VennDiagrams.Rmd

---
title: "VennDiagrams"
author: "Rodrigo Ortega Polo"
date: "August 30, 2017"
output:
  word_document: default
  html_document: default
bibliography: 2-4-8_library.bib
---

## Venn diagrams

__AMR__: AMR reports resulting from Coverage Sampler analyses were processed by 
filtering out those results with a gene fraction less than 75%, and also by 
filtering out housekeeping genes (genes present in the MEGARes database which 
require SNP confirmation). The filtered dataset was kept for further analyses.
Sets of unique taxa at each sequencing depth were obtained for each AMR level
(class, mechanism, group, gene) using Python 3.4.2. Venn diagrams were plotted using the `matplotlib_venn` package [@tretyakov_matplotlib-venn:_nodate] in Python 3.4.2.

__Microbiome__: 

Results for all Eukaryotes and for Enterobacteria phage phiX174 sensu lato were 
filtered out from the Kraken reports with Pavian [@breitwieser_pavian:_2016]. 
Complete taxonomic lineages were also added by Pavian.

Sets of unique taxa at each sequencing depth for each taxonomic level (i.e. 
phylum, class, family, order, genus, and species) were determined using Python 
3.4.2. Venn diagrams were plotted using the `matplotlib_venn` package 
[@tretyakov_matplotlib-venn:_nodate] in Python 3.4.2.

## References