Demo.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "import bacteriopop_utils\n",
    "import feature_selection_utils\n",
    "import load_data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "loaded_data = data = load_data.load_data()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(64755, 11)"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "loaded_data.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>kingdom</th>\n",
       "      <th>phylum</th>\n",
       "      <th>class</th>\n",
       "      <th>order</th>\n",
       "      <th>family</th>\n",
       "      <th>genus</th>\n",
       "      <th>length</th>\n",
       "      <th>oxygen</th>\n",
       "      <th>replicate</th>\n",
       "      <th>week</th>\n",
       "      <th>abundance</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>sampleID</th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1056013</th>\n",
       "      <td>Bacteria</td>\n",
       "      <td>Proteobacteria</td>\n",
       "      <td>Gammaproteobacteria</td>\n",
       "      <td>Methylococcales</td>\n",
       "      <td>Methylococcaceae</td>\n",
       "      <td>Methylobacter</td>\n",
       "      <td>9948861</td>\n",
       "      <td>Low</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>0.228531</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1056013</th>\n",
       "      <td>Bacteria</td>\n",
       "      <td>Proteobacteria</td>\n",
       "      <td>Betaproteobacteria</td>\n",
       "      <td>Methylophilales</td>\n",
       "      <td>Methylophilaceae</td>\n",
       "      <td>Methylotenera</td>\n",
       "      <td>5066955</td>\n",
       "      <td>Low</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>0.220860</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1056013</th>\n",
       "      <td>Bacteria</td>\n",
       "      <td>Bacteroidetes</td>\n",
       "      <td>Flavobacteriia</td>\n",
       "      <td>Flavobacteriales</td>\n",
       "      <td>Flavobacteriaceae</td>\n",
       "      <td>Flavobacterium</td>\n",
       "      <td>4654774</td>\n",
       "      <td>Low</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>0.054719</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1056013</th>\n",
       "      <td>Bacteria</td>\n",
       "      <td>Proteobacteria</td>\n",
       "      <td>Gammaproteobacteria</td>\n",
       "      <td>Methylococcales</td>\n",
       "      <td>Methylococcaceae</td>\n",
       "      <td>other</td>\n",
       "      <td>3046340</td>\n",
       "      <td>Low</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>0.047956</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1056013</th>\n",
       "      <td>Bacteria</td>\n",
       "      <td>Proteobacteria</td>\n",
       "      <td>Gammaproteobacteria</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>other</td>\n",
       "      <td>5620690</td>\n",
       "      <td>Low</td>\n",
       "      <td>1</td>\n",
       "      <td>4</td>\n",
       "      <td>0.040903</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "           kingdom          phylum                class             order  \\\n",
       "sampleID                                                                    \n",
       "1056013   Bacteria  Proteobacteria  Gammaproteobacteria   Methylococcales   \n",
       "1056013   Bacteria  Proteobacteria   Betaproteobacteria   Methylophilales   \n",
       "1056013   Bacteria   Bacteroidetes       Flavobacteriia  Flavobacteriales   \n",
       "1056013   Bacteria  Proteobacteria  Gammaproteobacteria   Methylococcales   \n",
       "1056013   Bacteria  Proteobacteria  Gammaproteobacteria               NaN   \n",
       "\n",
       "                     family           genus   length oxygen  replicate  week  \\\n",
       "sampleID                                                                       \n",
       "1056013    Methylococcaceae   Methylobacter  9948861    Low          1     4   \n",
       "1056013    Methylophilaceae   Methylotenera  5066955    Low          1     4   \n",
       "1056013   Flavobacteriaceae  Flavobacterium  4654774    Low          1     4   \n",
       "1056013    Methylococcaceae           other  3046340    Low          1     4   \n",
       "1056013                 NaN           other  5620690    Low          1     4   \n",
       "\n",
       "          abundance  \n",
       "sampleID             \n",
       "1056013    0.228531  \n",
       "1056013    0.220860  \n",
       "1056013    0.054719  \n",
       "1056013    0.047956  \n",
       "1056013    0.040903  "
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "loaded_data.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "extracted_features = bacteriopop_utils.extract_features(\n",
    "    dataframe = loaded_data,\n",
    "    column_list = ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'oxygen', 'abundance']\n",
    "    # default list was: ['kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'length', 'abundance', 'project']\n",
    "    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
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       "      <th>abundance</th>\n",
       "      <th>class=Acidobacteriia</th>\n",
       "      <th>class=Actinobacteria</th>\n",
       "      <th>class=Alphaproteobacteria</th>\n",
       "      <th>class=Anaerolineae</th>\n",
       "      <th>class=Aquificae</th>\n",
       "      <th>class=Archaeoglobi</th>\n",
       "      <th>class=Bacilli</th>\n",
       "      <th>class=Bacteroidia</th>\n",
       "      <th>class=Betaproteobacteria</th>\n",
       "      <th>...</th>\n",
       "      <th>phylum=Planctomycetes</th>\n",
       "      <th>phylum=Poribacteria</th>\n",
       "      <th>phylum=Proteobacteria</th>\n",
       "      <th>phylum=Spirochaetes</th>\n",
       "      <th>phylum=Synergistetes</th>\n",
       "      <th>phylum=Tenericutes</th>\n",
       "      <th>phylum=Thaumarchaeota</th>\n",
       "      <th>phylum=Thermodesulfobacteria</th>\n",
       "      <th>phylum=Thermotogae</th>\n",
       "      <th>phylum=Verrucomicrobia</th>\n",
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       "<p>5 rows × 1450 columns</p>\n",
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       "   abundance  class=Acidobacteriia  class=Actinobacteria  \\\n",
       "0   0.228531                     0                     0   \n",
       "1   0.220860                     0                     0   \n",
       "2   0.054719                     0                     0   \n",
       "3   0.047956                     0                     0   \n",
       "4   0.040903                     0                     0   \n",
       "\n",
       "   class=Alphaproteobacteria  class=Anaerolineae  class=Aquificae  \\\n",
       "0                          0                   0                0   \n",
       "1                          0                   0                0   \n",
       "2                          0                   0                0   \n",
       "3                          0                   0                0   \n",
       "4                          0                   0                0   \n",
       "\n",
       "   class=Archaeoglobi  class=Bacilli  class=Bacteroidia  \\\n",
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       "\n",
       "   class=Betaproteobacteria           ...            phylum=Planctomycetes  \\\n",
       "0                         0           ...                                0   \n",
       "1                         1           ...                                0   \n",
       "2                         0           ...                                0   \n",
       "3                         0           ...                                0   \n",
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       "\n",
       "   phylum=Poribacteria  phylum=Proteobacteria  phylum=Spirochaetes  \\\n",
       "0                    0                      1                    0   \n",
       "1                    0                      1                    0   \n",
       "2                    0                      0                    0   \n",
       "3                    0                      1                    0   \n",
       "4                    0                      1                    0   \n",
       "\n",
       "   phylum=Synergistetes  phylum=Tenericutes  phylum=Thaumarchaeota  \\\n",
       "0                     0                   0                      0   \n",
       "1                     0                   0                      0   \n",
       "2                     0                   0                      0   \n",
       "3                     0                   0                      0   \n",
       "4                     0                   0                      0   \n",
       "\n",
       "   phylum=Thermodesulfobacteria  phylum=Thermotogae  phylum=Verrucomicrobia  \n",
       "0                             0                   0                       0  \n",
       "1                             0                   0                       0  \n",
       "2                             0                   0                       0  \n",
       "3                             0                   0                       0  \n",
       "4                             0                   0                       0  \n",
       "\n",
       "[5 rows x 1450 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "extracted_features.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(64755, 1450)"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "extracted_features.shape"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Just do PCA on a tiny bit of the data as a demo"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "pca_results = feature_selection_utils.pca_bacteria(\n",
    "    data = extracted_features.head(100), n_components = 10)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
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     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
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   "source": [
    "pca_results.components_"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Do correlations for a tiny subset of the data."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
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      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "feature_selection_utils.calculate_features_target_correlation(\n",
    "    data = extracted_features.head(100),\n",
    "    features = extracted_features.columns.tolist(),\n",
    "    target='abundance',\n",
    "    method=\"Pearson\")"
   ]
  }
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