make_reports.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "9694965b",
   "metadata": {},
   "source": [
    "These data are derived from the Zenodo archive:\n",
    "\n",
    "[Upcycling Human Excrement: The Gut Microbiome to Soil Microbiome Axis (supporting data)](https://zenodo.org/records/13887457)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "85232fc5",
   "metadata": {},
   "outputs": [],
   "source": [
    "from qiime2 import Visualization\n",
    "from q2templates.reports import matryoshka_template"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "dff7e196",
   "metadata": {},
   "source": [
    "# Upstream\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "01cfc4c2",
   "metadata": {},
   "outputs": [],
   "source": [
    "table = Visualization.load('asv-table.qzv')\n",
    "seqs = Visualization.load('asv-seqs-ms10.qzv')\n",
    "metadata = Visualization.load('sample-metadata.qzv')\n",
    "\n",
    "upstream = Visualization.make_report(matryoshka_template, {\n",
    "    'Table Summary': table,\n",
    "    'ASV Summary': seqs,\n",
    "    'Sample Metadata': metadata,\n",
    "})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "48081ebc",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Upstream.qzv'"
      ]
     },
     "execution_count": 3,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "upstream.save('Upstream')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6e1ba7b3",
   "metadata": {},
   "source": [
    "# PCoA"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "4bcdff90",
   "metadata": {},
   "outputs": [],
   "source": [
    "jaccard = Visualization.load('jaccard.qzv')\n",
    "braycurtis = Visualization.load('braycurtis.qzv')\n",
    "uu = Visualization.load('unweighted_unifrac.qzv')\n",
    "wu = Visualization.load('weighted_unifrac.qzv')\n",
    "\n",
    "pcoa = Visualization.make_report(matryoshka_template, {\n",
    "    'Jaccard': jaccard,\n",
    "    'Bray-Curtis': braycurtis,\n",
    "    'Weighted UniFrac': wu,\n",
    "    'Unweighted UniFrac': uu\n",
    "})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "4146d97a",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'PCoA.qzv'"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "pcoa.save('PCoA')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "7c15971b",
   "metadata": {},
   "source": [
    "# Taxonomy"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "9d70c3b4",
   "metadata": {},
   "outputs": [],
   "source": [
    "bk2 = Visualization.load('taxa-bar-plots-bucket2-gtdb-r214.1-weighted-stool-taxonomy.qzv')\n",
    "bk3 = Visualization.load('taxa-bar-plots-bucket3-gtdb-r214.1-weighted-stool-taxonomy.qzv')\n",
    "\n",
    "\n",
    "taxa = Visualization.make_report(matryoshka_template, {\n",
    "    'Bucket 2': bk2,\n",
    "    'Bucket 3': bk3\n",
    "})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "3433a221",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Taxa.qzv'"
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "taxa.save('Taxa')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "fb93156d",
   "metadata": {},
   "source": [
    "# Other"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "7e21d73b",
   "metadata": {},
   "outputs": [],
   "source": [
    "rain = Visualization.load('hec-raincloud.qzv')\n",
    "\n",
    "other = Visualization.make_report(matryoshka_template, {\n",
    "    'Raincloud Plots': rain\n",
    "})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "cbbf877b",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'Other.qzv'"
      ]
     },
     "execution_count": 9,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "other.save('Other')"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "46910f12",
   "metadata": {},
   "source": [
    "# Full Collated Report"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "da882747",
   "metadata": {},
   "outputs": [],
   "source": [
    "final = Visualization.make_report(matryoshka_template, {\n",
    "    'Summary': upstream,\n",
    "    'PCoA': pcoa,\n",
    "    'Taxonomy': taxa,\n",
    "    'Additional': other\n",
    "})"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "a1e487f7",
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'FinalAnalysis(1) actually-finished_Copy(2).qzv'"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "final.save('FinalAnalysis(1) actually-finished_Copy(2)')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "acea4b35",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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