final_MICOM.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "c909cc0d-2178-4f8d-8b1d-ff3b4324c692",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d8858c9c-b619-438d-851e-b4482ba53a92",
   "metadata": {},
   "source": [
    "importing the manifest generated from MICOM from the previous notebook "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "11f01684-b446-4485-85ba-87583f717355",
   "metadata": {},
   "outputs": [],
   "source": [
    "pre_merged = pd.read_csv(\"/proj/gibbons/sswegle_micom/manifest.csv\").drop(\"Unnamed: 0\", axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "379c5033-2fef-4f30-913f-cc5e14fc4414",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>sample_id</th>\n",
       "      <th>description</th>\n",
       "      <th>time_point</th>\n",
       "      <th>file</th>\n",
       "      <th>found_taxa</th>\n",
       "      <th>total_taxa</th>\n",
       "      <th>found_fraction</th>\n",
       "      <th>found_abundance_fraction</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>SRR15032078</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>8</td>\n",
       "      <td>SRR15032078.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.889586</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>SRR15032079</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>4</td>\n",
       "      <td>SRR15032079.pickle</td>\n",
       "      <td>21.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>0.840000</td>\n",
       "      <td>0.942212</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SRR15032080</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>3</td>\n",
       "      <td>SRR15032080.pickle</td>\n",
       "      <td>16.0</td>\n",
       "      <td>27.0</td>\n",
       "      <td>0.592593</td>\n",
       "      <td>0.855661</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SRR15032082</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032082.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>33.0</td>\n",
       "      <td>0.696970</td>\n",
       "      <td>0.908204</td>\n",
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       "    <tr>\n",
       "      <th>...</th>\n",
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       "      <td>...</td>\n",
       "      <td>...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>306</th>\n",
       "      <td>SRR15032510</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032510.pickle</td>\n",
       "      <td>21.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>0.750000</td>\n",
       "      <td>0.881483</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>307</th>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>6</td>\n",
       "      <td>SRR15032511.pickle</td>\n",
       "      <td>22.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>0.687500</td>\n",
       "      <td>0.799526</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>308</th>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>309</th>\n",
       "      <td>SRR15032513</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>6</td>\n",
       "      <td>SRR15032513.pickle</td>\n",
       "      <td>19.0</td>\n",
       "      <td>30.0</td>\n",
       "      <td>0.633333</td>\n",
       "      <td>0.839063</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>310</th>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>9</td>\n",
       "      <td>SRR15032514.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.740106</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>311 rows × 8 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       sample_id               description  time_point                file  \\\n",
       "0    SRR15032078           High fiber diet           8  SRR15032078.pickle   \n",
       "1    SRR15032079           High fiber diet           4  SRR15032079.pickle   \n",
       "2    SRR15032080  High fermented food diet           3  SRR15032080.pickle   \n",
       "3    SRR15032081  High fermented food diet           2  SRR15032081.pickle   \n",
       "4    SRR15032082           High fiber diet           7  SRR15032082.pickle   \n",
       "..           ...                       ...         ...                 ...   \n",
       "306  SRR15032510  High fermented food diet           2  SRR15032510.pickle   \n",
       "307  SRR15032511           High fiber diet           6  SRR15032511.pickle   \n",
       "308  SRR15032512  High fermented food diet           7  SRR15032512.pickle   \n",
       "309  SRR15032513  High fermented food diet           6  SRR15032513.pickle   \n",
       "310  SRR15032514           High fiber diet           9  SRR15032514.pickle   \n",
       "\n",
       "     found_taxa  total_taxa  found_fraction  found_abundance_fraction  \n",
       "0          24.0        37.0        0.648649                  0.889586  \n",
       "1          21.0        25.0        0.840000                  0.942212  \n",
       "2          16.0        27.0        0.592593                  0.855661  \n",
       "3          11.0        17.0        0.647059                  0.898909  \n",
       "4          23.0        33.0        0.696970                  0.908204  \n",
       "..          ...         ...             ...                       ...  \n",
       "306        21.0        28.0        0.750000                  0.881483  \n",
       "307        22.0        32.0        0.687500                  0.799526  \n",
       "308        23.0        37.0        0.621622                  0.843232  \n",
       "309        19.0        30.0        0.633333                  0.839063  \n",
       "310        24.0        37.0        0.648649                  0.740106  \n",
       "\n",
       "[311 rows x 8 columns]"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pre_merged"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "9ed16ccf-8f60-4c21-91f5-1f9b103b618c",
   "metadata": {},
   "source": [
    "adding a column for the medium "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "e596cb90-8ef6-4b98-835e-520354734077",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>sample_id</th>\n",
       "      <th>description</th>\n",
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>SRR15032078</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>8</td>\n",
       "      <td>SRR15032078.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.889586</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>SRR15032079</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>4</td>\n",
       "      <td>SRR15032079.pickle</td>\n",
       "      <td>21.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>0.840000</td>\n",
       "      <td>0.942212</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SRR15032080</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>3</td>\n",
       "      <td>SRR15032080.pickle</td>\n",
       "      <td>16.0</td>\n",
       "      <td>27.0</td>\n",
       "      <td>0.592593</td>\n",
       "      <td>0.855661</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SRR15032082</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032082.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>33.0</td>\n",
       "      <td>0.696970</td>\n",
       "      <td>0.908204</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>...</th>\n",
       "      <td>...</td>\n",
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       "      <td>...</td>\n",
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       "    <tr>\n",
       "      <th>306</th>\n",
       "      <td>SRR15032510</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032510.pickle</td>\n",
       "      <td>21.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>0.750000</td>\n",
       "      <td>0.881483</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>307</th>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>6</td>\n",
       "      <td>SRR15032511.pickle</td>\n",
       "      <td>22.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>0.687500</td>\n",
       "      <td>0.799526</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>308</th>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>309</th>\n",
       "      <td>SRR15032513</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>6</td>\n",
       "      <td>SRR15032513.pickle</td>\n",
       "      <td>19.0</td>\n",
       "      <td>30.0</td>\n",
       "      <td>0.633333</td>\n",
       "      <td>0.839063</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>310</th>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>9</td>\n",
       "      <td>SRR15032514.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.740106</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>311 rows × 9 columns</p>\n",
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      ],
      "text/plain": [
       "       sample_id               description  time_point                file  \\\n",
       "0    SRR15032078           High fiber diet           8  SRR15032078.pickle   \n",
       "1    SRR15032079           High fiber diet           4  SRR15032079.pickle   \n",
       "2    SRR15032080  High fermented food diet           3  SRR15032080.pickle   \n",
       "3    SRR15032081  High fermented food diet           2  SRR15032081.pickle   \n",
       "4    SRR15032082           High fiber diet           7  SRR15032082.pickle   \n",
       "..           ...                       ...         ...                 ...   \n",
       "306  SRR15032510  High fermented food diet           2  SRR15032510.pickle   \n",
       "307  SRR15032511           High fiber diet           6  SRR15032511.pickle   \n",
       "308  SRR15032512  High fermented food diet           7  SRR15032512.pickle   \n",
       "309  SRR15032513  High fermented food diet           6  SRR15032513.pickle   \n",
       "310  SRR15032514           High fiber diet           9  SRR15032514.pickle   \n",
       "\n",
       "     found_taxa  total_taxa  found_fraction  found_abundance_fraction   medium  \n",
       "0          24.0        37.0        0.648649                  0.889586  western  \n",
       "1          21.0        25.0        0.840000                  0.942212  western  \n",
       "2          16.0        27.0        0.592593                  0.855661  western  \n",
       "3          11.0        17.0        0.647059                  0.898909  western  \n",
       "4          23.0        33.0        0.696970                  0.908204  western  \n",
       "..          ...         ...             ...                       ...      ...  \n",
       "306        21.0        28.0        0.750000                  0.881483  western  \n",
       "307        22.0        32.0        0.687500                  0.799526  western  \n",
       "308        23.0        37.0        0.621622                  0.843232  western  \n",
       "309        19.0        30.0        0.633333                  0.839063  western  \n",
       "310        24.0        37.0        0.648649                  0.740106  western  \n",
       "\n",
       "[311 rows x 9 columns]"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pre_merged[\"medium\"] = \"western\"\n",
    "pre_merged"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "82a8d134-5fba-454e-b408-8fc161d28fcb",
   "metadata": {},
   "source": [
    "meaning of the time points: \n",
    "\n",
    "- baseline = 0, 1, 3\n",
    "- ramp = 3\n",
    "- maintenance = 4, 5, 6, 7\n",
    "- choice = 8\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "65cba514-7381-4505-852a-61e11cae1d36",
   "metadata": {},
   "outputs": [],
   "source": [
    "pre_merged.loc[\n",
    "    pre_merged.time_point.between(3, 8) & \n",
    "    (pre_merged.description == \"High fiber diet\"), \"medium\"] = \"high_fiber\"\n",
    "\n",
    "pre_merged.loc[\n",
    "    pre_merged.time_point.between(3, 8) &\n",
    "    (pre_merged.description == \"High fermented food diet\"), \"medium\"] = \"fermented\"\n",
    "\n",
    "#pre_merged.loc[\n",
    "    #pre_merged.time_point.between(0, 2),\n",
    "    #\"medium\"] = \"western diet medium\""
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "be79284f-4a52-41ef-9cac-4e19c6c57b94",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>SRR15032078</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>8</td>\n",
       "      <td>SRR15032078.pickle</td>\n",
       "      <td>24.0</td>\n",
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       "      <td>0.648649</td>\n",
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       "      <td>high_fiber</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>SRR15032079</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>4</td>\n",
       "      <td>SRR15032079.pickle</td>\n",
       "      <td>21.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>0.840000</td>\n",
       "      <td>0.942212</td>\n",
       "      <td>high_fiber</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SRR15032080</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>3</td>\n",
       "      <td>SRR15032080.pickle</td>\n",
       "      <td>16.0</td>\n",
       "      <td>27.0</td>\n",
       "      <td>0.592593</td>\n",
       "      <td>0.855661</td>\n",
       "      <td>fermented</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SRR15032082</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032082.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>33.0</td>\n",
       "      <td>0.696970</td>\n",
       "      <td>0.908204</td>\n",
       "      <td>high_fiber</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>306</th>\n",
       "      <td>SRR15032510</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032510.pickle</td>\n",
       "      <td>21.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>0.750000</td>\n",
       "      <td>0.881483</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>307</th>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>6</td>\n",
       "      <td>SRR15032511.pickle</td>\n",
       "      <td>22.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>0.687500</td>\n",
       "      <td>0.799526</td>\n",
       "      <td>high_fiber</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>308</th>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "      <td>fermented</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>309</th>\n",
       "      <td>SRR15032513</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>6</td>\n",
       "      <td>SRR15032513.pickle</td>\n",
       "      <td>19.0</td>\n",
       "      <td>30.0</td>\n",
       "      <td>0.633333</td>\n",
       "      <td>0.839063</td>\n",
       "      <td>fermented</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>310</th>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>9</td>\n",
       "      <td>SRR15032514.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.740106</td>\n",
       "      <td>western</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>311 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "       sample_id               description  time_point                file  \\\n",
       "0    SRR15032078           High fiber diet           8  SRR15032078.pickle   \n",
       "1    SRR15032079           High fiber diet           4  SRR15032079.pickle   \n",
       "2    SRR15032080  High fermented food diet           3  SRR15032080.pickle   \n",
       "3    SRR15032081  High fermented food diet           2  SRR15032081.pickle   \n",
       "4    SRR15032082           High fiber diet           7  SRR15032082.pickle   \n",
       "..           ...                       ...         ...                 ...   \n",
       "306  SRR15032510  High fermented food diet           2  SRR15032510.pickle   \n",
       "307  SRR15032511           High fiber diet           6  SRR15032511.pickle   \n",
       "308  SRR15032512  High fermented food diet           7  SRR15032512.pickle   \n",
       "309  SRR15032513  High fermented food diet           6  SRR15032513.pickle   \n",
       "310  SRR15032514           High fiber diet           9  SRR15032514.pickle   \n",
       "\n",
       "     found_taxa  total_taxa  found_fraction  found_abundance_fraction  \\\n",
       "0          24.0        37.0        0.648649                  0.889586   \n",
       "1          21.0        25.0        0.840000                  0.942212   \n",
       "2          16.0        27.0        0.592593                  0.855661   \n",
       "3          11.0        17.0        0.647059                  0.898909   \n",
       "4          23.0        33.0        0.696970                  0.908204   \n",
       "..          ...         ...             ...                       ...   \n",
       "306        21.0        28.0        0.750000                  0.881483   \n",
       "307        22.0        32.0        0.687500                  0.799526   \n",
       "308        23.0        37.0        0.621622                  0.843232   \n",
       "309        19.0        30.0        0.633333                  0.839063   \n",
       "310        24.0        37.0        0.648649                  0.740106   \n",
       "\n",
       "         medium  \n",
       "0    high_fiber  \n",
       "1    high_fiber  \n",
       "2     fermented  \n",
       "3       western  \n",
       "4    high_fiber  \n",
       "..          ...  \n",
       "306     western  \n",
       "307  high_fiber  \n",
       "308   fermented  \n",
       "309   fermented  \n",
       "310     western  \n",
       "\n",
       "[311 rows x 9 columns]"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pre_merged"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "165d5417-6abc-4927-b3fb-7d3be2410170",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0    high_fiber\n",
       "1    high_fiber\n",
       "2     fermented\n",
       "3       western\n",
       "4    high_fiber\n",
       "Name: medium, dtype: object"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pre_merged.medium.head(5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "f8241230-7cbf-413e-9976-f24a7553606c",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "306       western\n",
       "307    high_fiber\n",
       "308     fermented\n",
       "309     fermented\n",
       "310       western\n",
       "Name: medium, dtype: object"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pre_merged.medium.tail(5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "a6d5a7d9-70fc-4c3b-abf9-72a9c0c8d240",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "high_fiber    105\n",
       "western       105\n",
       "fermented     101\n",
       "Name: medium, dtype: int64"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pre_merged.medium.value_counts()"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d8a16fc9-f7fb-44d9-af90-d8c88a9150cb",
   "metadata": {},
   "source": [
    "^ check to make sure it is merged"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "58af690a-0fb6-4f1c-b235-6871a7d8b234",
   "metadata": {},
   "outputs": [],
   "source": [
    "pre_merged.to_csv(\"metadata_swegle.csv\")"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "a12fb301-79c2-4e86-bf75-9512b3fcdf77",
   "metadata": {},
   "source": [
    "Importing the three mediums that will be used for MICOM"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "b3175ac8-0a8a-4e0c-b135-f0488b115187",
   "metadata": {},
   "outputs": [],
   "source": [
    "from micom.qiime_formats import load_qiime_medium"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "bfe18268-7e8c-41e0-8979-dfa52620095e",
   "metadata": {},
   "outputs": [],
   "source": [
    "uploaded_fiber = load_qiime_medium(\"/proj/gibbons/refs/micom_media/media/vmh_high_fiber_agora.qza\")\n",
    "uploaded_western = load_qiime_medium(\"/proj/gibbons/refs/micom_media/media/western_diet_gut_agora.qza\")\n",
    "uploaded_fermented = load_qiime_medium(\"/proj/gibbons/refs/micom_media/media/vmh_fermented_agora.qza\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "4a068969-37e7-46dd-ad9d-d59e95d7ba11",
   "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>reaction</th>\n",
       "      <th>metabolite</th>\n",
       "      <th>global_id</th>\n",
       "      <th>flux</th>\n",
       "      <th>medium</th>\n",
       "      <th>name</th>\n",
       "      <th>hmdb</th>\n",
       "      <th>kegg.compound</th>\n",
       "      <th>pubchem.compound</th>\n",
       "      <th>inchi</th>\n",
       "      <th>chebi</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>reaction</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>EX_4abz_m</th>\n",
       "      <td>EX_4abz_m</td>\n",
       "      <td>4abz_m</td>\n",
       "      <td>EX_4abz(e)</td>\n",
       "      <td>0.100000</td>\n",
       "      <td>western</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EX_4hbz_m</th>\n",
       "      <td>EX_4hbz_m</td>\n",
       "      <td>4hbz_m</td>\n",
       "      <td>EX_4hbz(e)</td>\n",
       "      <td>0.100000</td>\n",
       "      <td>western</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EX_ac_m</th>\n",
       "      <td>EX_ac_m</td>\n",
       "      <td>ac_m</td>\n",
       "      <td>EX_ac(e)</td>\n",
       "      <td>0.100000</td>\n",
       "      <td>western</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EX_acgam_m</th>\n",
       "      <td>EX_acgam_m</td>\n",
       "      <td>acgam_m</td>\n",
       "      <td>EX_acgam(e)</td>\n",
       "      <td>0.100000</td>\n",
       "      <td>western</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EX_ala_L_m</th>\n",
       "      <td>EX_ala_L_m</td>\n",
       "      <td>ala_L_m</td>\n",
       "      <td>EX_ala_L(e)</td>\n",
       "      <td>0.100000</td>\n",
       "      <td>western</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EX_acmana_m</th>\n",
       "      <td>EX_acmana_m</td>\n",
       "      <td>acmana</td>\n",
       "      <td>EX_acmana(e)</td>\n",
       "      <td>0.005002</td>\n",
       "      <td>fermented</td>\n",
       "      <td>N-acetyl-D-mannosamine</td>\n",
       "      <td>HMDB01129</td>\n",
       "      <td>C00645</td>\n",
       "      <td>439281.0</td>\n",
       "      <td>InChI=1S/C8H15NO6/c1-4(12)9-5(2-10)7(14)8(15)6...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EX_MGlcn188_m</th>\n",
       "      <td>EX_MGlcn188_m</td>\n",
       "      <td>MGlcn188</td>\n",
       "      <td>EX_MGlcn188(e)</td>\n",
       "      <td>0.004624</td>\n",
       "      <td>fermented</td>\n",
       "      <td>mucin-type O-glycan No 188</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EX_no2_m</th>\n",
       "      <td>EX_no2_m</td>\n",
       "      <td>no2</td>\n",
       "      <td>EX_no2(e)</td>\n",
       "      <td>0.001486</td>\n",
       "      <td>fermented</td>\n",
       "      <td>Nitrite</td>\n",
       "      <td>HMDB02786</td>\n",
       "      <td>C00088</td>\n",
       "      <td>24529.0</td>\n",
       "      <td>InChI=1S/HNO2/c2-1-3/h(H,2,3)/p-1</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EX_xan_m</th>\n",
       "      <td>EX_xan_m</td>\n",
       "      <td>xan</td>\n",
       "      <td>EX_xan(e)</td>\n",
       "      <td>0.054624</td>\n",
       "      <td>fermented</td>\n",
       "      <td>Xanthine</td>\n",
       "      <td>HMDB00292</td>\n",
       "      <td>C00385</td>\n",
       "      <td>1188.0</td>\n",
       "      <td>InChI=1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>EX_acald_m</th>\n",
       "      <td>EX_acald_m</td>\n",
       "      <td>acald</td>\n",
       "      <td>EX_acald(e)</td>\n",
       "      <td>0.000753</td>\n",
       "      <td>fermented</td>\n",
       "      <td>acetaldehyde</td>\n",
       "      <td>HMDB00990</td>\n",
       "      <td>C00084</td>\n",
       "      <td>177.0</td>\n",
       "      <td>InChI=1S/C2H4O/c1-2-3/h2H,1H3</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>460 rows × 11 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "                    reaction metabolite       global_id      flux     medium  \\\n",
       "reaction                                                                       \n",
       "EX_4abz_m          EX_4abz_m     4abz_m      EX_4abz(e)  0.100000    western   \n",
       "EX_4hbz_m          EX_4hbz_m     4hbz_m      EX_4hbz(e)  0.100000    western   \n",
       "EX_ac_m              EX_ac_m       ac_m        EX_ac(e)  0.100000    western   \n",
       "EX_acgam_m        EX_acgam_m    acgam_m     EX_acgam(e)  0.100000    western   \n",
       "EX_ala_L_m        EX_ala_L_m    ala_L_m     EX_ala_L(e)  0.100000    western   \n",
       "...                      ...        ...             ...       ...        ...   \n",
       "EX_acmana_m      EX_acmana_m     acmana    EX_acmana(e)  0.005002  fermented   \n",
       "EX_MGlcn188_m  EX_MGlcn188_m   MGlcn188  EX_MGlcn188(e)  0.004624  fermented   \n",
       "EX_no2_m            EX_no2_m        no2       EX_no2(e)  0.001486  fermented   \n",
       "EX_xan_m            EX_xan_m        xan       EX_xan(e)  0.054624  fermented   \n",
       "EX_acald_m        EX_acald_m      acald     EX_acald(e)  0.000753  fermented   \n",
       "\n",
       "                                     name       hmdb kegg.compound  \\\n",
       "reaction                                                             \n",
       "EX_4abz_m                             NaN        NaN           NaN   \n",
       "EX_4hbz_m                             NaN        NaN           NaN   \n",
       "EX_ac_m                               NaN        NaN           NaN   \n",
       "EX_acgam_m                            NaN        NaN           NaN   \n",
       "EX_ala_L_m                            NaN        NaN           NaN   \n",
       "...                                   ...        ...           ...   \n",
       "EX_acmana_m        N-acetyl-D-mannosamine  HMDB01129        C00645   \n",
       "EX_MGlcn188_m  mucin-type O-glycan No 188        NaN           NaN   \n",
       "EX_no2_m                          Nitrite  HMDB02786        C00088   \n",
       "EX_xan_m                         Xanthine  HMDB00292        C00385   \n",
       "EX_acald_m                   acetaldehyde  HMDB00990        C00084   \n",
       "\n",
       "               pubchem.compound  \\\n",
       "reaction                          \n",
       "EX_4abz_m                   NaN   \n",
       "EX_4hbz_m                   NaN   \n",
       "EX_ac_m                     NaN   \n",
       "EX_acgam_m                  NaN   \n",
       "EX_ala_L_m                  NaN   \n",
       "...                         ...   \n",
       "EX_acmana_m            439281.0   \n",
       "EX_MGlcn188_m               NaN   \n",
       "EX_no2_m                24529.0   \n",
       "EX_xan_m                 1188.0   \n",
       "EX_acald_m                177.0   \n",
       "\n",
       "                                                           inchi  chebi  \n",
       "reaction                                                                 \n",
       "EX_4abz_m                                                    NaN    NaN  \n",
       "EX_4hbz_m                                                    NaN    NaN  \n",
       "EX_ac_m                                                      NaN    NaN  \n",
       "EX_acgam_m                                                   NaN    NaN  \n",
       "EX_ala_L_m                                                   NaN    NaN  \n",
       "...                                                          ...    ...  \n",
       "EX_acmana_m    InChI=1S/C8H15NO6/c1-4(12)9-5(2-10)7(14)8(15)6...    NaN  \n",
       "EX_MGlcn188_m                                                NaN    NaN  \n",
       "EX_no2_m                       InChI=1S/HNO2/c2-1-3/h(H,2,3)/p-1    NaN  \n",
       "EX_xan_m       InChI=1S/C5H4N4O2/c10-4-2-3(7-1-6-2)8-5(11)9-4...    NaN  \n",
       "EX_acald_m                         InChI=1S/C2H4O/c1-2-3/h2H,1H3    NaN  \n",
       "\n",
       "[460 rows x 11 columns]"
      ]
     },
     "execution_count": 13,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "uploaded_western[\"medium\"] = \"western\"\n",
    "uploaded_fiber[\"medium\"] = \"high_fiber\"\n",
    "uploaded_fermented[\"medium\"] = \"fermented\"\n",
    "merged = pd.concat([uploaded_western, uploaded_fiber, uploaded_fermented])\n",
    "merged"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "199b7672-f86e-48d2-ad86-9addb1a10f11",
   "metadata": {},
   "outputs": [],
   "source": [
    "per_sample_medium = pd.merge(pre_merged, merged, on=\"medium\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "33cb9323-6e9d-4d27-9db2-6c780d92b863",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "    }\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>sample_id</th>\n",
       "      <th>description</th>\n",
       "      <th>time_point</th>\n",
       "      <th>file</th>\n",
       "      <th>found_taxa</th>\n",
       "      <th>total_taxa</th>\n",
       "      <th>found_fraction</th>\n",
       "      <th>found_abundance_fraction</th>\n",
       "      <th>medium</th>\n",
       "      <th>reaction</th>\n",
       "      <th>metabolite</th>\n",
       "      <th>global_id</th>\n",
       "      <th>flux</th>\n",
       "      <th>name</th>\n",
       "      <th>hmdb</th>\n",
       "      <th>kegg.compound</th>\n",
       "      <th>pubchem.compound</th>\n",
       "      <th>inchi</th>\n",
       "      <th>chebi</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>SRR15032078</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>8</td>\n",
       "      <td>SRR15032078.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.889586</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>EX_etoh_m</td>\n",
       "      <td>etoh</td>\n",
       "      <td>EX_etoh(e)</td>\n",
       "      <td>4.558439</td>\n",
       "      <td>ethanol</td>\n",
       "      <td>HMDB00108</td>\n",
       "      <td>C00469</td>\n",
       "      <td>702.0</td>\n",
       "      <td>InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>SRR15032078</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>8</td>\n",
       "      <td>SRR15032078.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.889586</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>EX_h2o_m</td>\n",
       "      <td>h2o</td>\n",
       "      <td>EX_h2o(e)</td>\n",
       "      <td>36334.267355</td>\n",
       "      <td>Water</td>\n",
       "      <td>HMDB02111</td>\n",
       "      <td>C00001</td>\n",
       "      <td>962.0</td>\n",
       "      <td>InChI=1S/H2O/h1H2</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>SRR15032078</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>8</td>\n",
       "      <td>SRR15032078.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.889586</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>EX_caro_m</td>\n",
       "      <td>caro</td>\n",
       "      <td>EX_caro(e)</td>\n",
       "      <td>0.002626</td>\n",
       "      <td>beta-carotene</td>\n",
       "      <td>HMDB00561</td>\n",
       "      <td>C02094</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>SRR15032078</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>8</td>\n",
       "      <td>SRR15032078.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.889586</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>EX_retinol_m</td>\n",
       "      <td>retinol</td>\n",
       "      <td>EX_retinol(e)</td>\n",
       "      <td>0.219932</td>\n",
       "      <td>retinol</td>\n",
       "      <td>HMDB00305</td>\n",
       "      <td>C00473</td>\n",
       "      <td>445354.0</td>\n",
       "      <td>InChI=1S/C20H30O/c1-16(8-6-9-17(2)13-15-21)11-...</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>SRR15032078</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>8</td>\n",
       "      <td>SRR15032078.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.889586</td>\n",
       "      <td>high_fiber</td>\n",
       "      <td>EX_thm_m</td>\n",
       "      <td>thm</td>\n",
       "      <td>EX_thm(e)</td>\n",
       "      <td>1.447120</td>\n",
       "      <td>Thiamin</td>\n",
       "      <td>HMDB00235</td>\n",
       "      <td>C00378</td>\n",
       "      <td>1130.0</td>\n",
       "      <td>InChI=1S/C12H17N4OS/c1-8-11(3-4-17)18-7-16(8)6...</td>\n",
       "      <td>NaN</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47711</th>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>9</td>\n",
       "      <td>SRR15032514.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.740106</td>\n",
       "      <td>western</td>\n",
       "      <td>EX_octa_m</td>\n",
       "      <td>octa_m</td>\n",
       "      <td>EX_octa(e)</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47712</th>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>9</td>\n",
       "      <td>SRR15032514.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.740106</td>\n",
       "      <td>western</td>\n",
       "      <td>EX_adpcbl_m</td>\n",
       "      <td>adpcbl_m</td>\n",
       "      <td>EX_adpcbl(e)</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47713</th>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>9</td>\n",
       "      <td>SRR15032514.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.740106</td>\n",
       "      <td>western</td>\n",
       "      <td>EX_fe3dcit_m</td>\n",
       "      <td>fe3dcit_m</td>\n",
       "      <td>EX_fe3dcit(e)</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47714</th>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>9</td>\n",
       "      <td>SRR15032514.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.740106</td>\n",
       "      <td>western</td>\n",
       "      <td>EX_pydx5p_m</td>\n",
       "      <td>pydx5p_m</td>\n",
       "      <td>EX_pydx5p(e)</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>47715</th>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>9</td>\n",
       "      <td>SRR15032514.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.740106</td>\n",
       "      <td>western</td>\n",
       "      <td>EX_glu_D_m</td>\n",
       "      <td>glu_D_m</td>\n",
       "      <td>EX_glu_D(e)</td>\n",
       "      <td>0.000000</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>47716 rows × 19 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "         sample_id      description  time_point                file  \\\n",
       "0      SRR15032078  High fiber diet           8  SRR15032078.pickle   \n",
       "1      SRR15032078  High fiber diet           8  SRR15032078.pickle   \n",
       "2      SRR15032078  High fiber diet           8  SRR15032078.pickle   \n",
       "3      SRR15032078  High fiber diet           8  SRR15032078.pickle   \n",
       "4      SRR15032078  High fiber diet           8  SRR15032078.pickle   \n",
       "...            ...              ...         ...                 ...   \n",
       "47711  SRR15032514  High fiber diet           9  SRR15032514.pickle   \n",
       "47712  SRR15032514  High fiber diet           9  SRR15032514.pickle   \n",
       "47713  SRR15032514  High fiber diet           9  SRR15032514.pickle   \n",
       "47714  SRR15032514  High fiber diet           9  SRR15032514.pickle   \n",
       "47715  SRR15032514  High fiber diet           9  SRR15032514.pickle   \n",
       "\n",
       "       found_taxa  total_taxa  found_fraction  found_abundance_fraction  \\\n",
       "0            24.0        37.0        0.648649                  0.889586   \n",
       "1            24.0        37.0        0.648649                  0.889586   \n",
       "2            24.0        37.0        0.648649                  0.889586   \n",
       "3            24.0        37.0        0.648649                  0.889586   \n",
       "4            24.0        37.0        0.648649                  0.889586   \n",
       "...           ...         ...             ...                       ...   \n",
       "47711        24.0        37.0        0.648649                  0.740106   \n",
       "47712        24.0        37.0        0.648649                  0.740106   \n",
       "47713        24.0        37.0        0.648649                  0.740106   \n",
       "47714        24.0        37.0        0.648649                  0.740106   \n",
       "47715        24.0        37.0        0.648649                  0.740106   \n",
       "\n",
       "           medium      reaction metabolite      global_id          flux  \\\n",
       "0      high_fiber     EX_etoh_m       etoh     EX_etoh(e)      4.558439   \n",
       "1      high_fiber      EX_h2o_m        h2o      EX_h2o(e)  36334.267355   \n",
       "2      high_fiber     EX_caro_m       caro     EX_caro(e)      0.002626   \n",
       "3      high_fiber  EX_retinol_m    retinol  EX_retinol(e)      0.219932   \n",
       "4      high_fiber      EX_thm_m        thm      EX_thm(e)      1.447120   \n",
       "...           ...           ...        ...            ...           ...   \n",
       "47711     western     EX_octa_m     octa_m     EX_octa(e)      0.000000   \n",
       "47712     western   EX_adpcbl_m   adpcbl_m   EX_adpcbl(e)      0.000000   \n",
       "47713     western  EX_fe3dcit_m  fe3dcit_m  EX_fe3dcit(e)      0.000000   \n",
       "47714     western   EX_pydx5p_m   pydx5p_m   EX_pydx5p(e)      0.000000   \n",
       "47715     western    EX_glu_D_m    glu_D_m    EX_glu_D(e)      0.000000   \n",
       "\n",
       "                name       hmdb kegg.compound  pubchem.compound  \\\n",
       "0            ethanol  HMDB00108        C00469             702.0   \n",
       "1              Water  HMDB02111        C00001             962.0   \n",
       "2      beta-carotene  HMDB00561        C02094               NaN   \n",
       "3            retinol  HMDB00305        C00473          445354.0   \n",
       "4            Thiamin  HMDB00235        C00378            1130.0   \n",
       "...              ...        ...           ...               ...   \n",
       "47711            NaN        NaN           NaN               NaN   \n",
       "47712            NaN        NaN           NaN               NaN   \n",
       "47713            NaN        NaN           NaN               NaN   \n",
       "47714            NaN        NaN           NaN               NaN   \n",
       "47715            NaN        NaN           NaN               NaN   \n",
       "\n",
       "                                                   inchi  chebi  \n",
       "0                      InChI=1S/C2H6O/c1-2-3/h3H,2H2,1H3    NaN  \n",
       "1                                      InChI=1S/H2O/h1H2    NaN  \n",
       "2                                                    NaN    NaN  \n",
       "3      InChI=1S/C20H30O/c1-16(8-6-9-17(2)13-15-21)11-...    NaN  \n",
       "4      InChI=1S/C12H17N4OS/c1-8-11(3-4-17)18-7-16(8)6...    NaN  \n",
       "...                                                  ...    ...  \n",
       "47711                                                NaN    NaN  \n",
       "47712                                                NaN    NaN  \n",
       "47713                                                NaN    NaN  \n",
       "47714                                                NaN    NaN  \n",
       "47715                                                NaN    NaN  \n",
       "\n",
       "[47716 rows x 19 columns]"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "per_sample_medium"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "c7731e16-f4a9-4298-abe1-496551d709f1",
   "metadata": {
    "tags": []
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Index(['sample_id', 'description', 'time_point', 'file', 'found_taxa',\n",
      "       'total_taxa', 'found_fraction', 'found_abundance_fraction', 'medium',\n",
      "       'reaction', 'metabolite', 'global_id', 'flux', 'name', 'hmdb',\n",
      "       'kegg.compound', 'pubchem.compound', 'inchi', 'chebi'],\n",
      "      dtype='object')\n"
     ]
    }
   ],
   "source": [
    "print(per_sample_medium.columns)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "d1591f4e-62c4-4d76-8ad1-ef3422256a57",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "41582\n"
     ]
    }
   ],
   "source": [
    "from micom import load_pickle\n",
    "\n",
    "com = load_pickle(\"models2/SRR15032291.pickle\")\n",
    "print(len(com.reactions))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "5e2a32c8-b9fc-4f18-bdfe-90f86c9acb09",
   "metadata": {},
   "outputs": [],
   "source": [
    "manifest = pd.read_csv(\"manifest.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "22432539-cadf-44ad-9d97-bee0e2d8563e",
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Unnamed: 0</th>\n",
       "      <th>sample_id</th>\n",
       "      <th>description</th>\n",
       "      <th>time_point</th>\n",
       "      <th>file</th>\n",
       "      <th>found_taxa</th>\n",
       "      <th>total_taxa</th>\n",
       "      <th>found_fraction</th>\n",
       "      <th>found_abundance_fraction</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>0</td>\n",
       "      <td>SRR15032078</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>8</td>\n",
       "      <td>SRR15032078.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.889586</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>1</td>\n",
       "      <td>SRR15032079</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>4</td>\n",
       "      <td>SRR15032079.pickle</td>\n",
       "      <td>21.0</td>\n",
       "      <td>25.0</td>\n",
       "      <td>0.840000</td>\n",
       "      <td>0.942212</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032080</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>3</td>\n",
       "      <td>SRR15032080.pickle</td>\n",
       "      <td>16.0</td>\n",
       "      <td>27.0</td>\n",
       "      <td>0.592593</td>\n",
       "      <td>0.855661</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>3</td>\n",
       "      <td>SRR15032081</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032081.pickle</td>\n",
       "      <td>11.0</td>\n",
       "      <td>17.0</td>\n",
       "      <td>0.647059</td>\n",
       "      <td>0.898909</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>4</td>\n",
       "      <td>SRR15032082</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032082.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>33.0</td>\n",
       "      <td>0.696970</td>\n",
       "      <td>0.908204</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",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>306</th>\n",
       "      <td>306</td>\n",
       "      <td>SRR15032510</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>2</td>\n",
       "      <td>SRR15032510.pickle</td>\n",
       "      <td>21.0</td>\n",
       "      <td>28.0</td>\n",
       "      <td>0.750000</td>\n",
       "      <td>0.881483</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>307</th>\n",
       "      <td>307</td>\n",
       "      <td>SRR15032511</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>6</td>\n",
       "      <td>SRR15032511.pickle</td>\n",
       "      <td>22.0</td>\n",
       "      <td>32.0</td>\n",
       "      <td>0.687500</td>\n",
       "      <td>0.799526</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>308</th>\n",
       "      <td>308</td>\n",
       "      <td>SRR15032512</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>7</td>\n",
       "      <td>SRR15032512.pickle</td>\n",
       "      <td>23.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.621622</td>\n",
       "      <td>0.843232</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>309</th>\n",
       "      <td>309</td>\n",
       "      <td>SRR15032513</td>\n",
       "      <td>High fermented food diet</td>\n",
       "      <td>6</td>\n",
       "      <td>SRR15032513.pickle</td>\n",
       "      <td>19.0</td>\n",
       "      <td>30.0</td>\n",
       "      <td>0.633333</td>\n",
       "      <td>0.839063</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>310</th>\n",
       "      <td>310</td>\n",
       "      <td>SRR15032514</td>\n",
       "      <td>High fiber diet</td>\n",
       "      <td>9</td>\n",
       "      <td>SRR15032514.pickle</td>\n",
       "      <td>24.0</td>\n",
       "      <td>37.0</td>\n",
       "      <td>0.648649</td>\n",
       "      <td>0.740106</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "<p>311 rows × 9 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "     Unnamed: 0    sample_id               description  time_point  \\\n",
       "0             0  SRR15032078           High fiber diet           8   \n",
       "1             1  SRR15032079           High fiber diet           4   \n",
       "2             2  SRR15032080  High fermented food diet           3   \n",
       "3             3  SRR15032081  High fermented food diet           2   \n",
       "4             4  SRR15032082           High fiber diet           7   \n",
       "..          ...          ...                       ...         ...   \n",
       "306         306  SRR15032510  High fermented food diet           2   \n",
       "307         307  SRR15032511           High fiber diet           6   \n",
       "308         308  SRR15032512  High fermented food diet           7   \n",
       "309         309  SRR15032513  High fermented food diet           6   \n",
       "310         310  SRR15032514           High fiber diet           9   \n",
       "\n",
       "                   file  found_taxa  total_taxa  found_fraction  \\\n",
       "0    SRR15032078.pickle        24.0        37.0        0.648649   \n",
       "1    SRR15032079.pickle        21.0        25.0        0.840000   \n",
       "2    SRR15032080.pickle        16.0        27.0        0.592593   \n",
       "3    SRR15032081.pickle        11.0        17.0        0.647059   \n",
       "4    SRR15032082.pickle        23.0        33.0        0.696970   \n",
       "..                  ...         ...         ...             ...   \n",
       "306  SRR15032510.pickle        21.0        28.0        0.750000   \n",
       "307  SRR15032511.pickle        22.0        32.0        0.687500   \n",
       "308  SRR15032512.pickle        23.0        37.0        0.621622   \n",
       "309  SRR15032513.pickle        19.0        30.0        0.633333   \n",
       "310  SRR15032514.pickle        24.0        37.0        0.648649   \n",
       "\n",
       "     found_abundance_fraction  \n",
       "0                    0.889586  \n",
       "1                    0.942212  \n",
       "2                    0.855661  \n",
       "3                    0.898909  \n",
       "4                    0.908204  \n",
       "..                        ...  \n",
       "306                  0.881483  \n",
       "307                  0.799526  \n",
       "308                  0.843232  \n",
       "309                  0.839063  \n",
       "310                  0.740106  \n",
       "\n",
       "[311 rows x 9 columns]"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "manifest"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "5f9dafe4-2050-4d87-a618-ead68c1365ec",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "311"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "per_sample_medium.sample_id.nunique()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "f937af6a-2b50-49d6-96d4-245fab49956c",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "western       17955\n",
       "high_fiber    15015\n",
       "fermented     14746\n",
       "Name: medium, dtype: int64"
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "per_sample_medium.medium.value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "e0e5fe30-1788-4b5e-9c04-3d65cc054318",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "a89f60fcff7b4774bc4328446b473135",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Output()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"></pre>\n"
      ],
      "text/plain": []
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">\n",
       "</pre>\n"
      ],
      "text/plain": [
       "\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/users/sswegle/miniconda3/envs/micom/lib/python3.8/site-packages/micom/workflows/grow.py:199: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`\n",
      "  exchanges[\"taxon\"] = exchanges.index\n"
     ]
    }
   ],
   "source": [
    "from micom.workflows import grow\n",
    "\n",
    "res = grow(manifest, model_folder = \"models2\", medium = per_sample_medium, tradeoff = 0.5, threads = 20)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "ac511669-2628-4dd8-b14f-6132d3c33b33",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">Running <span style=\"color: #f92672; text-decoration-color: #f92672\">━━━━━━╸</span><span style=\"color: #3a3a3a; text-decoration-color: #3a3a3a\">━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━</span> <span style=\"color: #800080; text-decoration-color: #800080\"> 17%</span> <span style=\"color: #008080; text-decoration-color: #008080\">0:56:32</span>\n",
       "</pre>\n"
      ],
      "text/plain": [
       "Running \u001b[38;2;249;38;114m━━━━━━\u001b[0m\u001b[38;2;249;38;114m╸\u001b[0m\u001b[38;5;237m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[35m 17%\u001b[0m \u001b[36m0:56:32\u001b[0m\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"></pre>\n"
      ],
      "text/plain": []
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">\n",
       "</pre>\n"
      ],
      "text/plain": [
       "\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "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>abundance</th>\n",
       "      <th>growth_rate</th>\n",
       "      <th>reactions</th>\n",
       "      <th>metabolites</th>\n",
       "      <th>taxon</th>\n",
       "      <th>tradeoff</th>\n",
       "      <th>sample_id</th>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>compartments</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>Acidaminococcus</th>\n",
       "      <td>0.014058</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>1278</td>\n",
       "      <td>1090</td>\n",
       "      <td>Acidaminococcus</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SRR15032081</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Akkermansia</th>\n",
       "      <td>0.133546</td>\n",
       "      <td>3.765432e-12</td>\n",
       "      <td>2274</td>\n",
       "      <td>1386</td>\n",
       "      <td>Akkermansia</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SRR15032081</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Alistipes</th>\n",
       "      <td>0.064537</td>\n",
       "      <td>7.632440e+00</td>\n",
       "      <td>2650</td>\n",
       "      <td>1613</td>\n",
       "      <td>Alistipes</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SRR15032081</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Bacteroides</th>\n",
       "      <td>0.203834</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>3293</td>\n",
       "      <td>1883</td>\n",
       "      <td>Bacteroides</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SRR15032081</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>Bifidobacterium</th>\n",
       "      <td>0.007668</td>\n",
       "      <td>0.000000e+00</td>\n",
       "      <td>3108</td>\n",
       "      <td>1734</td>\n",
       "      <td>Bifidobacterium</td>\n",
       "      <td>NaN</td>\n",
       "      <td>SRR15032081</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                 abundance   growth_rate  reactions  metabolites  \\\n",
       "compartments                                                       \n",
       "Acidaminococcus   0.014058  0.000000e+00       1278         1090   \n",
       "Akkermansia       0.133546  3.765432e-12       2274         1386   \n",
       "Alistipes         0.064537  7.632440e+00       2650         1613   \n",
       "Bacteroides       0.203834  0.000000e+00       3293         1883   \n",
       "Bifidobacterium   0.007668  0.000000e+00       3108         1734   \n",
       "\n",
       "                           taxon  tradeoff    sample_id  \n",
       "compartments                                             \n",
       "Acidaminococcus  Acidaminococcus       NaN  SRR15032081  \n",
       "Akkermansia          Akkermansia       NaN  SRR15032081  \n",
       "Alistipes              Alistipes       NaN  SRR15032081  \n",
       "Bacteroides          Bacteroides       NaN  SRR15032081  \n",
       "Bifidobacterium  Bifidobacterium       NaN  SRR15032081  "
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "from micom.workflows import tradeoff\n",
    "\n",
    "tradeoff_rates = tradeoff(manifest, model_folder = \"models2\", medium = per_sample_medium, threads= 20)\n",
    "tradeoff_rates.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "6bb787e6-df78-4a92-af3a-efc56918462b",
   "metadata": {},
   "outputs": [],
   "source": [
    "tradeoff_rates.to_csv(\"tradeoff_swegle.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "73a44f6d-4ddd-49db-bc15-8e6b5f531c91",
   "metadata": {},
   "outputs": [],
   "source": [
    "from micom.viz import plot_tradeoff\n",
    "\n",
    "pl = plot_tradeoff(tradeoff_rates, filename=\"view_tradeoff_swegle.html\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "id": "1f9c1fa5-b0d5-4819-8eaf-20c9c8a6e659",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<micom.viz.core.Visualization at 0x7f989a42ea60>"
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pl"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "2815f8fe-30d8-4044-8efe-f43b331cb693",
   "metadata": {},
   "source": [
    "changing tradeoff to 0.7 based on tradeoff"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "id": "436a4b74-9e85-4ef8-badc-9d6eb51ede58",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "781581da480e4b3396a5dfe55807eeec",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "Output()"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\"></pre>\n"
      ],
      "text/plain": []
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "data": {
      "text/html": [
       "<pre style=\"white-space:pre;overflow-x:auto;line-height:normal;font-family:Menlo,'DejaVu Sans Mono',consolas,'Courier New',monospace\">\n",
       "</pre>\n"
      ],
      "text/plain": [
       "\n"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/users/sswegle/miniconda3/envs/micom/lib/python3.8/site-packages/micom/workflows/grow.py:199: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead. To get a de-fragmented frame, use `newframe = frame.copy()`\n",
      "  exchanges[\"taxon\"] = exchanges.index\n"
     ]
    }
   ],
   "source": [
    "from micom.workflows import grow\n",
    "\n",
    "res = grow(manifest, model_folder = \"models2\", medium = per_sample_medium, tradeoff = 0.7, threads = 20)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "8b23ef49-1f4c-4598-b6c4-c0154659b737",
   "metadata": {},
   "source": [
    "use results from grow (res) for visualizations "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 28,
   "id": "6301bc33-32b7-4800-aa94-d3a71d3409e3",
   "metadata": {},
   "outputs": [],
   "source": [
    "res.exchanges.to_csv(\"exchanges_swegle.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 29,
   "id": "ad5c3c94-c06f-44ee-a69b-da84b40a947f",
   "metadata": {},
   "outputs": [],
   "source": [
    "res.annotations.to_csv(\"annotations_swegle.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "id": "487c60e4-f6b9-4cb4-9e2a-a46f1acf8dd0",
   "metadata": {},
   "outputs": [],
   "source": [
    "res.growth_rates.to_csv(\"growth_rates_swegle.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "id": "1bb82108-890c-4927-a0db-2b3983660829",
   "metadata": {},
   "outputs": [],
   "source": [
    "from micom.viz import plot_growth\n",
    "\n",
    "pl = plot_growth(res, filename=\"final_growth_rates.html\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "id": "4890bbb1-4cad-454c-a549-a6f5ad941a4a",
   "metadata": {},
   "outputs": [],
   "source": [
    "from micom.viz import plot_exchanges_per_sample\n",
    "\n",
    "pl = plot_exchanges_per_sample(res, filename=\"final_consumption.html\")"
   ]
  }
 ],
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