sample-metadata-exploration.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/gregcaporaso/.conda/envs/data-analysis/lib/python3.5/site-packages/IPython/kernel/__main__.py:3: FutureWarning: convert_objects is deprecated.  Use the data-type specific converters pd.to_datetime, pd.to_timedelta and pd.to_numeric.\n",
      "  app.launch_new_instance()\n"
     ]
    }
   ],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "sample_md = pd.read_csv(\"./master-map.tsv\", sep='\\t', index_col=\"#SampleID\").replace(\"no_data\", np.nan).convert_objects(convert_numeric=True)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "['BarcodeSequence',\n",
       " 'LinkerPrimerSequence',\n",
       " 'OTU-WeightedUniFrac-PC1',\n",
       " 'OTU-UnweightedUniFrac-PC1',\n",
       " 'OTU-PD',\n",
       " 'Derep-WeightedUniFrac-PC1',\n",
       " 'Derep-WeightedUniFrac-PC2',\n",
       " 'Derep-WeightedUniFrac-PC3',\n",
       " 'Derep-UnweightedUniFrac-PC1',\n",
       " 'Derep-UnweightedUniFrac-PC2',\n",
       " 'Derep-UnweightedUniFrac-PC3',\n",
       " 'Derep-PD',\n",
       " 'MiSeqRun',\n",
       " 'control',\n",
       " 'ptid',\n",
       " 'nau_id',\n",
       " 'visit',\n",
       " 'treatmentgroup',\n",
       " 'pre_date_startcol',\n",
       " 'pre_date_endcol',\n",
       " 'pre_date_process',\n",
       " 'pre_col_days',\n",
       " 'post_date_startcol',\n",
       " 'post_date_endcol',\n",
       " 'post_date_process',\n",
       " 'post_col_days',\n",
       " 'col_timegap',\n",
       " 'proc_timegap',\n",
       " 'rs13161018',\n",
       " 'has_rs13161018',\n",
       " 'odc1',\n",
       " 'pre_tac_lc',\n",
       " 'pre_tac_dc',\n",
       " 'pre_tac_cd',\n",
       " 'pre_tac_ca',\n",
       " 'pre_tac_ud',\n",
       " 'pre_tac_uc',\n",
       " 'pre_tac_ot',\n",
       " 'pre_tacids',\n",
       " 'pre_tac_primary',\n",
       " 'pre_tac_secondary',\n",
       " 'pre_tac_tertiary',\n",
       " 'pre_tac_hydrophobic',\n",
       " 'pre_tac_hydrophilic',\n",
       " 'post_tac_lc',\n",
       " 'post_tac_dc',\n",
       " 'post_tac_cd',\n",
       " 'post_tac_ca',\n",
       " 'post_tac_ud',\n",
       " 'post_tac_uc',\n",
       " 'post_tac_ot',\n",
       " 'post_tacids',\n",
       " 'post_tac_primary',\n",
       " 'post_tac_secondary',\n",
       " 'post_tac_tertiary',\n",
       " 'post_tac_hydrophobic',\n",
       " 'post_tac_hydrophilic',\n",
       " 'hrrecrx',\n",
       " 'treatudca',\n",
       " 'pre_largest',\n",
       " 'pre_large',\n",
       " 'pre_number',\n",
       " 'pre_mult',\n",
       " 'pre_dist',\n",
       " 'pre_prox',\n",
       " 'pre_villous',\n",
       " 'male',\n",
       " 'age',\n",
       " 'white',\n",
       " 'grade',\n",
       " 'weight',\n",
       " 'height',\n",
       " 'bmi',\n",
       " 'waist',\n",
       " 'hip',\n",
       " 'whr',\n",
       " 'systolbp',\n",
       " 'diastlbp',\n",
       " 'smokenow',\n",
       " 'eversmoke',\n",
       " 'aspirin',\n",
       " 'prevplyp',\n",
       " 'famhxcrc',\n",
       " 'hhdiabete',\n",
       " 'glucose',\n",
       " 'trig',\n",
       " 'hdl',\n",
       " 'post_recur',\n",
       " 'post_cancer',\n",
       " 'post_largest',\n",
       " 'post_large',\n",
       " 'post_number',\n",
       " 'post_mult',\n",
       " 'post_dist',\n",
       " 'post_prox',\n",
       " 'post_villous',\n",
       " 'post_advanced',\n",
       " 'prot',\n",
       " 'tfat',\n",
       " 'carb',\n",
       " 'ener',\n",
       " 'alco',\n",
       " 'tfib',\n",
       " 'calc',\n",
       " 'magn',\n",
       " 'fola',\n",
       " 'sfat',\n",
       " 'mufa',\n",
       " 'pufa',\n",
       " 'sfolat',\n",
       " 'scalc',\n",
       " 'suppuse',\n",
       " 'redmeat',\n",
       " 'sucr',\n",
       " 'gluc',\n",
       " 'fruc',\n",
       " 'lact',\n",
       " 'malt',\n",
       " 'suga',\n",
       " 'gala',\n",
       " 'argi',\n",
       " 'putrescine',\n",
       " 'spermidine',\n",
       " 'spermine',\n",
       " 'poly',\n",
       " 'Days_Since_Epoch',\n",
       " 'Description1',\n",
       " 'Description',\n",
       " 'Begin_collect_date']"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "list(sample_md.columns)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "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></th>\n",
       "      <th></th>\n",
       "      <th>BarcodeSequence</th>\n",
       "      <th>LinkerPrimerSequence</th>\n",
       "      <th>OTU-WeightedUniFrac-PC1</th>\n",
       "      <th>OTU-UnweightedUniFrac-PC1</th>\n",
       "      <th>OTU-PD</th>\n",
       "      <th>Derep-WeightedUniFrac-PC1</th>\n",
       "      <th>Derep-WeightedUniFrac-PC2</th>\n",
       "      <th>Derep-WeightedUniFrac-PC3</th>\n",
       "      <th>Derep-UnweightedUniFrac-PC1</th>\n",
       "      <th>Derep-UnweightedUniFrac-PC2</th>\n",
       "      <th>...</th>\n",
       "      <th>gala</th>\n",
       "      <th>argi</th>\n",
       "      <th>putrescine</th>\n",
       "      <th>spermidine</th>\n",
       "      <th>spermine</th>\n",
       "      <th>poly</th>\n",
       "      <th>Days_Since_Epoch</th>\n",
       "      <th>Description1</th>\n",
       "      <th>Description</th>\n",
       "      <th>Begin_collect_date</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>male</th>\n",
       "      <th>treatmentgroup</th>\n",
       "      <th>visit</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",
       "      <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 rowspan=\"4\" valign=\"top\">0.0</th>\n",
       "      <th rowspan=\"2\" valign=\"top\">UDCA</th>\n",
       "      <th>post</th>\n",
       "      <td>63</td>\n",
       "      <td>63</td>\n",
       "      <td>53</td>\n",
       "      <td>53</td>\n",
       "      <td>53</td>\n",
       "      <td>57</td>\n",
       "      <td>57</td>\n",
       "      <td>57</td>\n",
       "      <td>57</td>\n",
       "      <td>57</td>\n",
       "      <td>...</td>\n",
       "      <td>63</td>\n",
       "      <td>63</td>\n",
       "      <td>63</td>\n",
       "      <td>63</td>\n",
       "      <td>63</td>\n",
       "      <td>63</td>\n",
       "      <td>11</td>\n",
       "      <td>43</td>\n",
       "      <td>63</td>\n",
       "      <td>62</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>pre</th>\n",
       "      <td>65</td>\n",
       "      <td>65</td>\n",
       "      <td>50</td>\n",
       "      <td>50</td>\n",
       "      <td>50</td>\n",
       "      <td>53</td>\n",
       "      <td>53</td>\n",
       "      <td>53</td>\n",
       "      <td>53</td>\n",
       "      <td>53</td>\n",
       "      <td>...</td>\n",
       "      <td>65</td>\n",
       "      <td>65</td>\n",
       "      <td>65</td>\n",
       "      <td>65</td>\n",
       "      <td>65</td>\n",
       "      <td>65</td>\n",
       "      <td>14</td>\n",
       "      <td>45</td>\n",
       "      <td>65</td>\n",
       "      <td>65</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"2\" valign=\"top\">placebo</th>\n",
       "      <th>post</th>\n",
       "      <td>90</td>\n",
       "      <td>90</td>\n",
       "      <td>77</td>\n",
       "      <td>77</td>\n",
       "      <td>77</td>\n",
       "      <td>84</td>\n",
       "      <td>84</td>\n",
       "      <td>84</td>\n",
       "      <td>84</td>\n",
       "      <td>84</td>\n",
       "      <td>...</td>\n",
       "      <td>90</td>\n",
       "      <td>90</td>\n",
       "      <td>90</td>\n",
       "      <td>90</td>\n",
       "      <td>90</td>\n",
       "      <td>90</td>\n",
       "      <td>16</td>\n",
       "      <td>67</td>\n",
       "      <td>90</td>\n",
       "      <td>89</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>pre</th>\n",
       "      <td>88</td>\n",
       "      <td>88</td>\n",
       "      <td>66</td>\n",
       "      <td>66</td>\n",
       "      <td>66</td>\n",
       "      <td>75</td>\n",
       "      <td>75</td>\n",
       "      <td>75</td>\n",
       "      <td>75</td>\n",
       "      <td>75</td>\n",
       "      <td>...</td>\n",
       "      <td>88</td>\n",
       "      <td>88</td>\n",
       "      <td>88</td>\n",
       "      <td>88</td>\n",
       "      <td>88</td>\n",
       "      <td>88</td>\n",
       "      <td>13</td>\n",
       "      <td>63</td>\n",
       "      <td>88</td>\n",
       "      <td>88</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"4\" valign=\"top\">1.0</th>\n",
       "      <th rowspan=\"2\" valign=\"top\">UDCA</th>\n",
       "      <th>post</th>\n",
       "      <td>190</td>\n",
       "      <td>190</td>\n",
       "      <td>164</td>\n",
       "      <td>164</td>\n",
       "      <td>164</td>\n",
       "      <td>184</td>\n",
       "      <td>184</td>\n",
       "      <td>184</td>\n",
       "      <td>184</td>\n",
       "      <td>184</td>\n",
       "      <td>...</td>\n",
       "      <td>190</td>\n",
       "      <td>190</td>\n",
       "      <td>190</td>\n",
       "      <td>190</td>\n",
       "      <td>190</td>\n",
       "      <td>190</td>\n",
       "      <td>19</td>\n",
       "      <td>151</td>\n",
       "      <td>190</td>\n",
       "      <td>188</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>pre</th>\n",
       "      <td>186</td>\n",
       "      <td>186</td>\n",
       "      <td>133</td>\n",
       "      <td>133</td>\n",
       "      <td>133</td>\n",
       "      <td>151</td>\n",
       "      <td>151</td>\n",
       "      <td>151</td>\n",
       "      <td>151</td>\n",
       "      <td>151</td>\n",
       "      <td>...</td>\n",
       "      <td>186</td>\n",
       "      <td>186</td>\n",
       "      <td>186</td>\n",
       "      <td>186</td>\n",
       "      <td>186</td>\n",
       "      <td>186</td>\n",
       "      <td>14</td>\n",
       "      <td>141</td>\n",
       "      <td>186</td>\n",
       "      <td>186</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th rowspan=\"2\" valign=\"top\">placebo</th>\n",
       "      <th>post</th>\n",
       "      <td>161</td>\n",
       "      <td>161</td>\n",
       "      <td>143</td>\n",
       "      <td>143</td>\n",
       "      <td>143</td>\n",
       "      <td>159</td>\n",
       "      <td>159</td>\n",
       "      <td>159</td>\n",
       "      <td>159</td>\n",
       "      <td>159</td>\n",
       "      <td>...</td>\n",
       "      <td>161</td>\n",
       "      <td>161</td>\n",
       "      <td>161</td>\n",
       "      <td>161</td>\n",
       "      <td>161</td>\n",
       "      <td>161</td>\n",
       "      <td>15</td>\n",
       "      <td>121</td>\n",
       "      <td>161</td>\n",
       "      <td>159</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>pre</th>\n",
       "      <td>163</td>\n",
       "      <td>163</td>\n",
       "      <td>124</td>\n",
       "      <td>124</td>\n",
       "      <td>124</td>\n",
       "      <td>138</td>\n",
       "      <td>138</td>\n",
       "      <td>138</td>\n",
       "      <td>138</td>\n",
       "      <td>138</td>\n",
       "      <td>...</td>\n",
       "      <td>163</td>\n",
       "      <td>163</td>\n",
       "      <td>163</td>\n",
       "      <td>163</td>\n",
       "      <td>163</td>\n",
       "      <td>163</td>\n",
       "      <td>17</td>\n",
       "      <td>118</td>\n",
       "      <td>163</td>\n",
       "      <td>163</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>8 rows × 126 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                           BarcodeSequence  LinkerPrimerSequence  \\\n",
       "male treatmentgroup visit                                          \n",
       "0.0  UDCA           post                63                    63   \n",
       "                    pre                 65                    65   \n",
       "     placebo        post                90                    90   \n",
       "                    pre                 88                    88   \n",
       "1.0  UDCA           post               190                   190   \n",
       "                    pre                186                   186   \n",
       "     placebo        post               161                   161   \n",
       "                    pre                163                   163   \n",
       "\n",
       "                           OTU-WeightedUniFrac-PC1  OTU-UnweightedUniFrac-PC1  \\\n",
       "male treatmentgroup visit                                                       \n",
       "0.0  UDCA           post                        53                         53   \n",
       "                    pre                         50                         50   \n",
       "     placebo        post                        77                         77   \n",
       "                    pre                         66                         66   \n",
       "1.0  UDCA           post                       164                        164   \n",
       "                    pre                        133                        133   \n",
       "     placebo        post                       143                        143   \n",
       "                    pre                        124                        124   \n",
       "\n",
       "                           OTU-PD  Derep-WeightedUniFrac-PC1  \\\n",
       "male treatmentgroup visit                                      \n",
       "0.0  UDCA           post       53                         57   \n",
       "                    pre        50                         53   \n",
       "     placebo        post       77                         84   \n",
       "                    pre        66                         75   \n",
       "1.0  UDCA           post      164                        184   \n",
       "                    pre       133                        151   \n",
       "     placebo        post      143                        159   \n",
       "                    pre       124                        138   \n",
       "\n",
       "                           Derep-WeightedUniFrac-PC2  \\\n",
       "male treatmentgroup visit                              \n",
       "0.0  UDCA           post                          57   \n",
       "                    pre                           53   \n",
       "     placebo        post                          84   \n",
       "                    pre                           75   \n",
       "1.0  UDCA           post                         184   \n",
       "                    pre                          151   \n",
       "     placebo        post                         159   \n",
       "                    pre                          138   \n",
       "\n",
       "                           Derep-WeightedUniFrac-PC3  \\\n",
       "male treatmentgroup visit                              \n",
       "0.0  UDCA           post                          57   \n",
       "                    pre                           53   \n",
       "     placebo        post                          84   \n",
       "                    pre                           75   \n",
       "1.0  UDCA           post                         184   \n",
       "                    pre                          151   \n",
       "     placebo        post                         159   \n",
       "                    pre                          138   \n",
       "\n",
       "                           Derep-UnweightedUniFrac-PC1  \\\n",
       "male treatmentgroup visit                                \n",
       "0.0  UDCA           post                            57   \n",
       "                    pre                             53   \n",
       "     placebo        post                            84   \n",
       "                    pre                             75   \n",
       "1.0  UDCA           post                           184   \n",
       "                    pre                            151   \n",
       "     placebo        post                           159   \n",
       "                    pre                            138   \n",
       "\n",
       "                           Derep-UnweightedUniFrac-PC2         ...          \\\n",
       "male treatmentgroup visit                                      ...           \n",
       "0.0  UDCA           post                            57         ...           \n",
       "                    pre                             53         ...           \n",
       "     placebo        post                            84         ...           \n",
       "                    pre                             75         ...           \n",
       "1.0  UDCA           post                           184         ...           \n",
       "                    pre                            151         ...           \n",
       "     placebo        post                           159         ...           \n",
       "                    pre                            138         ...           \n",
       "\n",
       "                           gala  argi  putrescine  spermidine  spermine  poly  \\\n",
       "male treatmentgroup visit                                                       \n",
       "0.0  UDCA           post     63    63          63          63        63    63   \n",
       "                    pre      65    65          65          65        65    65   \n",
       "     placebo        post     90    90          90          90        90    90   \n",
       "                    pre      88    88          88          88        88    88   \n",
       "1.0  UDCA           post    190   190         190         190       190   190   \n",
       "                    pre     186   186         186         186       186   186   \n",
       "     placebo        post    161   161         161         161       161   161   \n",
       "                    pre     163   163         163         163       163   163   \n",
       "\n",
       "                           Days_Since_Epoch  Description1  Description  \\\n",
       "male treatmentgroup visit                                                \n",
       "0.0  UDCA           post                 11            43           63   \n",
       "                    pre                  14            45           65   \n",
       "     placebo        post                 16            67           90   \n",
       "                    pre                  13            63           88   \n",
       "1.0  UDCA           post                 19           151          190   \n",
       "                    pre                  14           141          186   \n",
       "     placebo        post                 15           121          161   \n",
       "                    pre                  17           118          163   \n",
       "\n",
       "                           Begin_collect_date  \n",
       "male treatmentgroup visit                      \n",
       "0.0  UDCA           post                   62  \n",
       "                    pre                    65  \n",
       "     placebo        post                   89  \n",
       "                    pre                    88  \n",
       "1.0  UDCA           post                  188  \n",
       "                    pre                   186  \n",
       "     placebo        post                  159  \n",
       "                    pre                   163  \n",
       "\n",
       "[8 rows x 126 columns]"
      ]
     },
     "execution_count": 16,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "sample_md.groupby(['male', 'treatmentgroup', 'visit']).count()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "data-analysis-conda",
   "language": "python",
   "name": "auto_data-analysis-conda"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.5.1"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 0
}