Phyloseq (R)

Description

It is recommended to use an IDE of R such as Rstudio, for easier R analysis. https://www.rstudio.com/products/rstudio/download/

For further information about phyloseq, see these tutorials below:

1. Preparing QIIME Data for Phyloseq

First you must convert your OTU Table (.biom) into an older version. Future updates may fix this issue.

# Start macqiime
macqiime

# Convert to JSON format
# See http://biom-format.org/documentation/biom_conversion.html
biom convert \
-i otu_table.biom \
-o otu_table_json.biom \
--to-json \
--table-type='OTU Table'

2. Installing phyloseq and other R-packages

# Install packages
source("https://bioconductor.org/biocLite.R")
biocLite("phyloseq")
biocLite("metagenomeSeq")
biocLite("ggplot2")
biocLite("vegan")
biocLite("randomforests")
biocLite("ape")
biocLite("microbiome")
biocLite("dplyr")
biocLite("pheatmap")
biocLite("RColorBrewer")
biocLite("ggtree")

3. Importing QIIME into Phyloseq

# Load required libraries
library(phyloseq)
library(ggplot2)

# Import OTU table and tree
otutable <- import_biom(BIOMfilename = 'otu_table_json.biom', 
                        treefilename = 'rep_set.tre', 
                        parseFunction = parse_taxonomy_greengenes)

# Import mapping file
mapping <- import_qiime_sample_data(mapfilename = 'mapping_file.txt')

# Merge map and otu table into once phyloseq object
phylo <- merge_phyloseq(otutable, mapping)

# Remove zero sum OTU's 
phylo = prune_taxa(taxa_sums(phylo) > 0, phylo)

# Check sample + OTU count
phylo
Verify taxonomic lineage names are correct
rank_names(phylo) 
> [1] "Kingdom" "Phylum"  "Class"   "Order"   "Family"  "Genus"   "Species"

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