examples/pH_data/qiime2/read data.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T18:59:53.916880Z",
     "start_time": "2020-12-14T18:59:52.523503Z"
    }
   },
   "outputs": [],
   "source": [
    "import qiime2\n",
    "import pandas as pd\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T18:59:53.948936Z",
     "start_time": "2020-12-14T18:59:53.920509Z"
    }
   },
   "outputs": [],
   "source": [
    "metadata = pd.read_table('originals/88soils_modified_metadata.txt', index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T18:59:54.042479Z",
     "start_time": "2020-12-14T18:59:53.957046Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/html": [
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       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
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       "\n",
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       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>BarcodeSequence</th>\n",
       "      <th>LinkerPrimerSequence</th>\n",
       "      <th>barcode_read_group_tag</th>\n",
       "      <th>dna_extracted_prep</th>\n",
       "      <th>experiment_alias</th>\n",
       "      <th>experiment_center</th>\n",
       "      <th>experiment_design_description</th>\n",
       "      <th>experiment_title</th>\n",
       "      <th>instrument_name</th>\n",
       "      <th>key_seq</th>\n",
       "      <th>...</th>\n",
       "      <th>taxon_id</th>\n",
       "      <th>texture</th>\n",
       "      <th>title</th>\n",
       "      <th>tot_org_carb</th>\n",
       "      <th>tot_org_nitro</th>\n",
       "      <th>Description</th>\n",
       "      <th>ph2</th>\n",
       "      <th>ph3</th>\n",
       "      <th>ph4</th>\n",
       "      <th>ph_rounded</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",
       "      <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>103.BZ1</th>\n",
       "      <td>ACACATGTCTAC</td>\n",
       "      <td>CATGCTGCCTCCCGTAGGAGT</td>\n",
       "      <td>BZ1_V2</td>\n",
       "      <td>True</td>\n",
       "      <td>lauber_88_soils</td>\n",
       "      <td>CCME</td>\n",
       "      <td>bacterial biogeography</td>\n",
       "      <td>Pyrosequencing_based_assessment_of_soil_pH_as_...</td>\n",
       "      <td>Engencore</td>\n",
       "      <td>TCAG</td>\n",
       "      <td>...</td>\n",
       "      <td>410658</td>\n",
       "      <td>silt loam</td>\n",
       "      <td>Pyrosequencing-Based Assessment of Soil pH as ...</td>\n",
       "      <td>30.3</td>\n",
       "      <td>0.0</td>\n",
       "      <td>soil metagenome</td>\n",
       "      <td>26.2144</td>\n",
       "      <td>134.217728</td>\n",
       "      <td>687.194767</td>\n",
       "      <td>5_</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.CR1</th>\n",
       "      <td>ACCACATACATC</td>\n",
       "      <td>CATGCTGCCTCCCGTAGGAGT</td>\n",
       "      <td>CR1_V2</td>\n",
       "      <td>True</td>\n",
       "      <td>lauber_88_soils</td>\n",
       "      <td>CCME</td>\n",
       "      <td>bacterial biogeography</td>\n",
       "      <td>Pyrosequencing_based_assessment_of_soil_pH_as_...</td>\n",
       "      <td>Engencore</td>\n",
       "      <td>TCAG</td>\n",
       "      <td>...</td>\n",
       "      <td>410658</td>\n",
       "      <td>loam</td>\n",
       "      <td>Pyrosequencing-Based Assessment of Soil pH as ...</td>\n",
       "      <td>28.3</td>\n",
       "      <td>10.9</td>\n",
       "      <td>soil metagenome</td>\n",
       "      <td>64.0000</td>\n",
       "      <td>512.000000</td>\n",
       "      <td>4096.000000</td>\n",
       "      <td>8_</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.GB2</th>\n",
       "      <td>ACCTGTCTCTCT</td>\n",
       "      <td>CATGCTGCCTCCCGTAGGAGT</td>\n",
       "      <td>GB2_V2</td>\n",
       "      <td>True</td>\n",
       "      <td>lauber_88_soils</td>\n",
       "      <td>CCME</td>\n",
       "      <td>bacterial biogeography</td>\n",
       "      <td>Pyrosequencing_based_assessment_of_soil_pH_as_...</td>\n",
       "      <td>Engencore</td>\n",
       "      <td>TCAG</td>\n",
       "      <td>...</td>\n",
       "      <td>410658</td>\n",
       "      <td>loam</td>\n",
       "      <td>Pyrosequencing-Based Assessment of Soil pH as ...</td>\n",
       "      <td>68.9</td>\n",
       "      <td>0.0</td>\n",
       "      <td>soil metagenome</td>\n",
       "      <td>57.3049</td>\n",
       "      <td>433.798093</td>\n",
       "      <td>3283.851564</td>\n",
       "      <td>7_</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.GB3</th>\n",
       "      <td>ACGACGTCTTAG</td>\n",
       "      <td>CATGCTGCCTCCCGTAGGAGT</td>\n",
       "      <td>GB3_V2</td>\n",
       "      <td>True</td>\n",
       "      <td>lauber_88_soils</td>\n",
       "      <td>CCME</td>\n",
       "      <td>bacterial biogeography</td>\n",
       "      <td>Pyrosequencing_based_assessment_of_soil_pH_as_...</td>\n",
       "      <td>Engencore</td>\n",
       "      <td>TCAG</td>\n",
       "      <td>...</td>\n",
       "      <td>410658</td>\n",
       "      <td>clay loam</td>\n",
       "      <td>Pyrosequencing-Based Assessment of Soil pH as ...</td>\n",
       "      <td>57.1</td>\n",
       "      <td>0.0</td>\n",
       "      <td>soil metagenome</td>\n",
       "      <td>51.5524</td>\n",
       "      <td>370.146232</td>\n",
       "      <td>2657.649946</td>\n",
       "      <td>7_</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.GB1</th>\n",
       "      <td>ACCTCGATCAGA</td>\n",
       "      <td>CATGCTGCCTCCCGTAGGAGT</td>\n",
       "      <td>GB1_V2</td>\n",
       "      <td>True</td>\n",
       "      <td>lauber_88_soils</td>\n",
       "      <td>CCME</td>\n",
       "      <td>bacterial biogeography</td>\n",
       "      <td>Pyrosequencing_based_assessment_of_soil_pH_as_...</td>\n",
       "      <td>Engencore</td>\n",
       "      <td>TCAG</td>\n",
       "      <td>...</td>\n",
       "      <td>410658</td>\n",
       "      <td>clay loam</td>\n",
       "      <td>Pyrosequencing-Based Assessment of Soil pH as ...</td>\n",
       "      <td>28.2</td>\n",
       "      <td>0.0</td>\n",
       "      <td>soil metagenome</td>\n",
       "      <td>46.7856</td>\n",
       "      <td>320.013504</td>\n",
       "      <td>2188.892367</td>\n",
       "      <td>6_</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.SV1</th>\n",
       "      <td>AGCTCTCAGAGG</td>\n",
       "      <td>CATGCTGCCTCCCGTAGGAGT</td>\n",
       "      <td>SV1_V2</td>\n",
       "      <td>True</td>\n",
       "      <td>lauber_88_soils</td>\n",
       "      <td>CCME</td>\n",
       "      <td>bacterial biogeography</td>\n",
       "      <td>Pyrosequencing_based_assessment_of_soil_pH_as_...</td>\n",
       "      <td>Engencore</td>\n",
       "      <td>TCAG</td>\n",
       "      <td>...</td>\n",
       "      <td>410658</td>\n",
       "      <td>sandy loam</td>\n",
       "      <td>Pyrosequencing-Based Assessment of Soil pH as ...</td>\n",
       "      <td>3.0</td>\n",
       "      <td>5.3</td>\n",
       "      <td>soil metagenome</td>\n",
       "      <td>69.0561</td>\n",
       "      <td>573.856191</td>\n",
       "      <td>4768.744947</td>\n",
       "      <td>8_</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.HI4</th>\n",
       "      <td>ACGCTCATGGAT</td>\n",
       "      <td>CATGCTGCCTCCCGTAGGAGT</td>\n",
       "      <td>HI4_V2</td>\n",
       "      <td>True</td>\n",
       "      <td>lauber_88_soils</td>\n",
       "      <td>CCME</td>\n",
       "      <td>bacterial biogeography</td>\n",
       "      <td>Pyrosequencing_based_assessment_of_soil_pH_as_...</td>\n",
       "      <td>Engencore</td>\n",
       "      <td>TCAG</td>\n",
       "      <td>...</td>\n",
       "      <td>410658</td>\n",
       "      <td>loam</td>\n",
       "      <td>Pyrosequencing-Based Assessment of Soil pH as ...</td>\n",
       "      <td>108.2</td>\n",
       "      <td>0.0</td>\n",
       "      <td>soil metagenome</td>\n",
       "      <td>24.2064</td>\n",
       "      <td>119.095488</td>\n",
       "      <td>585.949801</td>\n",
       "      <td>4_</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.HI1</th>\n",
       "      <td>ACGCGATACTGG</td>\n",
       "      <td>CATGCTGCCTCCCGTAGGAGT</td>\n",
       "      <td>HI1_V2</td>\n",
       "      <td>True</td>\n",
       "      <td>lauber_88_soils</td>\n",
       "      <td>CCME</td>\n",
       "      <td>bacterial biogeography</td>\n",
       "      <td>Pyrosequencing_based_assessment_of_soil_pH_as_...</td>\n",
       "      <td>Engencore</td>\n",
       "      <td>TCAG</td>\n",
       "      <td>...</td>\n",
       "      <td>410658</td>\n",
       "      <td>loam</td>\n",
       "      <td>Pyrosequencing-Based Assessment of Soil pH as ...</td>\n",
       "      <td>11.4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>soil metagenome</td>\n",
       "      <td>41.6025</td>\n",
       "      <td>268.336125</td>\n",
       "      <td>1730.768006</td>\n",
       "      <td>6_</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.HI2</th>\n",
       "      <td>ACGCGCAGATAC</td>\n",
       "      <td>CATGCTGCCTCCCGTAGGAGT</td>\n",
       "      <td>HI2_V2</td>\n",
       "      <td>True</td>\n",
       "      <td>lauber_88_soils</td>\n",
       "      <td>CCME</td>\n",
       "      <td>bacterial biogeography</td>\n",
       "      <td>Pyrosequencing_based_assessment_of_soil_pH_as_...</td>\n",
       "      <td>Engencore</td>\n",
       "      <td>TCAG</td>\n",
       "      <td>...</td>\n",
       "      <td>410658</td>\n",
       "      <td>sandy loam</td>\n",
       "      <td>Pyrosequencing-Based Assessment of Soil pH as ...</td>\n",
       "      <td>158.8</td>\n",
       "      <td>0.0</td>\n",
       "      <td>soil metagenome</td>\n",
       "      <td>39.9424</td>\n",
       "      <td>252.435968</td>\n",
       "      <td>1595.395318</td>\n",
       "      <td>6_</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.HI3</th>\n",
       "      <td>ACGCTATCTGGA</td>\n",
       "      <td>CATGCTGCCTCCCGTAGGAGT</td>\n",
       "      <td>HI3_V2</td>\n",
       "      <td>True</td>\n",
       "      <td>lauber_88_soils</td>\n",
       "      <td>CCME</td>\n",
       "      <td>bacterial biogeography</td>\n",
       "      <td>Pyrosequencing_based_assessment_of_soil_pH_as_...</td>\n",
       "      <td>Engencore</td>\n",
       "      <td>TCAG</td>\n",
       "      <td>...</td>\n",
       "      <td>410658</td>\n",
       "      <td>loamy sand</td>\n",
       "      <td>Pyrosequencing-Based Assessment of Soil pH as ...</td>\n",
       "      <td>182.4</td>\n",
       "      <td>0.0</td>\n",
       "      <td>soil metagenome</td>\n",
       "      <td>42.6409</td>\n",
       "      <td>278.445077</td>\n",
       "      <td>1818.246353</td>\n",
       "      <td>6_</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>89 rows × 69 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "          BarcodeSequence   LinkerPrimerSequence barcode_read_group_tag  \\\n",
       "#SampleID                                                                 \n",
       "103.BZ1      ACACATGTCTAC  CATGCTGCCTCCCGTAGGAGT                 BZ1_V2   \n",
       "103.CR1      ACCACATACATC  CATGCTGCCTCCCGTAGGAGT                 CR1_V2   \n",
       "103.GB2      ACCTGTCTCTCT  CATGCTGCCTCCCGTAGGAGT                 GB2_V2   \n",
       "103.GB3      ACGACGTCTTAG  CATGCTGCCTCCCGTAGGAGT                 GB3_V2   \n",
       "103.GB1      ACCTCGATCAGA  CATGCTGCCTCCCGTAGGAGT                 GB1_V2   \n",
       "...                   ...                    ...                    ...   \n",
       "103.SV1      AGCTCTCAGAGG  CATGCTGCCTCCCGTAGGAGT                 SV1_V2   \n",
       "103.HI4      ACGCTCATGGAT  CATGCTGCCTCCCGTAGGAGT                 HI4_V2   \n",
       "103.HI1      ACGCGATACTGG  CATGCTGCCTCCCGTAGGAGT                 HI1_V2   \n",
       "103.HI2      ACGCGCAGATAC  CATGCTGCCTCCCGTAGGAGT                 HI2_V2   \n",
       "103.HI3      ACGCTATCTGGA  CATGCTGCCTCCCGTAGGAGT                 HI3_V2   \n",
       "\n",
       "           dna_extracted_prep experiment_alias experiment_center  \\\n",
       "#SampleID                                                          \n",
       "103.BZ1                  True  lauber_88_soils              CCME   \n",
       "103.CR1                  True  lauber_88_soils              CCME   \n",
       "103.GB2                  True  lauber_88_soils              CCME   \n",
       "103.GB3                  True  lauber_88_soils              CCME   \n",
       "103.GB1                  True  lauber_88_soils              CCME   \n",
       "...                       ...              ...               ...   \n",
       "103.SV1                  True  lauber_88_soils              CCME   \n",
       "103.HI4                  True  lauber_88_soils              CCME   \n",
       "103.HI1                  True  lauber_88_soils              CCME   \n",
       "103.HI2                  True  lauber_88_soils              CCME   \n",
       "103.HI3                  True  lauber_88_soils              CCME   \n",
       "\n",
       "          experiment_design_description  \\\n",
       "#SampleID                                 \n",
       "103.BZ1          bacterial biogeography   \n",
       "103.CR1          bacterial biogeography   \n",
       "103.GB2          bacterial biogeography   \n",
       "103.GB3          bacterial biogeography   \n",
       "103.GB1          bacterial biogeography   \n",
       "...                                 ...   \n",
       "103.SV1          bacterial biogeography   \n",
       "103.HI4          bacterial biogeography   \n",
       "103.HI1          bacterial biogeography   \n",
       "103.HI2          bacterial biogeography   \n",
       "103.HI3          bacterial biogeography   \n",
       "\n",
       "                                            experiment_title instrument_name  \\\n",
       "#SampleID                                                                      \n",
       "103.BZ1    Pyrosequencing_based_assessment_of_soil_pH_as_...       Engencore   \n",
       "103.CR1    Pyrosequencing_based_assessment_of_soil_pH_as_...       Engencore   \n",
       "103.GB2    Pyrosequencing_based_assessment_of_soil_pH_as_...       Engencore   \n",
       "103.GB3    Pyrosequencing_based_assessment_of_soil_pH_as_...       Engencore   \n",
       "103.GB1    Pyrosequencing_based_assessment_of_soil_pH_as_...       Engencore   \n",
       "...                                                      ...             ...   \n",
       "103.SV1    Pyrosequencing_based_assessment_of_soil_pH_as_...       Engencore   \n",
       "103.HI4    Pyrosequencing_based_assessment_of_soil_pH_as_...       Engencore   \n",
       "103.HI1    Pyrosequencing_based_assessment_of_soil_pH_as_...       Engencore   \n",
       "103.HI2    Pyrosequencing_based_assessment_of_soil_pH_as_...       Engencore   \n",
       "103.HI3    Pyrosequencing_based_assessment_of_soil_pH_as_...       Engencore   \n",
       "\n",
       "          key_seq  ...  taxon_id     texture  \\\n",
       "#SampleID          ...                         \n",
       "103.BZ1      TCAG  ...    410658   silt loam   \n",
       "103.CR1      TCAG  ...    410658        loam   \n",
       "103.GB2      TCAG  ...    410658        loam   \n",
       "103.GB3      TCAG  ...    410658   clay loam   \n",
       "103.GB1      TCAG  ...    410658   clay loam   \n",
       "...           ...  ...       ...         ...   \n",
       "103.SV1      TCAG  ...    410658  sandy loam   \n",
       "103.HI4      TCAG  ...    410658        loam   \n",
       "103.HI1      TCAG  ...    410658        loam   \n",
       "103.HI2      TCAG  ...    410658  sandy loam   \n",
       "103.HI3      TCAG  ...    410658  loamy sand   \n",
       "\n",
       "                                                       title  tot_org_carb  \\\n",
       "#SampleID                                                                    \n",
       "103.BZ1    Pyrosequencing-Based Assessment of Soil pH as ...          30.3   \n",
       "103.CR1    Pyrosequencing-Based Assessment of Soil pH as ...          28.3   \n",
       "103.GB2    Pyrosequencing-Based Assessment of Soil pH as ...          68.9   \n",
       "103.GB3    Pyrosequencing-Based Assessment of Soil pH as ...          57.1   \n",
       "103.GB1    Pyrosequencing-Based Assessment of Soil pH as ...          28.2   \n",
       "...                                                      ...           ...   \n",
       "103.SV1    Pyrosequencing-Based Assessment of Soil pH as ...           3.0   \n",
       "103.HI4    Pyrosequencing-Based Assessment of Soil pH as ...         108.2   \n",
       "103.HI1    Pyrosequencing-Based Assessment of Soil pH as ...          11.4   \n",
       "103.HI2    Pyrosequencing-Based Assessment of Soil pH as ...         158.8   \n",
       "103.HI3    Pyrosequencing-Based Assessment of Soil pH as ...         182.4   \n",
       "\n",
       "          tot_org_nitro      Description      ph2         ph3          ph4  \\\n",
       "#SampleID                                                                    \n",
       "103.BZ1             0.0  soil metagenome  26.2144  134.217728   687.194767   \n",
       "103.CR1            10.9  soil metagenome  64.0000  512.000000  4096.000000   \n",
       "103.GB2             0.0  soil metagenome  57.3049  433.798093  3283.851564   \n",
       "103.GB3             0.0  soil metagenome  51.5524  370.146232  2657.649946   \n",
       "103.GB1             0.0  soil metagenome  46.7856  320.013504  2188.892367   \n",
       "...                 ...              ...      ...         ...          ...   \n",
       "103.SV1             5.3  soil metagenome  69.0561  573.856191  4768.744947   \n",
       "103.HI4             0.0  soil metagenome  24.2064  119.095488   585.949801   \n",
       "103.HI1             0.0  soil metagenome  41.6025  268.336125  1730.768006   \n",
       "103.HI2             0.0  soil metagenome  39.9424  252.435968  1595.395318   \n",
       "103.HI3             0.0  soil metagenome  42.6409  278.445077  1818.246353   \n",
       "\n",
       "          ph_rounded  \n",
       "#SampleID             \n",
       "103.BZ1           5_  \n",
       "103.CR1           8_  \n",
       "103.GB2           7_  \n",
       "103.GB3           7_  \n",
       "103.GB1           6_  \n",
       "...              ...  \n",
       "103.SV1           8_  \n",
       "103.HI4           4_  \n",
       "103.HI1           6_  \n",
       "103.HI2           6_  \n",
       "103.HI3           6_  \n",
       "\n",
       "[89 rows x 69 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T18:59:54.054891Z",
     "start_time": "2020-12-14T18:59:54.045947Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "(89,)"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "y = metadata[\"ph\"].values\n",
    "y.shape"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T19:00:24.620542Z",
     "start_time": "2020-12-14T18:59:54.064530Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Imported originals/238_otu_table.biom as BIOMV210DirFmt to news/88soils.biom.qza\n",
      "Imported originals/88soils_taxonomy.txt as TSVTaxonomyDirectoryFormat to news/88soils_taxonomy.qza\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "qiime tools import \\\n",
    "    --input-path originals/238_otu_table.biom \\\n",
    "    --output-path news/88soils.biom.qza \\\n",
    "    --type FeatureTable[Frequency]\n",
    "\n",
    "qiime tools import \\\n",
    "    --input-path originals/88soils_taxonomy.txt \\\n",
    "    --output-path news/88soils_taxonomy.qza \\\n",
    "    --type FeatureData[Taxonomy]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T19:00:31.124280Z",
     "start_time": "2020-12-14T19:00:24.625851Z"
    }
   },
   "outputs": [],
   "source": [
    "# Load the table\n",
    "table_art = qiime2.Artifact.load('news/88soils.biom.qza')\n",
    "table = table_art.view(pd.DataFrame)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T19:00:31.187473Z",
     "start_time": "2020-12-14T19:00:31.127657Z"
    },
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>1124701</th>\n",
       "      <th>244336</th>\n",
       "      <th>973124</th>\n",
       "      <th>809489</th>\n",
       "      <th>533625</th>\n",
       "      <th>2725587</th>\n",
       "      <th>623634</th>\n",
       "      <th>114076</th>\n",
       "      <th>511344</th>\n",
       "      <th>544561</th>\n",
       "      <th>...</th>\n",
       "      <th>620041</th>\n",
       "      <th>2970431</th>\n",
       "      <th>3897749</th>\n",
       "      <th>369734</th>\n",
       "      <th>823633</th>\n",
       "      <th>4433961</th>\n",
       "      <th>160412</th>\n",
       "      <th>3893085</th>\n",
       "      <th>2063454</th>\n",
       "      <th>848259</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>103.CA2</th>\n",
       "      <td>15.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
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       "      <th>103.CO3</th>\n",
       "      <td>14.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "    <tr>\n",
       "      <th>103.SR3</th>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.IE2</th>\n",
       "      <td>8.0</td>\n",
       "      <td>1.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "    <tr>\n",
       "      <th>103.BP1</th>\n",
       "      <td>13.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>103.CF3</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "    <tr>\n",
       "      <th>103.AR1</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>2.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.TL1</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
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       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.HI4</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>3.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.BB1</th>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>...</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "      <td>0.0</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>89 rows × 7396 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "         1124701  244336  973124  809489  533625  2725587  623634  114076  \\\n",
       "103.CA2     15.0     0.0     0.0     0.0     0.0      0.0     0.0     0.0   \n",
       "103.CO3     14.0     0.0     0.0     0.0     0.0      0.0     0.0     0.0   \n",
       "103.SR3      1.0     0.0     0.0     0.0     0.0      0.0     0.0     1.0   \n",
       "103.IE2      8.0     1.0     0.0     0.0     0.0      0.0     0.0     0.0   \n",
       "103.BP1     13.0     0.0     0.0     0.0     0.0      0.0     0.0     0.0   \n",
       "...          ...     ...     ...     ...     ...      ...     ...     ...   \n",
       "103.CF3      0.0     0.0     0.0     0.0     0.0      0.0     0.0     0.0   \n",
       "103.AR1      0.0     0.0     0.0     0.0     0.0      0.0     0.0     0.0   \n",
       "103.TL1      0.0     0.0     0.0     0.0     0.0      0.0     0.0     0.0   \n",
       "103.HI4      0.0     0.0     0.0     0.0     0.0      0.0     0.0     0.0   \n",
       "103.BB1      0.0     0.0     0.0     0.0     0.0      0.0     0.0     0.0   \n",
       "\n",
       "         511344  544561  ...  620041  2970431  3897749  369734  823633  \\\n",
       "103.CA2     0.0     0.0  ...     0.0      0.0      0.0     0.0     0.0   \n",
       "103.CO3     0.0     0.0  ...     1.0      0.0      0.0     0.0     1.0   \n",
       "103.SR3     0.0     0.0  ...     2.0      0.0      1.0     0.0     1.0   \n",
       "103.IE2     0.0     0.0  ...     0.0      0.0      0.0     0.0     1.0   \n",
       "103.BP1     0.0     0.0  ...     0.0      0.0      0.0     0.0     1.0   \n",
       "...         ...     ...  ...     ...      ...      ...     ...     ...   \n",
       "103.CF3     0.0     0.0  ...     0.0      0.0      0.0     0.0     0.0   \n",
       "103.AR1     0.0     0.0  ...     0.0      0.0      2.0     0.0     0.0   \n",
       "103.TL1     0.0     0.0  ...     0.0      0.0      0.0     0.0     0.0   \n",
       "103.HI4     0.0     0.0  ...     0.0      3.0      0.0     0.0     0.0   \n",
       "103.BB1     0.0     0.0  ...     0.0      0.0      0.0     0.0     0.0   \n",
       "\n",
       "         4433961  160412  3893085  2063454  848259  \n",
       "103.CA2      0.0     0.0      0.0      0.0     0.0  \n",
       "103.CO3      0.0     0.0      0.0      0.0     0.0  \n",
       "103.SR3      0.0     0.0      0.0      0.0     0.0  \n",
       "103.IE2      0.0     0.0      0.0      0.0     0.0  \n",
       "103.BP1      0.0     0.0      0.0      0.0     0.0  \n",
       "...          ...     ...      ...      ...     ...  \n",
       "103.CF3      0.0     0.0      0.0      0.0     0.0  \n",
       "103.AR1      0.0     0.0      0.0      0.0     0.0  \n",
       "103.TL1      0.0     0.0      0.0      0.0     0.0  \n",
       "103.HI4      0.0     0.0      0.0      0.0     0.0  \n",
       "103.BB1      0.0     0.0      0.0      0.0     0.0  \n",
       "\n",
       "[89 rows x 7396 columns]"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "table"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T19:00:40.418369Z",
     "start_time": "2020-12-14T19:00:31.189770Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Saved FeatureTable[Frequency] to: news/88soils_filt100.biom.qza\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "qiime feature-table filter-features \\\n",
    "    --i-table news/88soils.biom.qza \\\n",
    "    --o-filtered-table news/88soils_filt100.biom.qza \\\n",
    "    --p-min-frequency 100"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T19:01:18.637989Z",
     "start_time": "2020-12-14T19:00:40.422304Z"
    }
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Saved Hierarchy to: news/ph_tree.nwk.qza\n",
      "Saved FeatureTable[Composition] to: news/88soils_composition.biom.qza\n",
      "Saved FeatureTable[Balance] to: news/88soils_balances.qza\n"
     ]
    }
   ],
   "source": [
    "%%bash\n",
    "qiime gneiss gradient-clustering \\\n",
    "    --i-table news/88soils_filt100.biom.qza \\\n",
    "    --m-gradient-file originals/88soils_metadata.txt \\\n",
    "    --m-gradient-column ph \\\n",
    "    --o-clustering news/ph_tree.nwk.qza \\\n",
    "    --p-no-weighted\n",
    "    \n",
    "qiime composition add-pseudocount \\\n",
    "    --i-table news/88soils_filt100.biom.qza \\\n",
    "    --p-pseudocount 1 \\\n",
    "    --o-composition-table news/88soils_composition.biom.qza\n",
    "    \n",
    "qiime gneiss ilr-hierarchical\\\n",
    "    --i-table news/88soils_composition.biom.qza \\\n",
    "    --i-tree news/ph_tree.nwk.qza \\\n",
    "    --o-balances news/88soils_balances.qza"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T19:01:18.704761Z",
     "start_time": "2020-12-14T19:01:18.641399Z"
    }
   },
   "outputs": [],
   "source": [
    "# Load the table\n",
    "table_art = qiime2.Artifact.load('news/88soils_balances.qza')\n",
    "table = table_art.view(pd.DataFrame)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T19:01:18.752808Z",
     "start_time": "2020-12-14T19:01:18.707009Z"
    }
   },
   "outputs": [
    {
     "data": {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>y0</th>\n",
       "      <th>y2</th>\n",
       "      <th>y1</th>\n",
       "      <th>y5</th>\n",
       "      <th>y6</th>\n",
       "      <th>y4</th>\n",
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       "      <th>...</th>\n",
       "      <th>y109</th>\n",
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       "      <th>y116</th>\n",
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       "  </thead>\n",
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       "    <tr>\n",
       "      <th>103.CA2</th>\n",
       "      <td>6.017405</td>\n",
       "      <td>1.300712</td>\n",
       "      <td>-1.583031e+00</td>\n",
       "      <td>1.163362e-15</td>\n",
       "      <td>0.367869</td>\n",
       "      <td>1.592500e-01</td>\n",
       "      <td>-1.860294e+00</td>\n",
       "      <td>9.724289e-15</td>\n",
       "      <td>1.046054e-17</td>\n",
       "      <td>4.783170e-01</td>\n",
       "      <td>...</td>\n",
       "      <td>4.410147e-16</td>\n",
       "      <td>-4.183063e-16</td>\n",
       "      <td>4.508377e-16</td>\n",
       "      <td>4.114228e-16</td>\n",
       "      <td>-4.901291e-01</td>\n",
       "      <td>2.419823e-16</td>\n",
       "      <td>2.070660e-16</td>\n",
       "      <td>4.472881e-16</td>\n",
       "      <td>4.374651e-16</td>\n",
       "      <td>4.455133e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.CO3</th>\n",
       "      <td>4.283538</td>\n",
       "      <td>2.598426</td>\n",
       "      <td>-3.668994e+00</td>\n",
       "      <td>2.394468e-01</td>\n",
       "      <td>0.699803</td>\n",
       "      <td>-9.002491e-01</td>\n",
       "      <td>-7.907558e-01</td>\n",
       "      <td>1.018747e-01</td>\n",
       "      <td>2.465209e-01</td>\n",
       "      <td>-4.844185e-01</td>\n",
       "      <td>...</td>\n",
       "      <td>7.768362e-01</td>\n",
       "      <td>-4.825355e-16</td>\n",
       "      <td>5.241435e-16</td>\n",
       "      <td>-1.138044e+00</td>\n",
       "      <td>-6.479154e-01</td>\n",
       "      <td>2.368225e-16</td>\n",
       "      <td>-2.829762e-01</td>\n",
       "      <td>4.982947e-16</td>\n",
       "      <td>5.022776e-16</td>\n",
       "      <td>4.901291e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.SR3</th>\n",
       "      <td>4.056506</td>\n",
       "      <td>1.714048</td>\n",
       "      <td>7.462289e-01</td>\n",
       "      <td>3.142954e-01</td>\n",
       "      <td>0.631482</td>\n",
       "      <td>-1.222708e-01</td>\n",
       "      <td>-6.067223e-01</td>\n",
       "      <td>8.141817e-15</td>\n",
       "      <td>6.939455e-01</td>\n",
       "      <td>5.622562e-01</td>\n",
       "      <td>...</td>\n",
       "      <td>3.578523e-16</td>\n",
       "      <td>-3.897978e-16</td>\n",
       "      <td>4.056806e-16</td>\n",
       "      <td>4.016062e-16</td>\n",
       "      <td>7.768362e-01</td>\n",
       "      <td>2.157880e-16</td>\n",
       "      <td>1.736781e-16</td>\n",
       "      <td>3.980561e-16</td>\n",
       "      <td>4.057389e-16</td>\n",
       "      <td>3.942438e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.IE2</th>\n",
       "      <td>-2.967948</td>\n",
       "      <td>4.117410</td>\n",
       "      <td>-8.637628e-01</td>\n",
       "      <td>9.103348e-01</td>\n",
       "      <td>-0.681679</td>\n",
       "      <td>-4.402988e-01</td>\n",
       "      <td>2.046386e-15</td>\n",
       "      <td>6.105419e-01</td>\n",
       "      <td>-2.118836e-01</td>\n",
       "      <td>-1.176515e+00</td>\n",
       "      <td>...</td>\n",
       "      <td>1.138044e+00</td>\n",
       "      <td>-5.135196e-16</td>\n",
       "      <td>-4.901291e-01</td>\n",
       "      <td>7.153099e-01</td>\n",
       "      <td>5.469243e-16</td>\n",
       "      <td>8.970132e-01</td>\n",
       "      <td>8.970132e-01</td>\n",
       "      <td>5.310527e-16</td>\n",
       "      <td>5.230585e-16</td>\n",
       "      <td>-9.802581e-01</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.BP1</th>\n",
       "      <td>4.604773</td>\n",
       "      <td>2.291494</td>\n",
       "      <td>-3.761451e+00</td>\n",
       "      <td>3.647582e-01</td>\n",
       "      <td>0.589138</td>\n",
       "      <td>-1.509287e+00</td>\n",
       "      <td>-3.140556e-01</td>\n",
       "      <td>9.807120e-15</td>\n",
       "      <td>8.948492e-02</td>\n",
       "      <td>2.235710e-01</td>\n",
       "      <td>...</td>\n",
       "      <td>4.386532e-16</td>\n",
       "      <td>-4.736894e-16</td>\n",
       "      <td>4.428474e-16</td>\n",
       "      <td>-9.802581e-01</td>\n",
       "      <td>-4.901291e-01</td>\n",
       "      <td>2.389037e-16</td>\n",
       "      <td>2.533204e-16</td>\n",
       "      <td>4.819035e-16</td>\n",
       "      <td>4.472767e-16</td>\n",
       "      <td>4.307041e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.CF3</th>\n",
       "      <td>-4.244988</td>\n",
       "      <td>-5.018429</td>\n",
       "      <td>-9.333141e-15</td>\n",
       "      <td>-2.785376e+00</td>\n",
       "      <td>0.102171</td>\n",
       "      <td>-1.173204e-15</td>\n",
       "      <td>1.930747e-15</td>\n",
       "      <td>6.948292e-01</td>\n",
       "      <td>-1.996018e+00</td>\n",
       "      <td>-2.391585e-02</td>\n",
       "      <td>...</td>\n",
       "      <td>2.867071e-01</td>\n",
       "      <td>-1.138044e+00</td>\n",
       "      <td>-4.901291e-01</td>\n",
       "      <td>5.312056e-16</td>\n",
       "      <td>4.991581e-16</td>\n",
       "      <td>-2.300393e+00</td>\n",
       "      <td>-1.803775e-01</td>\n",
       "      <td>2.590529e+00</td>\n",
       "      <td>1.708309e+00</td>\n",
       "      <td>9.442095e-02</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.AR1</th>\n",
       "      <td>-0.425366</td>\n",
       "      <td>2.999198</td>\n",
       "      <td>-1.521950e+00</td>\n",
       "      <td>6.052052e-01</td>\n",
       "      <td>0.438425</td>\n",
       "      <td>-1.343861e+00</td>\n",
       "      <td>1.441635e-15</td>\n",
       "      <td>1.933831e-01</td>\n",
       "      <td>3.539671e-01</td>\n",
       "      <td>-1.086118e+00</td>\n",
       "      <td>...</td>\n",
       "      <td>3.483796e-16</td>\n",
       "      <td>-3.398883e-16</td>\n",
       "      <td>3.771164e-16</td>\n",
       "      <td>3.612083e-01</td>\n",
       "      <td>3.752868e-16</td>\n",
       "      <td>2.159226e-16</td>\n",
       "      <td>2.071010e-16</td>\n",
       "      <td>-1.138044e+00</td>\n",
       "      <td>3.380178e-16</td>\n",
       "      <td>3.266145e-16</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.TL1</th>\n",
       "      <td>-2.865096</td>\n",
       "      <td>-0.886588</td>\n",
       "      <td>-2.167928e-01</td>\n",
       "      <td>4.692166e-01</td>\n",
       "      <td>-1.907804</td>\n",
       "      <td>-3.364331e-01</td>\n",
       "      <td>1.446390e-15</td>\n",
       "      <td>1.162202e+00</td>\n",
       "      <td>1.696757e+00</td>\n",
       "      <td>3.026021e+00</td>\n",
       "      <td>...</td>\n",
       "      <td>-4.901291e-01</td>\n",
       "      <td>-4.121643e-16</td>\n",
       "      <td>-4.901291e-01</td>\n",
       "      <td>3.845207e-16</td>\n",
       "      <td>4.093179e-16</td>\n",
       "      <td>-5.659523e-01</td>\n",
       "      <td>-1.516059e+00</td>\n",
       "      <td>1.375966e+00</td>\n",
       "      <td>-2.336151e-16</td>\n",
       "      <td>-2.625892e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.HI4</th>\n",
       "      <td>-4.370944</td>\n",
       "      <td>-2.429179</td>\n",
       "      <td>-9.815676e-15</td>\n",
       "      <td>-1.428797e+00</td>\n",
       "      <td>-1.713023</td>\n",
       "      <td>-1.774091e-15</td>\n",
       "      <td>1.829604e-15</td>\n",
       "      <td>1.885191e-01</td>\n",
       "      <td>7.984236e-02</td>\n",
       "      <td>-1.392083e+00</td>\n",
       "      <td>...</td>\n",
       "      <td>1.813693e+00</td>\n",
       "      <td>-5.536801e-16</td>\n",
       "      <td>5.186180e-16</td>\n",
       "      <td>-1.418956e-01</td>\n",
       "      <td>5.536076e-16</td>\n",
       "      <td>2.523826e+00</td>\n",
       "      <td>-3.830470e-01</td>\n",
       "      <td>-1.266965e+00</td>\n",
       "      <td>5.026218e-16</td>\n",
       "      <td>-2.217129e+00</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>103.BB1</th>\n",
       "      <td>-0.042682</td>\n",
       "      <td>0.100777</td>\n",
       "      <td>-9.532878e-17</td>\n",
       "      <td>2.115894e-18</td>\n",
       "      <td>0.126551</td>\n",
       "      <td>-1.202002e-17</td>\n",
       "      <td>2.159697e-17</td>\n",
       "      <td>1.095055e-16</td>\n",
       "      <td>4.670720e-18</td>\n",
       "      <td>1.058619e-18</td>\n",
       "      <td>...</td>\n",
       "      <td>5.053658e-18</td>\n",
       "      <td>-4.873572e-18</td>\n",
       "      <td>5.316955e-18</td>\n",
       "      <td>5.119170e-18</td>\n",
       "      <td>4.799681e-18</td>\n",
       "      <td>2.208088e-18</td>\n",
       "      <td>2.054394e-18</td>\n",
       "      <td>5.459939e-18</td>\n",
       "      <td>5.196642e-18</td>\n",
       "      <td>5.097750e-18</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>89 rows × 118 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "               y0        y2            y1            y5        y6  \\\n",
       "103.CA2  6.017405  1.300712 -1.583031e+00  1.163362e-15  0.367869   \n",
       "103.CO3  4.283538  2.598426 -3.668994e+00  2.394468e-01  0.699803   \n",
       "103.SR3  4.056506  1.714048  7.462289e-01  3.142954e-01  0.631482   \n",
       "103.IE2 -2.967948  4.117410 -8.637628e-01  9.103348e-01 -0.681679   \n",
       "103.BP1  4.604773  2.291494 -3.761451e+00  3.647582e-01  0.589138   \n",
       "...           ...       ...           ...           ...       ...   \n",
       "103.CF3 -4.244988 -5.018429 -9.333141e-15 -2.785376e+00  0.102171   \n",
       "103.AR1 -0.425366  2.999198 -1.521950e+00  6.052052e-01  0.438425   \n",
       "103.TL1 -2.865096 -0.886588 -2.167928e-01  4.692166e-01 -1.907804   \n",
       "103.HI4 -4.370944 -2.429179 -9.815676e-15 -1.428797e+00 -1.713023   \n",
       "103.BB1 -0.042682  0.100777 -9.532878e-17  2.115894e-18  0.126551   \n",
       "\n",
       "                   y4            y3           y12           y11           y13  \\\n",
       "103.CA2  1.592500e-01 -1.860294e+00  9.724289e-15  1.046054e-17  4.783170e-01   \n",
       "103.CO3 -9.002491e-01 -7.907558e-01  1.018747e-01  2.465209e-01 -4.844185e-01   \n",
       "103.SR3 -1.222708e-01 -6.067223e-01  8.141817e-15  6.939455e-01  5.622562e-01   \n",
       "103.IE2 -4.402988e-01  2.046386e-15  6.105419e-01 -2.118836e-01 -1.176515e+00   \n",
       "103.BP1 -1.509287e+00 -3.140556e-01  9.807120e-15  8.948492e-02  2.235710e-01   \n",
       "...               ...           ...           ...           ...           ...   \n",
       "103.CF3 -1.173204e-15  1.930747e-15  6.948292e-01 -1.996018e+00 -2.391585e-02   \n",
       "103.AR1 -1.343861e+00  1.441635e-15  1.933831e-01  3.539671e-01 -1.086118e+00   \n",
       "103.TL1 -3.364331e-01  1.446390e-15  1.162202e+00  1.696757e+00  3.026021e+00   \n",
       "103.HI4 -1.774091e-15  1.829604e-15  1.885191e-01  7.984236e-02 -1.392083e+00   \n",
       "103.BB1 -1.202002e-17  2.159697e-17  1.095055e-16  4.670720e-18  1.058619e-18   \n",
       "\n",
       "         ...          y109          y102          y103          y112  \\\n",
       "103.CA2  ...  4.410147e-16 -4.183063e-16  4.508377e-16  4.114228e-16   \n",
       "103.CO3  ...  7.768362e-01 -4.825355e-16  5.241435e-16 -1.138044e+00   \n",
       "103.SR3  ...  3.578523e-16 -3.897978e-16  4.056806e-16  4.016062e-16   \n",
       "103.IE2  ...  1.138044e+00 -5.135196e-16 -4.901291e-01  7.153099e-01   \n",
       "103.BP1  ...  4.386532e-16 -4.736894e-16  4.428474e-16 -9.802581e-01   \n",
       "...      ...           ...           ...           ...           ...   \n",
       "103.CF3  ...  2.867071e-01 -1.138044e+00 -4.901291e-01  5.312056e-16   \n",
       "103.AR1  ...  3.483796e-16 -3.398883e-16  3.771164e-16  3.612083e-01   \n",
       "103.TL1  ... -4.901291e-01 -4.121643e-16 -4.901291e-01  3.845207e-16   \n",
       "103.HI4  ...  1.813693e+00 -5.536801e-16  5.186180e-16 -1.418956e-01   \n",
       "103.BB1  ...  5.053658e-18 -4.873572e-18  5.316955e-18  5.119170e-18   \n",
       "\n",
       "                 y101          y114          y113          y115          y117  \\\n",
       "103.CA2 -4.901291e-01  2.419823e-16  2.070660e-16  4.472881e-16  4.374651e-16   \n",
       "103.CO3 -6.479154e-01  2.368225e-16 -2.829762e-01  4.982947e-16  5.022776e-16   \n",
       "103.SR3  7.768362e-01  2.157880e-16  1.736781e-16  3.980561e-16  4.057389e-16   \n",
       "103.IE2  5.469243e-16  8.970132e-01  8.970132e-01  5.310527e-16  5.230585e-16   \n",
       "103.BP1 -4.901291e-01  2.389037e-16  2.533204e-16  4.819035e-16  4.472767e-16   \n",
       "...               ...           ...           ...           ...           ...   \n",
       "103.CF3  4.991581e-16 -2.300393e+00 -1.803775e-01  2.590529e+00  1.708309e+00   \n",
       "103.AR1  3.752868e-16  2.159226e-16  2.071010e-16 -1.138044e+00  3.380178e-16   \n",
       "103.TL1  4.093179e-16 -5.659523e-01 -1.516059e+00  1.375966e+00 -2.336151e-16   \n",
       "103.HI4  5.536076e-16  2.523826e+00 -3.830470e-01 -1.266965e+00  5.026218e-16   \n",
       "103.BB1  4.799681e-18  2.208088e-18  2.054394e-18  5.459939e-18  5.196642e-18   \n",
       "\n",
       "                 y116  \n",
       "103.CA2  4.455133e-16  \n",
       "103.CO3  4.901291e-01  \n",
       "103.SR3  3.942438e-16  \n",
       "103.IE2 -9.802581e-01  \n",
       "103.BP1  4.307041e-16  \n",
       "...               ...  \n",
       "103.CF3  9.442095e-02  \n",
       "103.AR1  3.266145e-16  \n",
       "103.TL1 -2.625892e+00  \n",
       "103.HI4 -2.217129e+00  \n",
       "103.BB1  5.097750e-18  \n",
       "\n",
       "[89 rows x 118 columns]"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
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    "table"
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   "cell_type": "code",
   "execution_count": 12,
   "metadata": {
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     "end_time": "2020-12-14T19:01:18.764117Z",
     "start_time": "2020-12-14T19:01:18.755782Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['y0', 'y2', 'y1', 'y5', 'y6', 'y4', 'y3', 'y12', 'y11', 'y13',\n",
       "       ...\n",
       "       'y109', 'y102', 'y103', 'y112', 'y101', 'y114', 'y113', 'y115', 'y117',\n",
       "       'y116'],\n",
       "      dtype='object', length=118)"
      ]
     },
     "execution_count": 12,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
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    "table.columns"
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  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T19:01:18.800529Z",
     "start_time": "2020-12-14T19:01:18.766635Z"
    }
   },
   "outputs": [],
   "source": [
    "tax = pd.read_table('originals/88soils_taxonomy.txt', index_col=0)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T19:01:18.816490Z",
     "start_time": "2020-12-14T19:01:18.802777Z"
    }
   },
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Taxon</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Feature ID</th>\n",
       "      <th></th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>1000512</th>\n",
       "      <td>k__Bacteria;p__Actinobacteria;c__Thermoleophil...</td>\n",
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       "    <tr>\n",
       "      <th>1000547</th>\n",
       "      <td>k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactob...</td>\n",
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       "    <tr>\n",
       "      <th>1000654</th>\n",
       "      <td>k__Bacteria;p__Bacteroidetes;c__Sphingobacteri...</td>\n",
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       "    <tr>\n",
       "      <th>1000757</th>\n",
       "      <td>k__Bacteria;p__Proteobacteria;c__Alphaproteoba...</td>\n",
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       "      <th>1000876</th>\n",
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       "      <th>997544</th>\n",
       "      <td>k__Bacteria;p__Bacteroidetes;c__[Saprospirae];...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>999784</th>\n",
       "      <td>k__Bacteria;p__Actinobacteria;c__Thermoleophil...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>99987</th>\n",
       "      <td>k__Bacteria;p__Actinobacteria;c__Actinobacteri...</td>\n",
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       "    <tr>\n",
       "      <th>999870</th>\n",
       "      <td>k__Bacteria;p__Proteobacteria;c__Gammaproteoba...</td>\n",
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       "    <tr>\n",
       "      <th>999876</th>\n",
       "      <td>k__Bacteria;p__Bacteroidetes;c__[Saprospirae];...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>7396 rows × 1 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                                                        Taxon\n",
       "Feature ID                                                   \n",
       "1000512     k__Bacteria;p__Actinobacteria;c__Thermoleophil...\n",
       "1000547     k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactob...\n",
       "1000654     k__Bacteria;p__Bacteroidetes;c__Sphingobacteri...\n",
       "1000757     k__Bacteria;p__Proteobacteria;c__Alphaproteoba...\n",
       "1000876     k__Bacteria;p__Actinobacteria;c__Actinobacteri...\n",
       "...                                                       ...\n",
       "997544      k__Bacteria;p__Bacteroidetes;c__[Saprospirae];...\n",
       "999784      k__Bacteria;p__Actinobacteria;c__Thermoleophil...\n",
       "99987       k__Bacteria;p__Actinobacteria;c__Actinobacteri...\n",
       "999870      k__Bacteria;p__Proteobacteria;c__Gammaproteoba...\n",
       "999876      k__Bacteria;p__Bacteroidetes;c__[Saprospirae];...\n",
       "\n",
       "[7396 rows x 1 columns]"
      ]
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     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tax"
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  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T19:01:18.829551Z",
     "start_time": "2020-12-14T19:01:18.820004Z"
    }
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Index(['y0', 'y2', 'y1', 'y5', 'y6', 'y4', 'y3', 'y12', 'y11', 'y13',\n",
       "       ...\n",
       "       'y109', 'y102', 'y103', 'y112', 'y101', 'y114', 'y113', 'y115', 'y117',\n",
       "       'y116'],\n",
       "      dtype='object', length=118)"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "table.columns"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "ExecuteTime": {
     "end_time": "2020-12-14T19:01:38.669784Z",
     "start_time": "2020-12-14T19:01:38.613225Z"
    }
   },
   "outputs": [],
   "source": [
    "table.to_csv('news/table.csv')"
   ]
  }
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