S29_alpha_diversity.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "9e6d5f66-4ebb-4dc6-9de9-8e293c77c489",
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import numpy as np\n",
    "\n",
    "\n",
    "df_quant = pd.read_csv(\"/Users/delser/Desktop/PhD/Phytochemistry/FBMN/alltissues/FEATURE-BASED-MOLECULAR-NETWORKING-cf822b6c-15072021/alltissues15072021-quant-py-dil.csv\",index_col='row ID', sep=\",\") # mzmine quant table\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "92d7b249-271a-49c7-ab1c-25e156ec4caf",
   "metadata": {},
   "outputs": [
    {
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       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>row m/z</th>\n",
       "      <th>row retention time</th>\n",
       "      <th>07 Nrep</th>\n",
       "      <th>07 Nnes</th>\n",
       "      <th>07 Nrxs</th>\n",
       "      <th>07 Nsto</th>\n",
       "      <th>07 Ntab</th>\n",
       "      <th>08 Nglu</th>\n",
       "      <th>10 Nben</th>\n",
       "      <th>10 Ncle</th>\n",
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       "      <th>-Ncle03-Caly</th>\n",
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       "      <th>Solvent_RA3</th>\n",
       "      <th>Solvent_RA4</th>\n",
       "      <th>-Natt03-Caly</th>\n",
       "      <th>Solvent_RA5</th>\n",
       "      <th>Solvent_RA26</th>\n",
       "      <th>Solvent_RA7</th>\n",
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       "<p>17901 rows × 114 columns</p>\n",
       "</div>"
      ],
      "text/plain": [
       "            row m/z  row retention time      07 Nrep     07 Nnes     07 Nrxs  \\\n",
       "row ID                                                                         \n",
       "1465      98.961427           46.090285  1912255.595  1819513.95  193807.138   \n",
       "11687    105.069960            1.335580     2979.690        0.00     399.556   \n",
       "23160    105.069976            1.476290        0.000     1289.97     599.280   \n",
       "13348    117.057295            0.636114        0.000      804.72       0.000   \n",
       "30656    117.057306            0.839741        0.000        0.00       0.000   \n",
       "...             ...                 ...          ...         ...         ...   \n",
       "24054   1430.721213           34.435048        0.000        0.00       0.000   \n",
       "13546   1430.721947           34.060064        0.000        0.00       0.000   \n",
       "15535   1430.722023           34.364866        0.000        0.00       0.000   \n",
       "14344   1435.675877           34.239693        0.000        0.00       0.000   \n",
       "13731   1458.753099           35.250299        0.000        0.00       0.000   \n",
       "\n",
       "           07 Nsto      07 Ntab      08 Nglu      10 Nben      10 Ncle  ...  \\\n",
       "row ID                                                                  ...   \n",
       "1465    1134014.55  225382.0585  169589.5770  128196.2975   87604.5795  ...   \n",
       "11687         0.00    1295.0300       0.0000  139611.8360  130091.3065  ...   \n",
       "23160         0.00     780.6560     338.1000    1953.2210    2100.7460  ...   \n",
       "13348      4006.46   18954.3080   37212.5555  173275.2150  421706.8330  ...   \n",
       "30656         0.00     999.4080     536.3860    5039.4610   53901.9645  ...   \n",
       "...            ...          ...          ...          ...          ...  ...   \n",
       "24054         0.00    6286.9545       0.0000       0.0000    5802.2190  ...   \n",
       "13546         0.00       0.0000       0.0000       0.0000  589619.7345  ...   \n",
       "15535         0.00       0.0000       0.0000       0.0000    3771.0110  ...   \n",
       "14344         0.00       0.0000       0.0000       0.0000   74666.5180  ...   \n",
       "13731         0.00       0.0000     122.4720       0.0000  197619.4325  ...   \n",
       "\n",
       "        -Ncle03-Caly  Solvent_RA1  -Nben03-Caly  Solvent_RA2  Solvent_RA3  \\\n",
       "row ID                                                                      \n",
       "1465    0.000000e+00     569.1535       249.555       0.0000     885.5805   \n",
       "11687   0.000000e+00       0.0000      1368.220       0.0000    1294.2630   \n",
       "23160   8.149567e+05       0.0000   2656672.966     154.5080     792.4800   \n",
       "13348   2.044090e+06       0.0000   1737524.104   12516.2695    2254.5635   \n",
       "30656   3.916763e+06       0.0000   1315696.120    3870.7565    2773.6960   \n",
       "...              ...          ...           ...          ...          ...   \n",
       "24054   1.475248e+03       0.0000         0.000       0.0000       0.0000   \n",
       "13546   1.610320e+05       0.0000         0.000       0.0000       0.0000   \n",
       "15535   7.933500e+02       0.0000         0.000       0.0000       0.0000   \n",
       "14344   4.350744e+03       0.0000         0.000      98.3280       0.0000   \n",
       "13731   4.086368e+04       0.0000         0.000       0.0000       0.0000   \n",
       "\n",
       "        Solvent_RA4  -Natt03-Caly  Solvent_RA5  Solvent_RA26  Solvent_RA7  \n",
       "row ID                                                                     \n",
       "1465       656.0620  8.086200e+02       0.0000       263.604     134.2345  \n",
       "11687     4001.5840  2.439269e+03    1378.2065         0.000     342.2805  \n",
       "23160        0.0000  1.003830e+06     795.6285       152.646     699.4875  \n",
       "13348     2145.2640  1.358149e+06       0.0000      9782.190    5743.9425  \n",
       "30656     3490.2665  2.066143e+06    2644.5225      3030.446    1771.9900  \n",
       "...             ...           ...          ...           ...          ...  \n",
       "24054        0.0000  0.000000e+00       0.0000         0.000       0.0000  \n",
       "13546        0.0000  0.000000e+00       0.0000         0.000       0.0000  \n",
       "15535        0.0000  1.788020e+02       0.0000         0.000       0.0000  \n",
       "14344        0.0000  0.000000e+00      82.2780         0.000       0.0000  \n",
       "13731        0.0000  0.000000e+00       0.0000         0.000       0.0000  \n",
       "\n",
       "[17901 rows x 114 columns]"
      ]
     },
     "execution_count": 2,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_quant"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "bf0b7a3b-dc3c-4668-b958-152fa12f8acf",
   "metadata": {},
   "outputs": [],
   "source": [
    "empty=[]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "0547e2ba-0b8a-4f5b-a830-d7bf72d3f5dc",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_nrep=df_quant[[\"07 Nrep\",\"Nrep03-Root_\",\"-Nrep03-MeJ_\",\"-Nrep03-Ctrl\",\"-Nrep03-Caly\"]].astype('int')\n",
    "df_nrep_t=df_nrep.T\n",
    "counts=df_nrep_t.to_numpy()\n",
    "ids=[\"07 Nrep\",\"Nrep03-Root_\",\"-Nrep03-MeJ_\",\"-Nrep03-Ctrl\",\"-Nrep03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "63d4af4f-475a-455c-b809-c225b9604b5b",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Nnes=df_quant[[\"07 Nnes\",\"Nnes03-Root_\",\"-Nnes03-MeJ_\",\"-Nnes03-Ctrl\",\"-Nnes03-Caly\"]].astype('int')\n",
    "df_Nnes_t=df_Nnes.T\n",
    "counts=df_Nnes_t.to_numpy()\n",
    "ids=[\"07 Nnes\",\"Nnes03-Root_\",\"-Nnes03-MeJ_\",\"-Nnes03-Ctrl\",\"-Nnes03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "91d5e9ff-f648-4de3-a0fd-71a1058605ce",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Nsto=df_quant[[\"07 Nsto\",\"Nsto03-Root_\",\"-Nsto03-MeJ_\",\"-Nsto03-Ctrl\",\"-Nsto03-Caly\"]].astype('int')\n",
    "df_Nsto_t=df_Nsto.T\n",
    "counts=df_Nsto_t.to_numpy()\n",
    "ids=[\"07 Nsto\",\"Nsto03-Root_\",\"-Nsto03-MeJ_\",\"-Nsto03-Ctrl\",\"-Nsto03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "2f9e99cd-4fdf-4fbb-b46f-fa82d3ccb2ac",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Nrxs=df_quant[[\"07 Nrxs\",\"Nrxs03-Root_\",\"-Nrxs03-MeJ_\",\"-Nrxs03-Ctrl\",\"-Nrxs03-Caly\"]].astype('int')\n",
    "df_Nrxs_t=df_Nrxs.T\n",
    "counts=df_Nrxs_t.to_numpy()\n",
    "ids=[\"07 Nrxs\",\"Nrxs03-Root_\",\"-Nrxs03-MeJ_\",\"-Nrxs03-Ctrl\",\"-Nrxs03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "7846a114-d40a-4b19-9e4f-8c46170cacaf",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Ntab=df_quant[[\"07 Ntab\",\"-Ntab03-Root\",\"-Ntab03-MeJ_\",\"-Ntab03-Ctrl\",\"-Ntab03-Caly\"]].astype('int')\n",
    "df_Ntab_t=df_Ntab.T\n",
    "counts=df_Ntab_t.to_numpy()\n",
    "ids=[\"07 Ntab\",\"-Ntab03-Root\",\"-Ntab03-MeJ_\",\"-Ntab03-Ctrl\",\"-Ntab03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "f381501c-d830-4440-8640-b8fcbf15c29d",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Nglu=df_quant[[\"08 Nglu\",\"Nglu03-Root_\",\"-Nglu03-MeJ_\",\"-Nglu03-Ctrl\",\"-Nglu03-Caly\"]].astype('int')\n",
    "df_Nglu_t=df_Nglu.T\n",
    "counts=df_Nglu_t.to_numpy()\n",
    "ids=[\"08 Nglu\",\"Nglu03-Root_\",\"-Nglu03-MeJ_\",\"-Nglu03-Ctrl\",\"-Nglu03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "5b32b198-5f3f-4372-bf7a-02ea6fd2611b",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Nben=df_quant[[\"10 Nben\",\"-Nben03-Root\",\"-Nben03-MeJ_\",\"-Nben03-Ctrl\",\"-Nben03-Caly\"]].astype('int')\n",
    "df_Nben_t=df_Nben.T\n",
    "counts=df_Nben_t.to_numpy()\n",
    "ids=[\"10 Nben\",\"Nben03-Root_\",\"-Nben03-MeJ_\",\"-Nben03-Ctrl\",\"-Nben03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "96357924-e2f3-4ab2-b6cf-c6aa2ab34a3a",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Ncle=df_quant[[\"10 Ncle\",\"-Ncle03-Root\",\"-Ncle03-MeJ_\",\"-Ncle03-Ctrl\",\"-Ncle03-Caly\"]].astype('int')\n",
    "df_Ncle_t=df_Ncle.T\n",
    "counts=df_Ncle_t.to_numpy()\n",
    "ids=[\"10 Ncle\",\"-Ncle03-Root\",\"-Ncle03-MeJ_\",\"-Ncle03-Ctrl\",\"-Ncle03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "a570be7b-2321-453e-8770-8443034af155",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Ngla=df_quant[[\"10 Ngla\",\"-Ngla03-Root\",\"-Ngla03-MeJ_\",\"-Ngla03-Ctrl\",\"-Ngla03-Caly\"]].astype('int')\n",
    "df_Ngla_t=df_Ngla.T\n",
    "counts=df_Ngla_t.to_numpy()\n",
    "ids=[\"10 Ngla\",\"-Ngla03-Root\",\"-Ngla03-MeJ_\",\"-Ngla03-Ctrl\",\"-Ngla03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "32337541-03cd-4b65-b545-a79c84765616",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Ngoo=df_quant[[\"10 Ngoo\",\"-Ngoo03-Root\",\"-Ngoo03-MeJ_\",\"-Ngoo03-Ctrl\",\"-Ngoo03-Caly\"]].astype('int')\n",
    "df_Ngoo_t=df_Ngoo.T\n",
    "counts=df_Ngoo_t.to_numpy()\n",
    "ids=[\"10 Ngoo\",\"-Ngoo03-Root\",\"-Ngoo03-MeJ_\",\"-Ngoo03-Ctrl\",\"-Ngoo03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "dd3c1536-324f-4248-baa9-cf4bba58c883",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Natt=df_quant[[\"10 Nnat\",\"-Natt03-Root\",\"-Natt03-MeJ_\",\"-Natt03-Ctrl\",\"-Natt03-Caly\"]].astype('int')\n",
    "df_Natt_t=df_Natt.T\n",
    "counts=df_Natt_t.to_numpy()\n",
    "ids=[\"10 Nnat\",\"-Natt03-Root\",\"-Natt03-MeJ_\",\"-Natt03-Ctrl\",\"-Natt03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "a9739d94-8a82-4904-bfe6-80082b2974d3",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Nnud=df_quant[[\"10 Nnud\",\"Nnud03-Root_\",\"-Nnud03-MeJ_\",\"-Nnud03-Ctrl\",\"-Nnud03-Caly\"]].astype('int')\n",
    "df_Nnud_t=df_Nnud.T\n",
    "counts=df_Nnud_t.to_numpy()\n",
    "ids=[\"10 Nnud\",\"Nnud03-Root_\",\"-Nnud03-MeJ_\",\"-Nnud03-Ctrl\",\"-Nnud03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "41179c58-2bc7-4ab7-a8fe-619da33c5008",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Nobt=df_quant[[\"10 Nobt\",\"Nobt03-Root_\",\"-Nobt03-MeJ_\",\"-Nobt03-Ctrl\",\"-Nobt03-Caly\"]].astype('int')\n",
    "df_Nobt_t=df_Nobt.T\n",
    "counts=df_Nobt_t.to_numpy()\n",
    "ids=[\"10 Nobt\",\"Nobt03-Root_\",\"-Nobt03-MeJ_\",\"-Nobt03-Ctrl\",\"-Nobt03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "d46845a9-8223-4a01-9f4b-a37be19acf2b",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Npal=df_quant[[\"10 Npal\",\"-Npal03-Root\",\"-Npal03-MeJ_\",\"-Npal03-Ctrl\",\"-Npal03-Caly\"]].astype('int')\n",
    "df_Npal_t=df_Npal.T\n",
    "counts=df_Npal_t.to_numpy()\n",
    "ids=[\"10 Npal\",\"Npal03-Root_\",\"-Npal03-MeJ_\",\"-Npal03-Ctrl\",\"-Npal03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "fec2e9b2-c86d-4f3f-a9a5-bb10c35c5f9d",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Npan=df_quant[[\"10 Npan\",\"-Npan03-Root\",\"-Npan03-MeJ_\",\"-Npan03-Ctrl\",\"-Npan03-Caly\"]].astype('int')\n",
    "df_Npan_t=df_Npan.T\n",
    "counts=df_Npan_t.to_numpy()\n",
    "ids=[\"10 Npan\",\"-Npan03-Root\",\"-Npan03-MeJ_\",\"-Npan03-Ctrl\",\"-Npan03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "8b8545fd-e906-4649-8584-1d30790254d6",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Nplu=df_quant[[\"10 Nplu\",\"-Nplu03-Root\",\"-Nplu03-MeJ_\",\"-Nplu03-Ctrl\",\"-Nplu03-Caly\"]].astype('int')\n",
    "df_Nplu_t=df_Nplu.T\n",
    "counts=df_Nplu_t.to_numpy()\n",
    "ids=[\"10 Nplu\",\"-Nplu03-Root\",\"-Nplu03-MeJ_\",\"-Nplu03-Ctrl\",\"-Nplu03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "id": "be000bb6-9f4b-4b62-9884-a6328babb49c",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Nrus=df_quant[[\"10 Nrus\",\"-Nrus03-Root\",\"-Nrus03-MeJ_\",\"-Nrus03-Ctrl\",\"-Nrus03-Caly\",\"10 Nrus02mf\"]].astype('int')\n",
    "df_Nrus_t=df_Nrus.T\n",
    "counts=df_Nrus_t.to_numpy()\n",
    "ids=[\"10 Nrus\",\"-Nrus03-Root\",\"-Nrus03-MeJ_\",\"-Nrus03-Ctrl\",\"-Nrus03-Caly\",\"10 Nrus02mf\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "id": "18b0e8e0-d51f-4660-9a83-9817d4e8e9be",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Nset=df_quant[[\"10 Nset\",\"-Nset03-Root\",\"-Nset03-MeJ_\",\"-Nset03-Ctrl\"]].astype('int')\n",
    "df_Nset_t=df_Nset.T\n",
    "counts=df_Nset_t.to_numpy()\n",
    "ids=[\"10 Nset\",\"-Nset03-Root\",\"-Nset03-MeJ_\",\"-Nset03-Ctrl\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "93eff657-4c53-4137-9a0b-56ffdfe9c508",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Nwut=df_quant[[\"10 Nwut\",\"Nwut03-Root_\",\"-Nwut03-MeJ_\",\"-Nwut03-Ctrl\",\"-Nwut03-Caly\"]].astype('int')\n",
    "df_Nwut_t=df_Nwut.T\n",
    "counts=df_Nwut_t.to_numpy()\n",
    "ids=[\"10 Nwut\",\"Nwut03-Root_\",\"-Nwut03-MeJ_\",\"-Nwut03-Ctrl\",\"-Nwut03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "id": "4085252d-a5b1-4e85-a481-acd00d94a6fd",
   "metadata": {},
   "outputs": [],
   "source": [
    "from skbio.diversity import alpha_diversity\n",
    "df_Nsyl=df_quant[[\"10 Nsyl\",\"Nsyl03-Root_\",\"-Nsyl03-MeJ_\",\"-Nsyl03-Ctrl\",\"-Nsyl03-Caly\"]].astype('int')\n",
    "df_Nsyl_t=df_Nsyl.T\n",
    "counts=df_Nsyl_t.to_numpy()\n",
    "ids=[\"10 Nsyl\",\"Nsyl03-Root_\",\"-Nsyl03-MeJ_\",\"-Nsyl03-Ctrl\",\"-Nsyl03-Caly\"]\n",
    "adiv_obs_otus = alpha_diversity('shannon', counts, ids)\n",
    "empty.append(adiv_obs_otus)\n",
    "adiv_obs_otus\n",
    "adiv_obs_otus = alpha_diversity('observed_otus', counts, ids)\n",
    "empty.append(adiv_obs_otus)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "id": "fbf00804-33ae-4f2a-9695-4729d9a30469",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "07 Nrep            3.724988\n",
       "Nrep03-Root_       7.655595\n",
       "-Nrep03-MeJ_       9.061189\n",
       "-Nrep03-Ctrl       8.876655\n",
       "-Nrep03-Caly       8.758468\n",
       "                   ...     \n",
       "10 Nsyl         6540.000000\n",
       "Nsyl03-Root_    7022.000000\n",
       "-Nsyl03-MeJ_    8942.000000\n",
       "-Nsyl03-Ctrl    8482.000000\n",
       "-Nsyl03-Caly    9364.000000\n",
       "Length: 200, dtype: float64"
      ]
     },
     "execution_count": 24,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "x=pd.concat(empty, axis=0, ignore_index=False)\n",
    "x"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "id": "83341f30-7d3f-4c73-9fc2-fbb92c9f505e",
   "metadata": {},
   "outputs": [],
   "source": [
    "x.to_csv(\"alpha_diversity_nicotiana.tsv\",sep=\"\\t\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "269eef13-2bad-4859-94a2-e61cb4a3733c",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
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  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
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   "file_extension": ".py",
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