "25                                            61   \n",
       "36                                           112   \n",
       "29                                            76   \n",
       "22                                            27   \n",
       "28                                             0   \n",
       "\n",
       "                CD16- CD56hi  ILRAplus NK Cells           NKT Population    \n",
       "25                                             0                     55556  \n",
       "36                                             0                     10921  \n",
       "29                                             0                      5388  \n",
       "22                                             0                     19233  \n",
       "28                                             0                     14239  \n",
       "\n",
       "[5 rows x 57 columns]"
      ]
     },
     "execution_count": 186,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "X_new = df.sample(5, random_state=99)\n",
    "X_new"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 189,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/srivastava/anaconda3/lib/python3.8/site-packages/sklearn/linear_model/_logistic.py:762: ConvergenceWarning: lbfgs failed to converge (status=1):\n",
      "STOP: TOTAL NO. of ITERATIONS REACHED LIMIT.\n",
      "\n",
      "Increase the number of iterations (max_iter) or scale the data as shown in:\n",
      "    https://scikit-learn.org/stable/modules/preprocessing.html\n",
      "Please also refer to the documentation for alternative solver options:\n",
      "    https://scikit-learn.org/stable/modules/linear_model.html#logistic-regression\n",
      "  n_iter_i = _check_optimize_result(\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "Pipeline(steps=[('columntransformer',\n",
       "                 ColumnTransformer(remainder='passthrough',\n",
       "                                   transformers=[('onehotencoder',\n",
       "                                                  OneHotEncoder(),\n",
       "                                                  ['Status'])])),\n",
       "                ('logisticregression', LogisticRegression())])"
      ]
     },
     "execution_count": 189,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pipe.fit(df, y)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 190,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array(['ND', 'CVID', 'CVID', 'ND', 'CVID'], dtype=object)"
      ]
     },
     "execution_count": 190,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pipe.predict(X_new)"
   ]
  }
 ],
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