examples/soils/check_soils.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "%matplotlib inline"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# standalone check"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "\u001b[34mlatent_dim_1_input_prior_1.00_output_prior_1.00_beta1_0.90_beta2_0.95\u001b[m\u001b[m\r\n",
      "latent_dim_1_input_prior_1.00_output_prior_1.00_beta1_0.90_beta2_0.95_embedding.txt\r\n",
      "latent_dim_1_input_prior_1.00_output_prior_1.00_beta1_0.90_beta2_0.95_ordination.txt\r\n",
      "latent_dim_1_input_prior_1.00_output_prior_1.00_beta1_0.90_beta2_0.95_ranks.txt\r\n"
     ]
    }
   ],
   "source": [
    "!ls summarydir"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "datadir = 'summarydir/latent_dim_1_input_prior_1.00_output_prior_1.00_beta1_0.90_beta2_0.95'\n",
    "ranks = pd.read_csv(datadir + '_ranks.txt', index_col=0, sep='\\t')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "featureid\n",
       "(2,3-dihydroxy-3-methylbutanoate)   -3.987261\n",
       "(2,5-diaminohexanoate)              -1.352668\n",
       "(3-hydroxypyridine)                 -0.020257\n",
       "(3-methyladenine)                    0.959734\n",
       "(4-oxoproline)                       2.986923\n",
       "Name: rplo 1 (Cyanobacteria), dtype: float64"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ranks['rplo 1 (Cyanobacteria)'].head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": [
    "microcoleus_metabolites = {'(3-methyladenine)', '7-methyladenine', '4-guanidinobutanoate', 'uracil',\n",
    "                           'xanthine', 'hypoxanthine', '(N6-acetyl-lysine)', 'cytosine',\n",
    "                           'N-acetylornithine', 'N-acetylornithine', 'succinate', \n",
    "                           'adenosine', 'guanine', 'adenine'}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "idx = ranks['rplo 1 (Cyanobacteria)'] > 0 \n",
    "detected_molecules = set(ranks.index[idx])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "{'(3-methyladenine)',\n",
       " '(N6-acetyl-lysine)',\n",
       " '4-guanidinobutanoate',\n",
       " '7-methyladenine',\n",
       " 'N-acetylornithine',\n",
       " 'adenine',\n",
       " 'adenosine',\n",
       " 'cytosine',\n",
       " 'guanine',\n",
       " 'hypoxanthine',\n",
       " 'succinate',\n",
       " 'uracil',\n",
       " 'xanthine'}"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "detected_molecules & microcoleus_metabolites"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "13"
      ]
     },
     "execution_count": 8,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(microcoleus_metabolites)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "13"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(detected_molecules & microcoleus_metabolites)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "featureid\n",
       "xanthine                0.642930\n",
       "(N6-acetyl-lysine)      4.409032\n",
       "succinate               0.878566\n",
       "guanine                 3.086299\n",
       "adenine                 4.947557\n",
       "N-acetylornithine       1.247694\n",
       "7-methyladenine         0.232607\n",
       "cytosine                3.205279\n",
       "hypoxanthine            0.661717\n",
       "4-guanidinobutanoate    3.998861\n",
       "(3-methyladenine)       0.959734\n",
       "adenosine               4.981767\n",
       "uracil                  1.782586\n",
       "Name: rplo 1 (Cyanobacteria), dtype: float64"
      ]
     },
     "execution_count": 10,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ranks['rplo 1 (Cyanobacteria)'].loc[microcoleus_metabolites]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [],
   "source": [
    "assert len(detected_molecules & microcoleus_metabolites) == 13"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# qiime2 check"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [],
   "source": [
    "import qiime2\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/Users/jmorton/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:516: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
      "  _np_qint8 = np.dtype([(\"qint8\", np.int8, 1)])\n",
      "/Users/jmorton/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
      "  _np_quint8 = np.dtype([(\"quint8\", np.uint8, 1)])\n",
      "/Users/jmorton/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
      "  _np_qint16 = np.dtype([(\"qint16\", np.int16, 1)])\n",
      "/Users/jmorton/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
      "  _np_quint16 = np.dtype([(\"quint16\", np.uint16, 1)])\n",
      "/Users/jmorton/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
      "  _np_qint32 = np.dtype([(\"qint32\", np.int32, 1)])\n",
      "/Users/jmorton/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:525: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
      "  np_resource = np.dtype([(\"resource\", np.ubyte, 1)])\n",
      "/Users/jmorton/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:541: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
      "  _np_qint8 = np.dtype([(\"qint8\", np.int8, 1)])\n",
      "/Users/jmorton/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:542: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
      "  _np_quint8 = np.dtype([(\"quint8\", np.uint8, 1)])\n",
      "/Users/jmorton/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:543: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
      "  _np_qint16 = np.dtype([(\"qint16\", np.int16, 1)])\n",
      "/Users/jmorton/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:544: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
      "  _np_quint16 = np.dtype([(\"quint16\", np.uint16, 1)])\n",
      "/Users/jmorton/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:545: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
      "  _np_qint32 = np.dtype([(\"qint32\", np.int32, 1)])\n",
      "/Users/jmorton/miniconda3/envs/qiime2-2019.7/lib/python3.6/site-packages/tensorboard/compat/tensorflow_stub/dtypes.py:550: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.\n",
      "  np_resource = np.dtype([(\"resource\", np.ubyte, 1)])\n"
     ]
    }
   ],
   "source": [
    "ranks = qiime2.Artifact.load('ranks.qza').view(pd.DataFrame)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [],
   "source": [
    "idx = ranks['rplo 1 (Cyanobacteria)'] > 0 \n",
    "detected_molecules = set(ranks.index[idx])\n",
    "assert len(detected_molecules & microcoleus_metabolites) == 13"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "featureid\n",
       "xanthine                0.742247\n",
       "(N6-acetyl-lysine)      4.348102\n",
       "succinate               0.720436\n",
       "guanine                 2.874898\n",
       "adenine                 4.852340\n",
       "N-acetylornithine       1.147904\n",
       "7-methyladenine         0.340129\n",
       "cytosine                3.000772\n",
       "hypoxanthine            0.522730\n",
       "4-guanidinobutanoate    3.888838\n",
       "(3-methyladenine)       0.750547\n",
       "adenosine               4.898254\n",
       "uracil                  1.723071\n",
       "Name: rplo 1 (Cyanobacteria), dtype: float64"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "ranks['rplo 1 (Cyanobacteria)'].loc[microcoleus_metabolites]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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