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joowkim/make-plots-taxonomy-composition-table.ipynb

Created April 2, 2018 06:04
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make-plots-taxonomy-composition-table.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Loading required package: ggplot2\n",
"Loading required package: tidyverse\n",
"Warning message:\n",
"\"package 'tidyverse' was built under R version 3.4.4\"-- Attaching packages --------------------------------------- tidyverse 1.2.1 --\n",
"√ tibble 1.4.2 √ purrr 0.2.4\n",
"√ tidyr 0.8.0 √ dplyr 0.7.4\n",
"√ readr 1.1.1 √ stringr 1.3.0\n",
"√ tibble 1.4.2 √ forcats 0.3.0\n",
"-- Conflicts ------------------------------------------ tidyverse_conflicts() --\n",
"x dplyr::filter() masks stats::filter()\n",
"x dplyr::lag() masks stats::lag()\n",
"Loading required package: RColorBrewer\n",
"Loading required package: vegan\n",
"Loading required package: permute\n",
"Loading required package: lattice\n",
"This is vegan 2.4-6\n",
"Loading required package: knitr\n",
"Loading required package: reshape2\n",
"\n",
"Attaching package: 'reshape2'\n",
"\n",
"The following object is masked from 'package:tidyr':\n",
"\n",
" smiths\n",
"\n",
"Loading required package: rJava\n",
"Loading required package: xlsxjars\n"
]
}
],
"source": [
"require(ggplot2)\n",
"require(tidyverse)\n",
"require(RColorBrewer)\n",
"require(vegan)\n",
"require(knitr)\n",
"require(reshape2)\n",
"library(xlsx)\n",
"library(RColorBrewer)"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>Gil34</th><th scope=col>Gil30</th><th scope=col>Gil31</th><th scope=col>Gil32</th><th scope=col>Gil33</th><th scope=col>IBD</th><th scope=col>Gil18</th><th scope=col>Gil19</th><th scope=col>Gil16</th><th scope=col>Gil17</th><th scope=col>...</th><th scope=col>Gil24</th><th scope=col>Gil8</th><th scope=col>Gil9</th><th scope=col>Gil4</th><th scope=col>Gil5</th><th scope=col>Gil6</th><th scope=col>Gil7</th><th scope=col>Gil1</th><th scope=col>Gil2</th><th scope=col>Gil3</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter</th><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>4.159156e-06</td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>... </td><td>0 </td><td>2.448362e-04</td><td>1.436110e-03</td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td></tr>\n",
"\t<tr><th scope=row>k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera</th><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0.000000e+00</td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>... </td><td>0 </td><td>7.122507e-04</td><td>5.566317e-05</td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td></tr>\n",
"\t<tr><th scope=row>k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta</th><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0.000000e+00</td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>... </td><td>0 </td><td>1.112892e-05</td><td>1.113263e-05</td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td></tr>\n",
"\t<tr><th scope=row>k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina</th><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0.000000e+00</td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>... </td><td>0 </td><td>0.000000e+00</td><td>0.000000e+00</td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td></tr>\n",
"\t<tr><th scope=row>k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus</th><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0.000000e+00</td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>... </td><td>0 </td><td>0.000000e+00</td><td>0.000000e+00</td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td></tr>\n",
"\t<tr><th scope=row>k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24</th><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0.000000e+00</td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>... </td><td>0 </td><td>1.112892e-05</td><td>0.000000e+00</td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td><td>0 </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|lllllllllllllllllllllllllllllll}\n",
" & Gil34 & Gil30 & Gil31 & Gil32 & Gil33 & IBD & Gil18 & Gil19 & Gil16 & Gil17 & ... & Gil24 & Gil8 & Gil9 & Gil4 & Gil5 & Gil6 & Gil7 & Gil1 & Gil2 & Gil3\\\\\n",
"\\hline\n",
"\tk\\_\\_Archaea;p\\_\\_Euryarchaeota;c\\_\\_Methanobacteria;o\\_\\_Methanobacteriales;f\\_\\_Methanobacteriaceae;g\\_\\_Methanobrevibacter & 0 & 0 & 0 & 0 & 0 & 4.159156e-06 & 0 & 0 & 0 & 0 & ... & 0 & 2.448362e-04 & 1.436110e-03 & 0 & 0 & 0 & 0 & 0 & 0 & 0 \\\\\n",
"\tk\\_\\_Archaea;p\\_\\_Euryarchaeota;c\\_\\_Methanobacteria;o\\_\\_Methanobacteriales;f\\_\\_Methanobacteriaceae;g\\_\\_Methanosphaera & 0 & 0 & 0 & 0 & 0 & 0.000000e+00 & 0 & 0 & 0 & 0 & ... & 0 & 7.122507e-04 & 5.566317e-05 & 0 & 0 & 0 & 0 & 0 & 0 & 0 \\\\\n",
"\tk\\_\\_Archaea;p\\_\\_Euryarchaeota;c\\_\\_Methanomicrobia;o\\_\\_Methanosarcinales;f\\_\\_Methanosaetaceae;g\\_\\_Methanosaeta & 0 & 0 & 0 & 0 & 0 & 0.000000e+00 & 0 & 0 & 0 & 0 & ... & 0 & 1.112892e-05 & 1.113263e-05 & 0 & 0 & 0 & 0 & 0 & 0 & 0 \\\\\n",
"\tk\\_\\_Archaea;p\\_\\_Euryarchaeota;c\\_\\_Methanomicrobia;o\\_\\_Methanosarcinales;f\\_\\_Methanosarcinaceae;g\\_\\_Methanosarcina & 0 & 0 & 0 & 0 & 0 & 0.000000e+00 & 0 & 0 & 0 & 0 & ... & 0 & 0.000000e+00 & 0.000000e+00 & 0 & 0 & 0 & 0 & 0 & 0 & 0 \\\\\n",
"\tk\\_\\_Archaea;p\\_\\_Euryarchaeota;c\\_\\_Thermoplasmata;o\\_\\_Thermoplasmatales;f\\_\\_Thermoplasmatales Incertae Sedis;g\\_\\_Methanomassiliicoccus & 0 & 0 & 0 & 0 & 0 & 0.000000e+00 & 0 & 0 & 0 & 0 & ... & 0 & 0.000000e+00 & 0.000000e+00 & 0 & 0 & 0 & 0 & 0 & 0 & 0 \\\\\n",
"\tk\\_\\_Bacteria;p\\_\\_Acidobacteria;c\\_\\_Blastocatellia;o\\_\\_Blastocatellales;f\\_\\_Blastocatellaceae (Subgroup 4);g\\_\\_11-24 & 0 & 0 & 0 & 0 & 0 & 0.000000e+00 & 0 & 0 & 0 & 0 & ... & 0 & 1.112892e-05 & 0.000000e+00 & 0 & 0 & 0 & 0 & 0 & 0 & 0 \\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | Gil34 | Gil30 | Gil31 | Gil32 | Gil33 | IBD | Gil18 | Gil19 | Gil16 | Gil17 | ... | Gil24 | Gil8 | Gil9 | Gil4 | Gil5 | Gil6 | Gil7 | Gil1 | Gil2 | Gil3 | \n",
"|---|---|---|---|---|---|\n",
"| k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter | 0 | 0 | 0 | 0 | 0 | 4.159156e-06 | 0 | 0 | 0 | 0 | ... | 0 | 2.448362e-04 | 1.436110e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | \n",
"| k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera | 0 | 0 | 0 | 0 | 0 | 0.000000e+00 | 0 | 0 | 0 | 0 | ... | 0 | 7.122507e-04 | 5.566317e-05 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | \n",
"| k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta | 0 | 0 | 0 | 0 | 0 | 0.000000e+00 | 0 | 0 | 0 | 0 | ... | 0 | 1.112892e-05 | 1.113263e-05 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | \n",
"| k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina | 0 | 0 | 0 | 0 | 0 | 0.000000e+00 | 0 | 0 | 0 | 0 | ... | 0 | 0.000000e+00 | 0.000000e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | \n",
"| k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus | 0 | 0 | 0 | 0 | 0 | 0.000000e+00 | 0 | 0 | 0 | 0 | ... | 0 | 0.000000e+00 | 0.000000e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | \n",
"| k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 | 0 | 0 | 0 | 0 | 0 | 0.000000e+00 | 0 | 0 | 0 | 0 | ... | 0 | 1.112892e-05 | 0.000000e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | \n",
"\n",
"\n"
],
"text/plain": [
" Gil34\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil30\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil31\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil32\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil33\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" IBD \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 4.159156e-06\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0.000000e+00\n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0.000000e+00\n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0.000000e+00\n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0.000000e+00\n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0.000000e+00\n",
" Gil18\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil19\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil16\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil17\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" ...\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter ...\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera ...\n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta ...\n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina ...\n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus ...\n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 ...\n",
" Gil24\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil8 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 2.448362e-04\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 7.122507e-04\n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 1.112892e-05\n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0.000000e+00\n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0.000000e+00\n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 1.112892e-05\n",
" Gil9 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 1.436110e-03\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 5.566317e-05\n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 1.113263e-05\n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0.000000e+00\n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0.000000e+00\n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0.000000e+00\n",
" Gil4\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil5\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil6\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil7\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil1\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil2\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 \n",
" Gil3\n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanosphaera 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosaetaceae;g__Methanosaeta 0 \n",
"k__Archaea;p__Euryarchaeota;c__Methanomicrobia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina 0 \n",
"k__Archaea;p__Euryarchaeota;c__Thermoplasmata;o__Thermoplasmatales;f__Thermoplasmatales Incertae Sedis;g__Methanomassiliicoccus 0 \n",
"k__Bacteria;p__Acidobacteria;c__Blastocatellia;o__Blastocatellales;f__Blastocatellaceae (Subgroup 4);g__11-24 0 "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"taxa <- read.delim(\"Description_otu_table_L6.txt\", sep='\\t', row=1)\n",
"head(taxa)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"split <- strsplit(rownames(taxa),\";\")"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<ol>\n",
"\t<li><ol class=list-inline>\n",
"\t<li>'k__Archaea'</li>\n",
"\t<li>'p__Euryarchaeota'</li>\n",
"\t<li>'c__Methanobacteria'</li>\n",
"\t<li>'o__Methanobacteriales'</li>\n",
"\t<li>'f__Methanobacteriaceae'</li>\n",
"\t<li>'g__Methanobrevibacter'</li>\n",
"</ol>\n",
"</li>\n",
"\t<li><ol class=list-inline>\n",
"\t<li>'k__Archaea'</li>\n",
"\t<li>'p__Euryarchaeota'</li>\n",
"\t<li>'c__Methanobacteria'</li>\n",
"\t<li>'o__Methanobacteriales'</li>\n",
"\t<li>'f__Methanobacteriaceae'</li>\n",
"\t<li>'g__Methanosphaera'</li>\n",
"</ol>\n",
"</li>\n",
"\t<li><ol class=list-inline>\n",
"\t<li>'k__Archaea'</li>\n",
"\t<li>'p__Euryarchaeota'</li>\n",
"\t<li>'c__Methanomicrobia'</li>\n",
"\t<li>'o__Methanosarcinales'</li>\n",
"\t<li>'f__Methanosaetaceae'</li>\n",
"\t<li>'g__Methanosaeta'</li>\n",
"</ol>\n",
"</li>\n",
"\t<li><ol class=list-inline>\n",
"\t<li>'k__Archaea'</li>\n",
"\t<li>'p__Euryarchaeota'</li>\n",
"\t<li>'c__Methanomicrobia'</li>\n",
"\t<li>'o__Methanosarcinales'</li>\n",
"\t<li>'f__Methanosarcinaceae'</li>\n",
"\t<li>'g__Methanosarcina'</li>\n",
"</ol>\n",
"</li>\n",
"\t<li><ol class=list-inline>\n",
"\t<li>'k__Archaea'</li>\n",
"\t<li>'p__Euryarchaeota'</li>\n",
"\t<li>'c__Thermoplasmata'</li>\n",
"\t<li>'o__Thermoplasmatales'</li>\n",
"\t<li>'f__Thermoplasmatales Incertae Sedis'</li>\n",
"\t<li>'g__Methanomassiliicoccus'</li>\n",
"</ol>\n",
"</li>\n",
"\t<li><ol class=list-inline>\n",
"\t<li>'k__Bacteria'</li>\n",
"\t<li>'p__Acidobacteria'</li>\n",
"\t<li>'c__Blastocatellia'</li>\n",
"\t<li>'o__Blastocatellales'</li>\n",
"\t<li>'f__Blastocatellaceae (Subgroup 4)'</li>\n",
"\t<li>'g__11-24'</li>\n",
"</ol>\n",
"</li>\n",
"</ol>\n"
],
"text/latex": [
"\\begin{enumerate}\n",
"\\item \\begin{enumerate*}\n",
"\\item 'k\\_\\_Archaea'\n",
"\\item 'p\\_\\_Euryarchaeota'\n",
"\\item 'c\\_\\_Methanobacteria'\n",
"\\item 'o\\_\\_Methanobacteriales'\n",
"\\item 'f\\_\\_Methanobacteriaceae'\n",
"\\item 'g\\_\\_Methanobrevibacter'\n",
"\\end{enumerate*}\n",
"\n",
"\\item \\begin{enumerate*}\n",
"\\item 'k\\_\\_Archaea'\n",
"\\item 'p\\_\\_Euryarchaeota'\n",
"\\item 'c\\_\\_Methanobacteria'\n",
"\\item 'o\\_\\_Methanobacteriales'\n",
"\\item 'f\\_\\_Methanobacteriaceae'\n",
"\\item 'g\\_\\_Methanosphaera'\n",
"\\end{enumerate*}\n",
"\n",
"\\item \\begin{enumerate*}\n",
"\\item 'k\\_\\_Archaea'\n",
"\\item 'p\\_\\_Euryarchaeota'\n",
"\\item 'c\\_\\_Methanomicrobia'\n",
"\\item 'o\\_\\_Methanosarcinales'\n",
"\\item 'f\\_\\_Methanosaetaceae'\n",
"\\item 'g\\_\\_Methanosaeta'\n",
"\\end{enumerate*}\n",
"\n",
"\\item \\begin{enumerate*}\n",
"\\item 'k\\_\\_Archaea'\n",
"\\item 'p\\_\\_Euryarchaeota'\n",
"\\item 'c\\_\\_Methanomicrobia'\n",
"\\item 'o\\_\\_Methanosarcinales'\n",
"\\item 'f\\_\\_Methanosarcinaceae'\n",
"\\item 'g\\_\\_Methanosarcina'\n",
"\\end{enumerate*}\n",
"\n",
"\\item \\begin{enumerate*}\n",
"\\item 'k\\_\\_Archaea'\n",
"\\item 'p\\_\\_Euryarchaeota'\n",
"\\item 'c\\_\\_Thermoplasmata'\n",
"\\item 'o\\_\\_Thermoplasmatales'\n",
"\\item 'f\\_\\_Thermoplasmatales Incertae Sedis'\n",
"\\item 'g\\_\\_Methanomassiliicoccus'\n",
"\\end{enumerate*}\n",
"\n",
"\\item \\begin{enumerate*}\n",
"\\item 'k\\_\\_Bacteria'\n",
"\\item 'p\\_\\_Acidobacteria'\n",
"\\item 'c\\_\\_Blastocatellia'\n",
"\\item 'o\\_\\_Blastocatellales'\n",
"\\item 'f\\_\\_Blastocatellaceae (Subgroup 4)'\n",
"\\item 'g\\_\\_11-24'\n",
"\\end{enumerate*}\n",
"\n",
"\\end{enumerate}\n"
],
"text/markdown": [
"1. 1. 'k__Archaea'\n",
"2. 'p__Euryarchaeota'\n",
"3. 'c__Methanobacteria'\n",
"4. 'o__Methanobacteriales'\n",
"5. 'f__Methanobacteriaceae'\n",
"6. 'g__Methanobrevibacter'\n",
"\n",
"\n",
"\n",
"2. 1. 'k__Archaea'\n",
"2. 'p__Euryarchaeota'\n",
"3. 'c__Methanobacteria'\n",
"4. 'o__Methanobacteriales'\n",
"5. 'f__Methanobacteriaceae'\n",
"6. 'g__Methanosphaera'\n",
"\n",
"\n",
"\n",
"3. 1. 'k__Archaea'\n",
"2. 'p__Euryarchaeota'\n",
"3. 'c__Methanomicrobia'\n",
"4. 'o__Methanosarcinales'\n",
"5. 'f__Methanosaetaceae'\n",
"6. 'g__Methanosaeta'\n",
"\n",
"\n",
"\n",
"4. 1. 'k__Archaea'\n",
"2. 'p__Euryarchaeota'\n",
"3. 'c__Methanomicrobia'\n",
"4. 'o__Methanosarcinales'\n",
"5. 'f__Methanosarcinaceae'\n",
"6. 'g__Methanosarcina'\n",
"\n",
"\n",
"\n",
"5. 1. 'k__Archaea'\n",
"2. 'p__Euryarchaeota'\n",
"3. 'c__Thermoplasmata'\n",
"4. 'o__Thermoplasmatales'\n",
"5. 'f__Thermoplasmatales Incertae Sedis'\n",
"6. 'g__Methanomassiliicoccus'\n",
"\n",
"\n",
"\n",
"6. 1. 'k__Bacteria'\n",
"2. 'p__Acidobacteria'\n",
"3. 'c__Blastocatellia'\n",
"4. 'o__Blastocatellales'\n",
"5. 'f__Blastocatellaceae (Subgroup 4)'\n",
"6. 'g__11-24'\n",
"\n",
"\n",
"\n",
"\n",
"\n"
],
"text/plain": [
"[[1]]\n",
"[1] \"k__Archaea\" \"p__Euryarchaeota\" \"c__Methanobacteria\" \n",
"[4] \"o__Methanobacteriales\" \"f__Methanobacteriaceae\" \"g__Methanobrevibacter\" \n",
"\n",
"[[2]]\n",
"[1] \"k__Archaea\" \"p__Euryarchaeota\" \"c__Methanobacteria\" \n",
"[4] \"o__Methanobacteriales\" \"f__Methanobacteriaceae\" \"g__Methanosphaera\" \n",
"\n",
"[[3]]\n",
"[1] \"k__Archaea\" \"p__Euryarchaeota\" \"c__Methanomicrobia\" \n",
"[4] \"o__Methanosarcinales\" \"f__Methanosaetaceae\" \"g__Methanosaeta\" \n",
"\n",
"[[4]]\n",
"[1] \"k__Archaea\" \"p__Euryarchaeota\" \"c__Methanomicrobia\" \n",
"[4] \"o__Methanosarcinales\" \"f__Methanosarcinaceae\" \"g__Methanosarcina\" \n",
"\n",
"[[5]]\n",
"[1] \"k__Archaea\" \"p__Euryarchaeota\" \n",
"[3] \"c__Thermoplasmata\" \"o__Thermoplasmatales\" \n",
"[5] \"f__Thermoplasmatales Incertae Sedis\" \"g__Methanomassiliicoccus\" \n",
"\n",
"[[6]]\n",
"[1] \"k__Bacteria\" \"p__Acidobacteria\" \n",
"[3] \"c__Blastocatellia\" \"o__Blastocatellales\" \n",
"[5] \"f__Blastocatellaceae (Subgroup 4)\" \"g__11-24\" \n"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"head(split)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"taxaStrings <- sapply(split,function(x) paste(x[1:6],collapse=\";\"))\n",
"gtaxa <- taxa\n",
"splitg <- strsplit(rownames(gtaxa),\";\") # Split and rejoin on lv7\n",
"gtaxaStrings <- sapply(splitg,function(x) paste(x[1:6],collapse=\";\")) # level 7 is species, 8 is strain\n",
"gtaxa <- rowsum(gtaxa,gtaxaStrings) # Collapse by taxonomy name\n",
"gtaxa <- sweep(gtaxa,2,colSums(gtaxa),'/')\n",
"gtaxa <- gtaxa[order(rowMeans(gtaxa),decreasing=T),]"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>Bacteroides</th><th scope=col>Prevotella 9</th><th scope=col>Faecalibacterium</th><th scope=col>Bifidobacterium</th><th scope=col>Blautia</th><th scope=col>Parabacteroides</th><th scope=col>[Eubacterium] coprostanoligenes group</th><th scope=col>Alistipes</th><th scope=col>uncultured bacterium</th><th scope=col>Escherichia-Shigella</th><th scope=col>Roseburia</th><th scope=col>Ruminococcaceae UCG-002</th><th scope=col>Lachnospiraceae UCG-008</th><th scope=col>Akkermansia</th><th scope=col>Prevotella 2</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>Gil34</th><td>23.07988 </td><td>0.000000000</td><td>11.094204 </td><td>0.04149952 </td><td>3.4229415 </td><td> 1.58159266</td><td>2.201011359</td><td>6.36940717 </td><td>7.66204024 </td><td>0.02612932 </td><td>1.507816 </td><td>2.7389680 </td><td>0.5932894 </td><td>6.7828653 </td><td>0.000000 </td></tr>\n",
"\t<tr><th scope=row>Gil30</th><td>16.68995 </td><td>3.247942866</td><td> 5.905915 </td><td>7.91026238 </td><td>6.2241888 </td><td> 8.27977022</td><td>6.613879832</td><td>1.28706723 </td><td>0.00776277 </td><td>0.00000000 </td><td>1.892563 </td><td>1.3553796 </td><td>1.2358329 </td><td>0.0000000 </td><td>4.196553 </td></tr>\n",
"\t<tr><th scope=row>Gil31</th><td>66.39226 </td><td>0.000000000</td><td> 2.881272 </td><td>2.81740118 </td><td>2.2875121 </td><td> 0.01892461</td><td>0.001182788</td><td>0.06741892 </td><td>0.23182646 </td><td>2.76535850 </td><td>1.088165 </td><td>0.0000000 </td><td>0.7912852 </td><td>0.0000000 </td><td>0.000000 </td></tr>\n",
"\t<tr><th scope=row>Gil32</th><td>40.40468 </td><td>0.000000000</td><td>22.978358 </td><td>1.72348245 </td><td>2.4359678 </td><td> 3.55397851</td><td>0.832171672</td><td>0.74205494 </td><td>0.12672665 </td><td>0.08448443 </td><td>2.403582 </td><td>0.0000000 </td><td>0.7448711 </td><td>0.0000000 </td><td>0.000000 </td></tr>\n",
"\t<tr><th scope=row>Gil33</th><td>38.18386 </td><td>0.000000000</td><td> 9.873941 </td><td>1.68217560 </td><td>7.3180879 </td><td>10.19983636</td><td>0.047150841</td><td>7.91856772 </td><td>0.14699968 </td><td>0.05131121 </td><td>2.268788 </td><td>0.0000000 </td><td>2.4227212 </td><td>0.0000000 </td><td>0.000000 </td></tr>\n",
"\t<tr><th scope=row>IBD</th><td>40.93182 </td><td>0.004159156</td><td>15.823146 </td><td>0.04824621 </td><td>0.9029009 </td><td> 1.09344221</td><td>0.068574090</td><td>2.85910806 </td><td>0.76523278 </td><td>0.50112635 </td><td>6.134496 </td><td>0.0729412 </td><td>0.6104602 </td><td>0.5219741 </td><td>0.000000 </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|lllllllllllllll}\n",
" & Bacteroides & Prevotella 9 & Faecalibacterium & Bifidobacterium & Blautia & Parabacteroides & {[}Eubacterium{]} coprostanoligenes group & Alistipes & uncultured bacterium & Escherichia-Shigella & Roseburia & Ruminococcaceae UCG-002 & Lachnospiraceae UCG-008 & Akkermansia & Prevotella 2\\\\\n",
"\\hline\n",
"\tGil34 & 23.07988 & 0.000000000 & 11.094204 & 0.04149952 & 3.4229415 & 1.58159266 & 2.201011359 & 6.36940717 & 7.66204024 & 0.02612932 & 1.507816 & 2.7389680 & 0.5932894 & 6.7828653 & 0.000000 \\\\\n",
"\tGil30 & 16.68995 & 3.247942866 & 5.905915 & 7.91026238 & 6.2241888 & 8.27977022 & 6.613879832 & 1.28706723 & 0.00776277 & 0.00000000 & 1.892563 & 1.3553796 & 1.2358329 & 0.0000000 & 4.196553 \\\\\n",
"\tGil31 & 66.39226 & 0.000000000 & 2.881272 & 2.81740118 & 2.2875121 & 0.01892461 & 0.001182788 & 0.06741892 & 0.23182646 & 2.76535850 & 1.088165 & 0.0000000 & 0.7912852 & 0.0000000 & 0.000000 \\\\\n",
"\tGil32 & 40.40468 & 0.000000000 & 22.978358 & 1.72348245 & 2.4359678 & 3.55397851 & 0.832171672 & 0.74205494 & 0.12672665 & 0.08448443 & 2.403582 & 0.0000000 & 0.7448711 & 0.0000000 & 0.000000 \\\\\n",
"\tGil33 & 38.18386 & 0.000000000 & 9.873941 & 1.68217560 & 7.3180879 & 10.19983636 & 0.047150841 & 7.91856772 & 0.14699968 & 0.05131121 & 2.268788 & 0.0000000 & 2.4227212 & 0.0000000 & 0.000000 \\\\\n",
"\tIBD & 40.93182 & 0.004159156 & 15.823146 & 0.04824621 & 0.9029009 & 1.09344221 & 0.068574090 & 2.85910806 & 0.76523278 & 0.50112635 & 6.134496 & 0.0729412 & 0.6104602 & 0.5219741 & 0.000000 \\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | Bacteroides | Prevotella 9 | Faecalibacterium | Bifidobacterium | Blautia | Parabacteroides | [Eubacterium] coprostanoligenes group | Alistipes | uncultured bacterium | Escherichia-Shigella | Roseburia | Ruminococcaceae UCG-002 | Lachnospiraceae UCG-008 | Akkermansia | Prevotella 2 | \n",
"|---|---|---|---|---|---|\n",
"| Gil34 | 23.07988 | 0.000000000 | 11.094204 | 0.04149952 | 3.4229415 | 1.58159266 | 2.201011359 | 6.36940717 | 7.66204024 | 0.02612932 | 1.507816 | 2.7389680 | 0.5932894 | 6.7828653 | 0.000000 | \n",
"| Gil30 | 16.68995 | 3.247942866 | 5.905915 | 7.91026238 | 6.2241888 | 8.27977022 | 6.613879832 | 1.28706723 | 0.00776277 | 0.00000000 | 1.892563 | 1.3553796 | 1.2358329 | 0.0000000 | 4.196553 | \n",
"| Gil31 | 66.39226 | 0.000000000 | 2.881272 | 2.81740118 | 2.2875121 | 0.01892461 | 0.001182788 | 0.06741892 | 0.23182646 | 2.76535850 | 1.088165 | 0.0000000 | 0.7912852 | 0.0000000 | 0.000000 | \n",
"| Gil32 | 40.40468 | 0.000000000 | 22.978358 | 1.72348245 | 2.4359678 | 3.55397851 | 0.832171672 | 0.74205494 | 0.12672665 | 0.08448443 | 2.403582 | 0.0000000 | 0.7448711 | 0.0000000 | 0.000000 | \n",
"| Gil33 | 38.18386 | 0.000000000 | 9.873941 | 1.68217560 | 7.3180879 | 10.19983636 | 0.047150841 | 7.91856772 | 0.14699968 | 0.05131121 | 2.268788 | 0.0000000 | 2.4227212 | 0.0000000 | 0.000000 | \n",
"| IBD | 40.93182 | 0.004159156 | 15.823146 | 0.04824621 | 0.9029009 | 1.09344221 | 0.068574090 | 2.85910806 | 0.76523278 | 0.50112635 | 6.134496 | 0.0729412 | 0.6104602 | 0.5219741 | 0.000000 | \n",
"\n",
"\n"
],
"text/plain": [
" Bacteroides Prevotella 9 Faecalibacterium Bifidobacterium Blautia \n",
"Gil34 23.07988 0.000000000 11.094204 0.04149952 3.4229415\n",
"Gil30 16.68995 3.247942866 5.905915 7.91026238 6.2241888\n",
"Gil31 66.39226 0.000000000 2.881272 2.81740118 2.2875121\n",
"Gil32 40.40468 0.000000000 22.978358 1.72348245 2.4359678\n",
"Gil33 38.18386 0.000000000 9.873941 1.68217560 7.3180879\n",
"IBD 40.93182 0.004159156 15.823146 0.04824621 0.9029009\n",
" Parabacteroides [Eubacterium] coprostanoligenes group Alistipes \n",
"Gil34 1.58159266 2.201011359 6.36940717\n",
"Gil30 8.27977022 6.613879832 1.28706723\n",
"Gil31 0.01892461 0.001182788 0.06741892\n",
"Gil32 3.55397851 0.832171672 0.74205494\n",
"Gil33 10.19983636 0.047150841 7.91856772\n",
"IBD 1.09344221 0.068574090 2.85910806\n",
" uncultured bacterium Escherichia-Shigella Roseburia\n",
"Gil34 7.66204024 0.02612932 1.507816 \n",
"Gil30 0.00776277 0.00000000 1.892563 \n",
"Gil31 0.23182646 2.76535850 1.088165 \n",
"Gil32 0.12672665 0.08448443 2.403582 \n",
"Gil33 0.14699968 0.05131121 2.268788 \n",
"IBD 0.76523278 0.50112635 6.134496 \n",
" Ruminococcaceae UCG-002 Lachnospiraceae UCG-008 Akkermansia Prevotella 2\n",
"Gil34 2.7389680 0.5932894 6.7828653 0.000000 \n",
"Gil30 1.3553796 1.2358329 0.0000000 4.196553 \n",
"Gil31 0.0000000 0.7912852 0.0000000 0.000000 \n",
"Gil32 0.0000000 0.7448711 0.0000000 0.000000 \n",
"Gil33 0.0000000 2.4227212 0.0000000 0.000000 \n",
"IBD 0.0729412 0.6104602 0.5219741 0.000000 "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"filtered.taxa <- gtaxa[1:15,] * 100\n",
"#filtered.taxa <- gtaxa * 100\n",
"#traspose to add to map for later use\n",
"filtered.taxa <- t(filtered.taxa)\n",
"colnames(filtered.taxa) <- gsub(\".*;g__?\", \"\", colnames(filtered.taxa))\n",
"colnames(filtered.taxa) <- gsub(\"_\", \"\", colnames(filtered.taxa))\n",
"colnames(filtered.taxa) <- gsub(\";.*\",\"\",colnames(filtered.taxa))\n",
"\n",
"head(filtered.taxa)"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {},
"outputs": [],
"source": [
"filtered.taxa.df <- as.data.frame(filtered.taxa)\n",
"\n",
"one.minus.sum <- function(row) { return(100 - sum(row)) }\n",
"\n",
"filtered.taxa.df$etc <- apply(filtered.taxa.df, 1, one.minus.sum)"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>Gil34</th><th scope=col>Gil30</th><th scope=col>Gil31</th><th scope=col>Gil32</th><th scope=col>Gil33</th><th scope=col>IBD</th><th scope=col>Gil18</th><th scope=col>Gil19</th><th scope=col>Gil16</th><th scope=col>Gil17</th><th scope=col>...</th><th scope=col>Gil24</th><th scope=col>Gil8</th><th scope=col>Gil9</th><th scope=col>Gil4</th><th scope=col>Gil5</th><th scope=col>Gil6</th><th scope=col>Gil7</th><th scope=col>Gil1</th><th scope=col>Gil2</th><th scope=col>Gil3</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>Bacteroides</th><td>23.08</td><td>16.69</td><td>66.39</td><td>40.40</td><td>38.18</td><td>40.93</td><td> 3.21</td><td>34.35</td><td>22.32</td><td>39.31</td><td>... </td><td> 5.00</td><td>7.53 </td><td>14.91</td><td>47.69</td><td>27.42</td><td>61.70</td><td> 2.39</td><td>16.60</td><td>35.38</td><td>38.66</td></tr>\n",
"\t<tr><th scope=row>Prevotella 9</th><td> 0.00</td><td> 3.25</td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td> 9.41</td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td>... </td><td>55.84</td><td>0.76 </td><td>30.14</td><td> 1.50</td><td> 0.00</td><td> 0.00</td><td>39.68</td><td> 0.00</td><td> 0.00</td><td> 6.98</td></tr>\n",
"\t<tr><th scope=row>Faecalibacterium</th><td>11.09</td><td> 5.91</td><td> 2.88</td><td>22.98</td><td> 9.87</td><td>15.82</td><td> 9.50</td><td> 5.08</td><td>22.89</td><td> 2.27</td><td>... </td><td> 2.92</td><td>4.77 </td><td> 7.87</td><td>11.80</td><td>20.27</td><td> 3.73</td><td> 0.98</td><td>11.36</td><td> 0.06</td><td>12.76</td></tr>\n",
"\t<tr><th scope=row>Bifidobacterium</th><td> 0.04</td><td> 7.91</td><td> 2.82</td><td> 1.72</td><td> 1.68</td><td> 0.05</td><td> 4.82</td><td> 4.40</td><td>18.77</td><td> 2.11</td><td>... </td><td> 0.69</td><td>0.03 </td><td> 0.69</td><td> 0.12</td><td> 6.26</td><td> 1.67</td><td> 0.35</td><td> 1.34</td><td>12.62</td><td> 0.83</td></tr>\n",
"\t<tr><th scope=row>Blautia</th><td> 3.42</td><td> 6.22</td><td> 2.29</td><td> 2.44</td><td> 7.32</td><td> 0.90</td><td> 1.81</td><td> 2.99</td><td> 2.70</td><td> 4.58</td><td>... </td><td> 0.90</td><td>3.79 </td><td> 1.06</td><td> 1.02</td><td> 0.12</td><td> 0.58</td><td> 0.29</td><td>22.14</td><td> 0.88</td><td>10.04</td></tr>\n",
"\t<tr><th scope=row>Parabacteroides</th><td> 1.58</td><td> 8.28</td><td> 0.02</td><td> 3.55</td><td>10.20</td><td> 1.09</td><td> 0.46</td><td> 1.61</td><td> 0.06</td><td> 9.34</td><td>... </td><td> 0.41</td><td>1.63 </td><td> 1.27</td><td> 0.61</td><td>16.91</td><td> 0.30</td><td> 2.28</td><td> 3.71</td><td> 3.19</td><td> 1.72</td></tr>\n",
"\t<tr><th scope=row>[Eubacterium] coprostanoligenes group</th><td> 2.20</td><td> 6.61</td><td> 0.00</td><td> 0.83</td><td> 0.05</td><td> 0.07</td><td>14.71</td><td> 0.00</td><td> 0.00</td><td> 0.01</td><td>... </td><td> 1.98</td><td>5.17 </td><td> 3.95</td><td> 4.03</td><td> 0.00</td><td> 0.57</td><td> 8.92</td><td> 0.14</td><td> 0.01</td><td> 0.00</td></tr>\n",
"\t<tr><th scope=row>Alistipes</th><td> 6.37</td><td> 1.29</td><td> 0.07</td><td> 0.74</td><td> 7.92</td><td> 2.86</td><td> 0.22</td><td> 1.11</td><td> 0.03</td><td> 1.64</td><td>... </td><td> 0.71</td><td>2.56 </td><td> 4.13</td><td> 0.22</td><td> 0.13</td><td> 3.04</td><td> 1.03</td><td> 0.68</td><td> 2.30</td><td> 4.18</td></tr>\n",
"\t<tr><th scope=row>uncultured bacterium</th><td> 7.66</td><td> 0.01</td><td> 0.23</td><td> 0.13</td><td> 0.15</td><td> 0.77</td><td> 0.61</td><td> 0.55</td><td> 0.00</td><td> 0.35</td><td>... </td><td> 5.42</td><td>5.50 </td><td> 8.86</td><td> 0.75</td><td> 0.29</td><td> 0.05</td><td> 7.69</td><td> 0.25</td><td> 1.62</td><td> 0.14</td></tr>\n",
"\t<tr><th scope=row>Escherichia-Shigella</th><td> 0.03</td><td> 0.00</td><td> 2.77</td><td> 0.08</td><td> 0.05</td><td> 0.50</td><td> 0.02</td><td> 9.52</td><td> 0.04</td><td> 2.21</td><td>... </td><td> 0.01</td><td>0.01 </td><td> 0.16</td><td> 0.12</td><td>13.09</td><td> 0.08</td><td> 0.06</td><td> 0.07</td><td> 1.62</td><td> 0.33</td></tr>\n",
"\t<tr><th scope=row>Roseburia</th><td> 1.51</td><td> 1.89</td><td> 1.09</td><td> 2.40</td><td> 2.27</td><td> 6.13</td><td> 4.51</td><td> 2.87</td><td> 0.96</td><td> 0.78</td><td>... </td><td> 2.02</td><td>1.82 </td><td> 2.38</td><td> 2.56</td><td> 0.01</td><td> 0.98</td><td> 1.02</td><td> 2.16</td><td> 0.00</td><td> 1.31</td></tr>\n",
"\t<tr><th scope=row>Ruminococcaceae UCG-002</th><td> 2.74</td><td> 1.36</td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td> 0.07</td><td> 0.13</td><td> 0.19</td><td> 0.01</td><td> 0.23</td><td>... </td><td> 2.57</td><td>2.89 </td><td> 0.45</td><td> 0.11</td><td> 0.00</td><td> 0.32</td><td>10.17</td><td> 0.05</td><td> 0.00</td><td> 0.06</td></tr>\n",
"\t<tr><th scope=row>Lachnospiraceae UCG-008</th><td> 0.59</td><td> 1.24</td><td> 0.79</td><td> 0.74</td><td> 2.42</td><td> 0.61</td><td> 1.80</td><td> 1.06</td><td> 2.01</td><td> 1.57</td><td>... </td><td> 1.10</td><td>0.65 </td><td> 0.49</td><td> 0.36</td><td> 0.04</td><td> 0.93</td><td> 0.31</td><td>11.21</td><td> 0.32</td><td> 5.07</td></tr>\n",
"\t<tr><th scope=row>Akkermansia</th><td> 6.78</td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td> 0.52</td><td> 0.02</td><td> 0.00</td><td> 0.00</td><td> 0.03</td><td>... </td><td> 0.00</td><td>0.38 </td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td> 0.01</td><td> 0.00</td><td> 0.00</td><td> 5.40</td><td> 0.00</td></tr>\n",
"\t<tr><th scope=row>Prevotella 2</th><td> 0.00</td><td> 4.20</td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td> 0.07</td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td>... </td><td> 0.54</td><td>0.07 </td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td> 1.50</td><td> 0.00</td><td> 0.00</td><td> 0.00</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|lllllllllllllllllllllllllllllll}\n",
" & Gil34 & Gil30 & Gil31 & Gil32 & Gil33 & IBD & Gil18 & Gil19 & Gil16 & Gil17 & ... & Gil24 & Gil8 & Gil9 & Gil4 & Gil5 & Gil6 & Gil7 & Gil1 & Gil2 & Gil3\\\\\n",
"\\hline\n",
"\tBacteroides & 23.08 & 16.69 & 66.39 & 40.40 & 38.18 & 40.93 & 3.21 & 34.35 & 22.32 & 39.31 & ... & 5.00 & 7.53 & 14.91 & 47.69 & 27.42 & 61.70 & 2.39 & 16.60 & 35.38 & 38.66\\\\\n",
"\tPrevotella 9 & 0.00 & 3.25 & 0.00 & 0.00 & 0.00 & 0.00 & 9.41 & 0.00 & 0.00 & 0.00 & ... & 55.84 & 0.76 & 30.14 & 1.50 & 0.00 & 0.00 & 39.68 & 0.00 & 0.00 & 6.98\\\\\n",
"\tFaecalibacterium & 11.09 & 5.91 & 2.88 & 22.98 & 9.87 & 15.82 & 9.50 & 5.08 & 22.89 & 2.27 & ... & 2.92 & 4.77 & 7.87 & 11.80 & 20.27 & 3.73 & 0.98 & 11.36 & 0.06 & 12.76\\\\\n",
"\tBifidobacterium & 0.04 & 7.91 & 2.82 & 1.72 & 1.68 & 0.05 & 4.82 & 4.40 & 18.77 & 2.11 & ... & 0.69 & 0.03 & 0.69 & 0.12 & 6.26 & 1.67 & 0.35 & 1.34 & 12.62 & 0.83\\\\\n",
"\tBlautia & 3.42 & 6.22 & 2.29 & 2.44 & 7.32 & 0.90 & 1.81 & 2.99 & 2.70 & 4.58 & ... & 0.90 & 3.79 & 1.06 & 1.02 & 0.12 & 0.58 & 0.29 & 22.14 & 0.88 & 10.04\\\\\n",
"\tParabacteroides & 1.58 & 8.28 & 0.02 & 3.55 & 10.20 & 1.09 & 0.46 & 1.61 & 0.06 & 9.34 & ... & 0.41 & 1.63 & 1.27 & 0.61 & 16.91 & 0.30 & 2.28 & 3.71 & 3.19 & 1.72\\\\\n",
"\t{[}Eubacterium{]} coprostanoligenes group & 2.20 & 6.61 & 0.00 & 0.83 & 0.05 & 0.07 & 14.71 & 0.00 & 0.00 & 0.01 & ... & 1.98 & 5.17 & 3.95 & 4.03 & 0.00 & 0.57 & 8.92 & 0.14 & 0.01 & 0.00\\\\\n",
"\tAlistipes & 6.37 & 1.29 & 0.07 & 0.74 & 7.92 & 2.86 & 0.22 & 1.11 & 0.03 & 1.64 & ... & 0.71 & 2.56 & 4.13 & 0.22 & 0.13 & 3.04 & 1.03 & 0.68 & 2.30 & 4.18\\\\\n",
"\tuncultured bacterium & 7.66 & 0.01 & 0.23 & 0.13 & 0.15 & 0.77 & 0.61 & 0.55 & 0.00 & 0.35 & ... & 5.42 & 5.50 & 8.86 & 0.75 & 0.29 & 0.05 & 7.69 & 0.25 & 1.62 & 0.14\\\\\n",
"\tEscherichia-Shigella & 0.03 & 0.00 & 2.77 & 0.08 & 0.05 & 0.50 & 0.02 & 9.52 & 0.04 & 2.21 & ... & 0.01 & 0.01 & 0.16 & 0.12 & 13.09 & 0.08 & 0.06 & 0.07 & 1.62 & 0.33\\\\\n",
"\tRoseburia & 1.51 & 1.89 & 1.09 & 2.40 & 2.27 & 6.13 & 4.51 & 2.87 & 0.96 & 0.78 & ... & 2.02 & 1.82 & 2.38 & 2.56 & 0.01 & 0.98 & 1.02 & 2.16 & 0.00 & 1.31\\\\\n",
"\tRuminococcaceae UCG-002 & 2.74 & 1.36 & 0.00 & 0.00 & 0.00 & 0.07 & 0.13 & 0.19 & 0.01 & 0.23 & ... & 2.57 & 2.89 & 0.45 & 0.11 & 0.00 & 0.32 & 10.17 & 0.05 & 0.00 & 0.06\\\\\n",
"\tLachnospiraceae UCG-008 & 0.59 & 1.24 & 0.79 & 0.74 & 2.42 & 0.61 & 1.80 & 1.06 & 2.01 & 1.57 & ... & 1.10 & 0.65 & 0.49 & 0.36 & 0.04 & 0.93 & 0.31 & 11.21 & 0.32 & 5.07\\\\\n",
"\tAkkermansia & 6.78 & 0.00 & 0.00 & 0.00 & 0.00 & 0.52 & 0.02 & 0.00 & 0.00 & 0.03 & ... & 0.00 & 0.38 & 0.00 & 0.00 & 0.00 & 0.01 & 0.00 & 0.00 & 5.40 & 0.00\\\\\n",
"\tPrevotella 2 & 0.00 & 4.20 & 0.00 & 0.00 & 0.00 & 0.00 & 0.07 & 0.00 & 0.00 & 0.00 & ... & 0.54 & 0.07 & 0.00 & 0.00 & 0.00 & 0.00 & 1.50 & 0.00 & 0.00 & 0.00\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | Gil34 | Gil30 | Gil31 | Gil32 | Gil33 | IBD | Gil18 | Gil19 | Gil16 | Gil17 | ... | Gil24 | Gil8 | Gil9 | Gil4 | Gil5 | Gil6 | Gil7 | Gil1 | Gil2 | Gil3 | \n",
"|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
"| Bacteroides | 23.08 | 16.69 | 66.39 | 40.40 | 38.18 | 40.93 | 3.21 | 34.35 | 22.32 | 39.31 | ... | 5.00 | 7.53 | 14.91 | 47.69 | 27.42 | 61.70 | 2.39 | 16.60 | 35.38 | 38.66 | \n",
"| Prevotella 9 | 0.00 | 3.25 | 0.00 | 0.00 | 0.00 | 0.00 | 9.41 | 0.00 | 0.00 | 0.00 | ... | 55.84 | 0.76 | 30.14 | 1.50 | 0.00 | 0.00 | 39.68 | 0.00 | 0.00 | 6.98 | \n",
"| Faecalibacterium | 11.09 | 5.91 | 2.88 | 22.98 | 9.87 | 15.82 | 9.50 | 5.08 | 22.89 | 2.27 | ... | 2.92 | 4.77 | 7.87 | 11.80 | 20.27 | 3.73 | 0.98 | 11.36 | 0.06 | 12.76 | \n",
"| Bifidobacterium | 0.04 | 7.91 | 2.82 | 1.72 | 1.68 | 0.05 | 4.82 | 4.40 | 18.77 | 2.11 | ... | 0.69 | 0.03 | 0.69 | 0.12 | 6.26 | 1.67 | 0.35 | 1.34 | 12.62 | 0.83 | \n",
"| Blautia | 3.42 | 6.22 | 2.29 | 2.44 | 7.32 | 0.90 | 1.81 | 2.99 | 2.70 | 4.58 | ... | 0.90 | 3.79 | 1.06 | 1.02 | 0.12 | 0.58 | 0.29 | 22.14 | 0.88 | 10.04 | \n",
"| Parabacteroides | 1.58 | 8.28 | 0.02 | 3.55 | 10.20 | 1.09 | 0.46 | 1.61 | 0.06 | 9.34 | ... | 0.41 | 1.63 | 1.27 | 0.61 | 16.91 | 0.30 | 2.28 | 3.71 | 3.19 | 1.72 | \n",
"| [Eubacterium] coprostanoligenes group | 2.20 | 6.61 | 0.00 | 0.83 | 0.05 | 0.07 | 14.71 | 0.00 | 0.00 | 0.01 | ... | 1.98 | 5.17 | 3.95 | 4.03 | 0.00 | 0.57 | 8.92 | 0.14 | 0.01 | 0.00 | \n",
"| Alistipes | 6.37 | 1.29 | 0.07 | 0.74 | 7.92 | 2.86 | 0.22 | 1.11 | 0.03 | 1.64 | ... | 0.71 | 2.56 | 4.13 | 0.22 | 0.13 | 3.04 | 1.03 | 0.68 | 2.30 | 4.18 | \n",
"| uncultured bacterium | 7.66 | 0.01 | 0.23 | 0.13 | 0.15 | 0.77 | 0.61 | 0.55 | 0.00 | 0.35 | ... | 5.42 | 5.50 | 8.86 | 0.75 | 0.29 | 0.05 | 7.69 | 0.25 | 1.62 | 0.14 | \n",
"| Escherichia-Shigella | 0.03 | 0.00 | 2.77 | 0.08 | 0.05 | 0.50 | 0.02 | 9.52 | 0.04 | 2.21 | ... | 0.01 | 0.01 | 0.16 | 0.12 | 13.09 | 0.08 | 0.06 | 0.07 | 1.62 | 0.33 | \n",
"| Roseburia | 1.51 | 1.89 | 1.09 | 2.40 | 2.27 | 6.13 | 4.51 | 2.87 | 0.96 | 0.78 | ... | 2.02 | 1.82 | 2.38 | 2.56 | 0.01 | 0.98 | 1.02 | 2.16 | 0.00 | 1.31 | \n",
"| Ruminococcaceae UCG-002 | 2.74 | 1.36 | 0.00 | 0.00 | 0.00 | 0.07 | 0.13 | 0.19 | 0.01 | 0.23 | ... | 2.57 | 2.89 | 0.45 | 0.11 | 0.00 | 0.32 | 10.17 | 0.05 | 0.00 | 0.06 | \n",
"| Lachnospiraceae UCG-008 | 0.59 | 1.24 | 0.79 | 0.74 | 2.42 | 0.61 | 1.80 | 1.06 | 2.01 | 1.57 | ... | 1.10 | 0.65 | 0.49 | 0.36 | 0.04 | 0.93 | 0.31 | 11.21 | 0.32 | 5.07 | \n",
"| Akkermansia | 6.78 | 0.00 | 0.00 | 0.00 | 0.00 | 0.52 | 0.02 | 0.00 | 0.00 | 0.03 | ... | 0.00 | 0.38 | 0.00 | 0.00 | 0.00 | 0.01 | 0.00 | 0.00 | 5.40 | 0.00 | \n",
"| Prevotella 2 | 0.00 | 4.20 | 0.00 | 0.00 | 0.00 | 0.00 | 0.07 | 0.00 | 0.00 | 0.00 | ... | 0.54 | 0.07 | 0.00 | 0.00 | 0.00 | 0.00 | 1.50 | 0.00 | 0.00 | 0.00 | \n",
"\n",
"\n"
],
"text/plain": [
" Gil34 Gil30 Gil31 Gil32 Gil33 IBD Gil18\n",
"Bacteroides 23.08 16.69 66.39 40.40 38.18 40.93 3.21\n",
"Prevotella 9 0.00 3.25 0.00 0.00 0.00 0.00 9.41\n",
"Faecalibacterium 11.09 5.91 2.88 22.98 9.87 15.82 9.50\n",
"Bifidobacterium 0.04 7.91 2.82 1.72 1.68 0.05 4.82\n",
"Blautia 3.42 6.22 2.29 2.44 7.32 0.90 1.81\n",
"Parabacteroides 1.58 8.28 0.02 3.55 10.20 1.09 0.46\n",
"[Eubacterium] coprostanoligenes group 2.20 6.61 0.00 0.83 0.05 0.07 14.71\n",
"Alistipes 6.37 1.29 0.07 0.74 7.92 2.86 0.22\n",
"uncultured bacterium 7.66 0.01 0.23 0.13 0.15 0.77 0.61\n",
"Escherichia-Shigella 0.03 0.00 2.77 0.08 0.05 0.50 0.02\n",
"Roseburia 1.51 1.89 1.09 2.40 2.27 6.13 4.51\n",
"Ruminococcaceae UCG-002 2.74 1.36 0.00 0.00 0.00 0.07 0.13\n",
"Lachnospiraceae UCG-008 0.59 1.24 0.79 0.74 2.42 0.61 1.80\n",
"Akkermansia 6.78 0.00 0.00 0.00 0.00 0.52 0.02\n",
"Prevotella 2 0.00 4.20 0.00 0.00 0.00 0.00 0.07\n",
" Gil19 Gil16 Gil17 ... Gil24 Gil8 Gil9 \n",
"Bacteroides 34.35 22.32 39.31 ... 5.00 7.53 14.91\n",
"Prevotella 9 0.00 0.00 0.00 ... 55.84 0.76 30.14\n",
"Faecalibacterium 5.08 22.89 2.27 ... 2.92 4.77 7.87\n",
"Bifidobacterium 4.40 18.77 2.11 ... 0.69 0.03 0.69\n",
"Blautia 2.99 2.70 4.58 ... 0.90 3.79 1.06\n",
"Parabacteroides 1.61 0.06 9.34 ... 0.41 1.63 1.27\n",
"[Eubacterium] coprostanoligenes group 0.00 0.00 0.01 ... 1.98 5.17 3.95\n",
"Alistipes 1.11 0.03 1.64 ... 0.71 2.56 4.13\n",
"uncultured bacterium 0.55 0.00 0.35 ... 5.42 5.50 8.86\n",
"Escherichia-Shigella 9.52 0.04 2.21 ... 0.01 0.01 0.16\n",
"Roseburia 2.87 0.96 0.78 ... 2.02 1.82 2.38\n",
"Ruminococcaceae UCG-002 0.19 0.01 0.23 ... 2.57 2.89 0.45\n",
"Lachnospiraceae UCG-008 1.06 2.01 1.57 ... 1.10 0.65 0.49\n",
"Akkermansia 0.00 0.00 0.03 ... 0.00 0.38 0.00\n",
"Prevotella 2 0.00 0.00 0.00 ... 0.54 0.07 0.00\n",
" Gil4 Gil5 Gil6 Gil7 Gil1 Gil2 Gil3 \n",
"Bacteroides 47.69 27.42 61.70 2.39 16.60 35.38 38.66\n",
"Prevotella 9 1.50 0.00 0.00 39.68 0.00 0.00 6.98\n",
"Faecalibacterium 11.80 20.27 3.73 0.98 11.36 0.06 12.76\n",
"Bifidobacterium 0.12 6.26 1.67 0.35 1.34 12.62 0.83\n",
"Blautia 1.02 0.12 0.58 0.29 22.14 0.88 10.04\n",
"Parabacteroides 0.61 16.91 0.30 2.28 3.71 3.19 1.72\n",
"[Eubacterium] coprostanoligenes group 4.03 0.00 0.57 8.92 0.14 0.01 0.00\n",
"Alistipes 0.22 0.13 3.04 1.03 0.68 2.30 4.18\n",
"uncultured bacterium 0.75 0.29 0.05 7.69 0.25 1.62 0.14\n",
"Escherichia-Shigella 0.12 13.09 0.08 0.06 0.07 1.62 0.33\n",
"Roseburia 2.56 0.01 0.98 1.02 2.16 0.00 1.31\n",
"Ruminococcaceae UCG-002 0.11 0.00 0.32 10.17 0.05 0.00 0.06\n",
"Lachnospiraceae UCG-008 0.36 0.04 0.93 0.31 11.21 0.32 5.07\n",
"Akkermansia 0.00 0.00 0.01 0.00 0.00 5.40 0.00\n",
"Prevotella 2 0.00 0.00 0.00 1.50 0.00 0.00 0.00"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"f.t <- t(filtered.taxa.df)\n",
"\n",
"f.t <- apply(f.t, 2,function(x) {round(x,2)})\n",
"head(f.t, 15)"
]
},
{
"cell_type": "code",
"execution_count": 83,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>Gil1</th><th scope=col>American</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>Blautia</th><td>22.14</td><td> 2.39</td></tr>\n",
"\t<tr><th scope=row>Bacteroides</th><td>16.60</td><td>25.42</td></tr>\n",
"\t<tr><th scope=row>Faecalibacterium</th><td>11.36</td><td> 5.98</td></tr>\n",
"\t<tr><th scope=row>Lachnospiraceae UCG-008</th><td>11.21</td><td> 0.28</td></tr>\n",
"\t<tr><th scope=row>Parabacteroides</th><td> 3.71</td><td> 1.20</td></tr>\n",
"\t<tr><th scope=row>[Ruminococcus] torques group</th><td> 3.12</td><td> 1.84</td></tr>\n",
"\t<tr><th scope=row>Erysipelotrichaceae UCG-003</th><td> 2.25</td><td> 0.41</td></tr>\n",
"\t<tr><th scope=row>Roseburia</th><td> 2.16</td><td> 1.78</td></tr>\n",
"\t<tr><th scope=row>Lachnoclostridium</th><td> 1.97</td><td> 1.42</td></tr>\n",
"\t<tr><th scope=row>uncultured</th><td> 1.86</td><td> 0.63</td></tr>\n",
"\t<tr><th scope=row>Phascolarctobacterium</th><td> 1.80</td><td> 0.35</td></tr>\n",
"\t<tr><th scope=row>[Eubacterium] rectale group</th><td> 1.76</td><td> 2.69</td></tr>\n",
"\t<tr><th scope=row>Coprococcus 3</th><td> 1.64</td><td> 0.60</td></tr>\n",
"\t<tr><th scope=row>Bifidobacterium</th><td> 1.34</td><td> 0.82</td></tr>\n",
"\t<tr><th scope=row>Holdemanella</th><td> 1.14</td><td> 0.61</td></tr>\n",
"\t<tr><th scope=row>Dorea</th><td> 1.11</td><td> 0.17</td></tr>\n",
"\t<tr><th scope=row>Christensenellaceae R-7 group</th><td> 1.05</td><td> 0.99</td></tr>\n",
"\t<tr><th scope=row>uncultured.1</th><td> 1.03</td><td> 0.13</td></tr>\n",
"\t<tr><th scope=row>Fusicatenibacter</th><td> 1.00</td><td> 0.71</td></tr>\n",
"\t<tr><th scope=row>Ruminococcaceae UCG-013</th><td> 1.00</td><td> 0.22</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|ll}\n",
" & Gil1 & American\\\\\n",
"\\hline\n",
"\tBlautia & 22.14 & 2.39\\\\\n",
"\tBacteroides & 16.60 & 25.42\\\\\n",
"\tFaecalibacterium & 11.36 & 5.98\\\\\n",
"\tLachnospiraceae UCG-008 & 11.21 & 0.28\\\\\n",
"\tParabacteroides & 3.71 & 1.20\\\\\n",
"\t{[}Ruminococcus{]} torques group & 3.12 & 1.84\\\\\n",
"\tErysipelotrichaceae UCG-003 & 2.25 & 0.41\\\\\n",
"\tRoseburia & 2.16 & 1.78\\\\\n",
"\tLachnoclostridium & 1.97 & 1.42\\\\\n",
"\tuncultured & 1.86 & 0.63\\\\\n",
"\tPhascolarctobacterium & 1.80 & 0.35\\\\\n",
"\t{[}Eubacterium{]} rectale group & 1.76 & 2.69\\\\\n",
"\tCoprococcus 3 & 1.64 & 0.60\\\\\n",
"\tBifidobacterium & 1.34 & 0.82\\\\\n",
"\tHoldemanella & 1.14 & 0.61\\\\\n",
"\tDorea & 1.11 & 0.17\\\\\n",
"\tChristensenellaceae R-7 group & 1.05 & 0.99\\\\\n",
"\tuncultured.1 & 1.03 & 0.13\\\\\n",
"\tFusicatenibacter & 1.00 & 0.71\\\\\n",
"\tRuminococcaceae UCG-013 & 1.00 & 0.22\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | Gil1 | American | \n",
"|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
"| Blautia | 22.14 | 2.39 | \n",
"| Bacteroides | 16.60 | 25.42 | \n",
"| Faecalibacterium | 11.36 | 5.98 | \n",
"| Lachnospiraceae UCG-008 | 11.21 | 0.28 | \n",
"| Parabacteroides | 3.71 | 1.20 | \n",
"| [Ruminococcus] torques group | 3.12 | 1.84 | \n",
"| Erysipelotrichaceae UCG-003 | 2.25 | 0.41 | \n",
"| Roseburia | 2.16 | 1.78 | \n",
"| Lachnoclostridium | 1.97 | 1.42 | \n",
"| uncultured | 1.86 | 0.63 | \n",
"| Phascolarctobacterium | 1.80 | 0.35 | \n",
"| [Eubacterium] rectale group | 1.76 | 2.69 | \n",
"| Coprococcus 3 | 1.64 | 0.60 | \n",
"| Bifidobacterium | 1.34 | 0.82 | \n",
"| Holdemanella | 1.14 | 0.61 | \n",
"| Dorea | 1.11 | 0.17 | \n",
"| Christensenellaceae R-7 group | 1.05 | 0.99 | \n",
"| uncultured.1 | 1.03 | 0.13 | \n",
"| Fusicatenibacter | 1.00 | 0.71 | \n",
"| Ruminococcaceae UCG-013 | 1.00 | 0.22 | \n",
"\n",
"\n"
],
"text/plain": [
" Gil1 American\n",
"Blautia 22.14 2.39 \n",
"Bacteroides 16.60 25.42 \n",
"Faecalibacterium 11.36 5.98 \n",
"Lachnospiraceae UCG-008 11.21 0.28 \n",
"Parabacteroides 3.71 1.20 \n",
"[Ruminococcus] torques group 3.12 1.84 \n",
"Erysipelotrichaceae UCG-003 2.25 0.41 \n",
"Roseburia 2.16 1.78 \n",
"Lachnoclostridium 1.97 1.42 \n",
"uncultured 1.86 0.63 \n",
"Phascolarctobacterium 1.80 0.35 \n",
"[Eubacterium] rectale group 1.76 2.69 \n",
"Coprococcus 3 1.64 0.60 \n",
"Bifidobacterium 1.34 0.82 \n",
"Holdemanella 1.14 0.61 \n",
"Dorea 1.11 0.17 \n",
"Christensenellaceae R-7 group 1.05 0.99 \n",
"uncultured.1 1.03 0.13 \n",
"Fusicatenibacter 1.00 0.71 \n",
"Ruminococcaceae UCG-013 1.00 0.22 "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"#sth <- f.t.df[order(f.t.df$Gil1, f.t.df$American, decreasing = TRUE),, drop=FALSE]\n",
"#head(sth, 20)"
]
},
{
"cell_type": "code",
"execution_count": 34,
"metadata": {
"scrolled": true
},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>Gil34</th><th scope=col>Gil30</th><th scope=col>Gil31</th><th scope=col>Gil32</th><th scope=col>Gil33</th><th scope=col>IBD</th><th scope=col>Gil18</th><th scope=col>Gil19</th><th scope=col>Gil16</th><th scope=col>Gil17</th><th scope=col>...</th><th scope=col>Gil24</th><th scope=col>Gil8</th><th scope=col>Gil9</th><th scope=col>Gil4</th><th scope=col>Gil5</th><th scope=col>Gil6</th><th scope=col>Gil7</th><th scope=col>Gil1</th><th scope=col>Gil2</th><th scope=col>Gil3</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>Bacteroides</th><td>23.08</td><td>16.69</td><td>66.39</td><td>40.40</td><td>38.18</td><td>40.93</td><td>3.21 </td><td>34.35</td><td>22.32</td><td>39.31</td><td>... </td><td> 5.00</td><td>7.53 </td><td>14.91</td><td>47.69</td><td>27.42</td><td>61.70</td><td> 2.39</td><td>16.60</td><td>35.38</td><td>38.66</td></tr>\n",
"\t<tr><th scope=row>Prevotella 9</th><td> 0.00</td><td> 3.25</td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td>9.41 </td><td> 0.00</td><td> 0.00</td><td> 0.00</td><td>... </td><td>55.84</td><td>0.76 </td><td>30.14</td><td> 1.50</td><td> 0.00</td><td> 0.00</td><td>39.68</td><td> 0.00</td><td> 0.00</td><td> 6.98</td></tr>\n",
"\t<tr><th scope=row>Faecalibacterium</th><td>11.09</td><td> 5.91</td><td> 2.88</td><td>22.98</td><td> 9.87</td><td>15.82</td><td>9.50 </td><td> 5.08</td><td>22.89</td><td> 2.27</td><td>... </td><td> 2.92</td><td>4.77 </td><td> 7.87</td><td>11.80</td><td>20.27</td><td> 3.73</td><td> 0.98</td><td>11.36</td><td> 0.06</td><td>12.76</td></tr>\n",
"\t<tr><th scope=row>Bifidobacterium</th><td> 0.04</td><td> 7.91</td><td> 2.82</td><td> 1.72</td><td> 1.68</td><td> 0.05</td><td>4.82 </td><td> 4.40</td><td>18.77</td><td> 2.11</td><td>... </td><td> 0.69</td><td>0.03 </td><td> 0.69</td><td> 0.12</td><td> 6.26</td><td> 1.67</td><td> 0.35</td><td> 1.34</td><td>12.62</td><td> 0.83</td></tr>\n",
"\t<tr><th scope=row>Blautia</th><td> 3.42</td><td> 6.22</td><td> 2.29</td><td> 2.44</td><td> 7.32</td><td> 0.90</td><td>1.81 </td><td> 2.99</td><td> 2.70</td><td> 4.58</td><td>... </td><td> 0.90</td><td>3.79 </td><td> 1.06</td><td> 1.02</td><td> 0.12</td><td> 0.58</td><td> 0.29</td><td>22.14</td><td> 0.88</td><td>10.04</td></tr>\n",
"\t<tr><th scope=row>Parabacteroides</th><td> 1.58</td><td> 8.28</td><td> 0.02</td><td> 3.55</td><td>10.20</td><td> 1.09</td><td>0.46 </td><td> 1.61</td><td> 0.06</td><td> 9.34</td><td>... </td><td> 0.41</td><td>1.63 </td><td> 1.27</td><td> 0.61</td><td>16.91</td><td> 0.30</td><td> 2.28</td><td> 3.71</td><td> 3.19</td><td> 1.72</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|lllllllllllllllllllllllllllllll}\n",
" & Gil34 & Gil30 & Gil31 & Gil32 & Gil33 & IBD & Gil18 & Gil19 & Gil16 & Gil17 & ... & Gil24 & Gil8 & Gil9 & Gil4 & Gil5 & Gil6 & Gil7 & Gil1 & Gil2 & Gil3\\\\\n",
"\\hline\n",
"\tBacteroides & 23.08 & 16.69 & 66.39 & 40.40 & 38.18 & 40.93 & 3.21 & 34.35 & 22.32 & 39.31 & ... & 5.00 & 7.53 & 14.91 & 47.69 & 27.42 & 61.70 & 2.39 & 16.60 & 35.38 & 38.66\\\\\n",
"\tPrevotella 9 & 0.00 & 3.25 & 0.00 & 0.00 & 0.00 & 0.00 & 9.41 & 0.00 & 0.00 & 0.00 & ... & 55.84 & 0.76 & 30.14 & 1.50 & 0.00 & 0.00 & 39.68 & 0.00 & 0.00 & 6.98\\\\\n",
"\tFaecalibacterium & 11.09 & 5.91 & 2.88 & 22.98 & 9.87 & 15.82 & 9.50 & 5.08 & 22.89 & 2.27 & ... & 2.92 & 4.77 & 7.87 & 11.80 & 20.27 & 3.73 & 0.98 & 11.36 & 0.06 & 12.76\\\\\n",
"\tBifidobacterium & 0.04 & 7.91 & 2.82 & 1.72 & 1.68 & 0.05 & 4.82 & 4.40 & 18.77 & 2.11 & ... & 0.69 & 0.03 & 0.69 & 0.12 & 6.26 & 1.67 & 0.35 & 1.34 & 12.62 & 0.83\\\\\n",
"\tBlautia & 3.42 & 6.22 & 2.29 & 2.44 & 7.32 & 0.90 & 1.81 & 2.99 & 2.70 & 4.58 & ... & 0.90 & 3.79 & 1.06 & 1.02 & 0.12 & 0.58 & 0.29 & 22.14 & 0.88 & 10.04\\\\\n",
"\tParabacteroides & 1.58 & 8.28 & 0.02 & 3.55 & 10.20 & 1.09 & 0.46 & 1.61 & 0.06 & 9.34 & ... & 0.41 & 1.63 & 1.27 & 0.61 & 16.91 & 0.30 & 2.28 & 3.71 & 3.19 & 1.72\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | Gil34 | Gil30 | Gil31 | Gil32 | Gil33 | IBD | Gil18 | Gil19 | Gil16 | Gil17 | ... | Gil24 | Gil8 | Gil9 | Gil4 | Gil5 | Gil6 | Gil7 | Gil1 | Gil2 | Gil3 | \n",
"|---|---|---|---|---|---|\n",
"| Bacteroides | 23.08 | 16.69 | 66.39 | 40.40 | 38.18 | 40.93 | 3.21 | 34.35 | 22.32 | 39.31 | ... | 5.00 | 7.53 | 14.91 | 47.69 | 27.42 | 61.70 | 2.39 | 16.60 | 35.38 | 38.66 | \n",
"| Prevotella 9 | 0.00 | 3.25 | 0.00 | 0.00 | 0.00 | 0.00 | 9.41 | 0.00 | 0.00 | 0.00 | ... | 55.84 | 0.76 | 30.14 | 1.50 | 0.00 | 0.00 | 39.68 | 0.00 | 0.00 | 6.98 | \n",
"| Faecalibacterium | 11.09 | 5.91 | 2.88 | 22.98 | 9.87 | 15.82 | 9.50 | 5.08 | 22.89 | 2.27 | ... | 2.92 | 4.77 | 7.87 | 11.80 | 20.27 | 3.73 | 0.98 | 11.36 | 0.06 | 12.76 | \n",
"| Bifidobacterium | 0.04 | 7.91 | 2.82 | 1.72 | 1.68 | 0.05 | 4.82 | 4.40 | 18.77 | 2.11 | ... | 0.69 | 0.03 | 0.69 | 0.12 | 6.26 | 1.67 | 0.35 | 1.34 | 12.62 | 0.83 | \n",
"| Blautia | 3.42 | 6.22 | 2.29 | 2.44 | 7.32 | 0.90 | 1.81 | 2.99 | 2.70 | 4.58 | ... | 0.90 | 3.79 | 1.06 | 1.02 | 0.12 | 0.58 | 0.29 | 22.14 | 0.88 | 10.04 | \n",
"| Parabacteroides | 1.58 | 8.28 | 0.02 | 3.55 | 10.20 | 1.09 | 0.46 | 1.61 | 0.06 | 9.34 | ... | 0.41 | 1.63 | 1.27 | 0.61 | 16.91 | 0.30 | 2.28 | 3.71 | 3.19 | 1.72 | \n",
"\n",
"\n"
],
"text/plain": [
" Gil34 Gil30 Gil31 Gil32 Gil33 IBD Gil18 Gil19 Gil16 Gil17\n",
"Bacteroides 23.08 16.69 66.39 40.40 38.18 40.93 3.21 34.35 22.32 39.31\n",
"Prevotella 9 0.00 3.25 0.00 0.00 0.00 0.00 9.41 0.00 0.00 0.00\n",
"Faecalibacterium 11.09 5.91 2.88 22.98 9.87 15.82 9.50 5.08 22.89 2.27\n",
"Bifidobacterium 0.04 7.91 2.82 1.72 1.68 0.05 4.82 4.40 18.77 2.11\n",
"Blautia 3.42 6.22 2.29 2.44 7.32 0.90 1.81 2.99 2.70 4.58\n",
"Parabacteroides 1.58 8.28 0.02 3.55 10.20 1.09 0.46 1.61 0.06 9.34\n",
" ... Gil24 Gil8 Gil9 Gil4 Gil5 Gil6 Gil7 Gil1 Gil2 Gil3 \n",
"Bacteroides ... 5.00 7.53 14.91 47.69 27.42 61.70 2.39 16.60 35.38 38.66\n",
"Prevotella 9 ... 55.84 0.76 30.14 1.50 0.00 0.00 39.68 0.00 0.00 6.98\n",
"Faecalibacterium ... 2.92 4.77 7.87 11.80 20.27 3.73 0.98 11.36 0.06 12.76\n",
"Bifidobacterium ... 0.69 0.03 0.69 0.12 6.26 1.67 0.35 1.34 12.62 0.83\n",
"Blautia ... 0.90 3.79 1.06 1.02 0.12 0.58 0.29 22.14 0.88 10.04\n",
"Parabacteroides ... 0.41 1.63 1.27 0.61 16.91 0.30 2.28 3.71 3.19 1.72"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"#sample.name <- 'Gil1'\n",
"\n",
"f.t.df <- as.data.frame(f.t)\n",
"#f.t.df <- f.t.df %>% select(sample.name, American)\n",
"head(f.t.df)"
]
},
{
"cell_type": "code",
"execution_count": 35,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>Genus</th><th scope=col>Sample</th><th scope=col>Proportion</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>Bacteroides </td><td>Gil34 </td><td>23.08 </td></tr>\n",
"\t<tr><td>Prevotella 9 </td><td>Gil34 </td><td> 0.00 </td></tr>\n",
"\t<tr><td>Faecalibacterium</td><td>Gil34 </td><td>11.09 </td></tr>\n",
"\t<tr><td>Bifidobacterium </td><td>Gil34 </td><td> 0.04 </td></tr>\n",
"\t<tr><td>Blautia </td><td>Gil34 </td><td> 3.42 </td></tr>\n",
"\t<tr><td>Parabacteroides </td><td>Gil34 </td><td> 1.58 </td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|lll}\n",
" Genus & Sample & Proportion\\\\\n",
"\\hline\n",
"\t Bacteroides & Gil34 & 23.08 \\\\\n",
"\t Prevotella 9 & Gil34 & 0.00 \\\\\n",
"\t Faecalibacterium & Gil34 & 11.09 \\\\\n",
"\t Bifidobacterium & Gil34 & 0.04 \\\\\n",
"\t Blautia & Gil34 & 3.42 \\\\\n",
"\t Parabacteroides & Gil34 & 1.58 \\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"Genus | Sample | Proportion | \n",
"|---|---|---|---|---|---|\n",
"| Bacteroides | Gil34 | 23.08 | \n",
"| Prevotella 9 | Gil34 | 0.00 | \n",
"| Faecalibacterium | Gil34 | 11.09 | \n",
"| Bifidobacterium | Gil34 | 0.04 | \n",
"| Blautia | Gil34 | 3.42 | \n",
"| Parabacteroides | Gil34 | 1.58 | \n",
"\n",
"\n"
],
"text/plain": [
" Genus Sample Proportion\n",
"1 Bacteroides Gil34 23.08 \n",
"2 Prevotella 9 Gil34 0.00 \n",
"3 Faecalibacterium Gil34 11.09 \n",
"4 Bifidobacterium Gil34 0.04 \n",
"5 Blautia Gil34 3.42 \n",
"6 Parabacteroides Gil34 1.58 "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"df <- melt(f.t, varnames=c(\"Genus\", \"Sample\"), value.name=\"Proportion\")\n",
"head(df)"
]
},
{
"cell_type": "code",
"execution_count": 36,
"metadata": {},
"outputs": [],
"source": [
"colourCount <- 21\n",
"getPalette = colorRampPalette(brewer.pal(7, \"Set3\"))"
]
},
{
"cell_type": "code",
"execution_count": 37,
"metadata": {},
"outputs": [],
"source": [
"sample.name <- 'Gil9'"
]
},
{
"cell_type": "code",
"execution_count": 38,
"metadata": {},
"outputs": [],
"source": [
"long <- df %>% filter(Sample==sample.name | Sample==\"American\")\n",
"wf <- f.t.df %>% select(sample.name,American)"
]
},
{
"cell_type": "code",
"execution_count": 39,
"metadata": {},
"outputs": [],
"source": [
"p <- ggplot(long) + geom_bar(aes(x=Sample, y=Proportion, fill=Genus), stat = \"identity\") + scale_fill_manual(values = getPalette(colourCount))"
]
},
{
"cell_type": "code",
"execution_count": 40,
"metadata": {},
"outputs": [],
"source": [
"wf <- f.t.df %>% select(sample.name,American)"
]
},
{
"cell_type": "code",
"execution_count": 41,
"metadata": {},
"outputs": [],
"source": [
"ggsave(filename = paste0(sample.name,\".png\"), plot = p ,width=5, height = 10, dpi= 100)"
]
},
{
"cell_type": "code",
"execution_count": 42,
"metadata": {},
"outputs": [],
"source": [
"write.xlsx(wf, paste0(sample.name, '.xlsx'))"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th></th><th scope=col>Gil9</th><th scope=col>American</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><th scope=row>Bacteroides</th><td>14.91</td><td>25.42</td></tr>\n",
"\t<tr><th scope=row>Prevotella 9</th><td>30.14</td><td> 3.59</td></tr>\n",
"\t<tr><th scope=row>Faecalibacterium</th><td> 7.87</td><td> 5.98</td></tr>\n",
"\t<tr><th scope=row>Bifidobacterium</th><td> 0.69</td><td> 0.82</td></tr>\n",
"\t<tr><th scope=row>Blautia</th><td> 1.06</td><td> 2.39</td></tr>\n",
"\t<tr><th scope=row>Parabacteroides</th><td> 1.27</td><td> 1.20</td></tr>\n",
"\t<tr><th scope=row>[Eubacterium] coprostanoligenes group</th><td> 3.95</td><td> 0.81</td></tr>\n",
"\t<tr><th scope=row>Alistipes</th><td> 4.13</td><td> 1.28</td></tr>\n",
"\t<tr><th scope=row>uncultured bacterium</th><td> 8.86</td><td> 0.05</td></tr>\n",
"\t<tr><th scope=row>Escherichia-Shigella</th><td> 0.16</td><td>16.10</td></tr>\n",
"\t<tr><th scope=row>Roseburia</th><td> 2.38</td><td> 1.78</td></tr>\n",
"\t<tr><th scope=row>Ruminococcaceae UCG-002</th><td> 0.45</td><td> 1.37</td></tr>\n",
"\t<tr><th scope=row>Lachnospiraceae UCG-008</th><td> 0.49</td><td> 0.28</td></tr>\n",
"\t<tr><th scope=row>Akkermansia</th><td> 0.00</td><td> 1.63</td></tr>\n",
"\t<tr><th scope=row>Prevotella 2</th><td> 0.00</td><td> 0.03</td></tr>\n",
"\t<tr><th scope=row>Dialister</th><td> 0.00</td><td> 1.44</td></tr>\n",
"\t<tr><th scope=row>Subdoligranulum</th><td> 0.56</td><td> 2.42</td></tr>\n",
"\t<tr><th scope=row>[Eubacterium] rectale group</th><td> 0.20</td><td> 2.69</td></tr>\n",
"\t<tr><th scope=row>Sutterella</th><td> 0.45</td><td> 0.18</td></tr>\n",
"\t<tr><th scope=row>Phascolarctobacterium</th><td> 0.75</td><td> 0.35</td></tr>\n",
"\t<tr><th scope=row>etc</th><td>21.70</td><td>30.18</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|ll}\n",
" & Gil9 & American\\\\\n",
"\\hline\n",
"\tBacteroides & 14.91 & 25.42\\\\\n",
"\tPrevotella 9 & 30.14 & 3.59\\\\\n",
"\tFaecalibacterium & 7.87 & 5.98\\\\\n",
"\tBifidobacterium & 0.69 & 0.82\\\\\n",
"\tBlautia & 1.06 & 2.39\\\\\n",
"\tParabacteroides & 1.27 & 1.20\\\\\n",
"\t{[}Eubacterium{]} coprostanoligenes group & 3.95 & 0.81\\\\\n",
"\tAlistipes & 4.13 & 1.28\\\\\n",
"\tuncultured bacterium & 8.86 & 0.05\\\\\n",
"\tEscherichia-Shigella & 0.16 & 16.10\\\\\n",
"\tRoseburia & 2.38 & 1.78\\\\\n",
"\tRuminococcaceae UCG-002 & 0.45 & 1.37\\\\\n",
"\tLachnospiraceae UCG-008 & 0.49 & 0.28\\\\\n",
"\tAkkermansia & 0.00 & 1.63\\\\\n",
"\tPrevotella 2 & 0.00 & 0.03\\\\\n",
"\tDialister & 0.00 & 1.44\\\\\n",
"\tSubdoligranulum & 0.56 & 2.42\\\\\n",
"\t{[}Eubacterium{]} rectale group & 0.20 & 2.69\\\\\n",
"\tSutterella & 0.45 & 0.18\\\\\n",
"\tPhascolarctobacterium & 0.75 & 0.35\\\\\n",
"\tetc & 21.70 & 30.18\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"| <!--/--> | Gil9 | American | \n",
"|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|\n",
"| Bacteroides | 14.91 | 25.42 | \n",
"| Prevotella 9 | 30.14 | 3.59 | \n",
"| Faecalibacterium | 7.87 | 5.98 | \n",
"| Bifidobacterium | 0.69 | 0.82 | \n",
"| Blautia | 1.06 | 2.39 | \n",
"| Parabacteroides | 1.27 | 1.20 | \n",
"| [Eubacterium] coprostanoligenes group | 3.95 | 0.81 | \n",
"| Alistipes | 4.13 | 1.28 | \n",
"| uncultured bacterium | 8.86 | 0.05 | \n",
"| Escherichia-Shigella | 0.16 | 16.10 | \n",
"| Roseburia | 2.38 | 1.78 | \n",
"| Ruminococcaceae UCG-002 | 0.45 | 1.37 | \n",
"| Lachnospiraceae UCG-008 | 0.49 | 0.28 | \n",
"| Akkermansia | 0.00 | 1.63 | \n",
"| Prevotella 2 | 0.00 | 0.03 | \n",
"| Dialister | 0.00 | 1.44 | \n",
"| Subdoligranulum | 0.56 | 2.42 | \n",
"| [Eubacterium] rectale group | 0.20 | 2.69 | \n",
"| Sutterella | 0.45 | 0.18 | \n",
"| Phascolarctobacterium | 0.75 | 0.35 | \n",
"| etc | 21.70 | 30.18 | \n",
"\n",
"\n"
],
"text/plain": [
" Gil9 American\n",
"Bacteroides 14.91 25.42 \n",
"Prevotella 9 30.14 3.59 \n",
"Faecalibacterium 7.87 5.98 \n",
"Bifidobacterium 0.69 0.82 \n",
"Blautia 1.06 2.39 \n",
"Parabacteroides 1.27 1.20 \n",
"[Eubacterium] coprostanoligenes group 3.95 0.81 \n",
"Alistipes 4.13 1.28 \n",
"uncultured bacterium 8.86 0.05 \n",
"Escherichia-Shigella 0.16 16.10 \n",
"Roseburia 2.38 1.78 \n",
"Ruminococcaceae UCG-002 0.45 1.37 \n",
"Lachnospiraceae UCG-008 0.49 0.28 \n",
"Akkermansia 0.00 1.63 \n",
"Prevotella 2 0.00 0.03 \n",
"Dialister 0.00 1.44 \n",
"Subdoligranulum 0.56 2.42 \n",
"[Eubacterium] rectale group 0.20 2.69 \n",
"Sutterella 0.45 0.18 \n",
"Phascolarctobacterium 0.75 0.35 \n",
"etc 21.70 30.18 "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"wf"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"<table>\n",
"<thead><tr><th scope=col>Gil9</th><th scope=col>American</th></tr></thead>\n",
"<tbody>\n",
"\t<tr><td>30.14</td><td> 3.59</td></tr>\n",
"\t<tr><td>14.91</td><td>25.42</td></tr>\n",
"\t<tr><td> 8.86</td><td> 0.05</td></tr>\n",
"\t<tr><td> 7.87</td><td> 5.98</td></tr>\n",
"\t<tr><td> 4.13</td><td> 1.28</td></tr>\n",
"\t<tr><td> 3.95</td><td> 0.81</td></tr>\n",
"</tbody>\n",
"</table>\n"
],
"text/latex": [
"\\begin{tabular}{r|ll}\n",
" Gil9 & American\\\\\n",
"\\hline\n",
"\t 30.14 & 3.59\\\\\n",
"\t 14.91 & 25.42\\\\\n",
"\t 8.86 & 0.05\\\\\n",
"\t 7.87 & 5.98\\\\\n",
"\t 4.13 & 1.28\\\\\n",
"\t 3.95 & 0.81\\\\\n",
"\\end{tabular}\n"
],
"text/markdown": [
"\n",
"Gil9 | American | \n",
"|---|---|---|---|---|---|\n",
"| 30.14 | 3.59 | \n",
"| 14.91 | 25.42 | \n",
"| 8.86 | 0.05 | \n",
"| 7.87 | 5.98 | \n",
"| 4.13 | 1.28 | \n",
"| 3.95 | 0.81 | \n",
"\n",
"\n"
],
"text/plain": [
" Gil9 American\n",
"1 30.14 3.59 \n",
"2 14.91 25.42 \n",
"3 8.86 0.05 \n",
"4 7.87 5.98 \n",
"5 4.13 1.28 \n",
"6 3.95 0.81 "
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"wf %>% arrange(desc(Gil9), desc(American)) %>% head"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "R",
"language": "R",
"name": "ir"
},
"language_info": {
"codemirror_mode": "r",
"file_extension": ".r",
"mimetype": "text/x-r-source",
"name": "R",
"pygments_lexer": "r",
"version": "3.4.3"
}
},
"nbformat": 4,
"nbformat_minor": 2
}
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