Creating a tsv file from your phyloseq object

By Angus ball

library(phyloseq)
library(tidyr)
library(dplyr)

Bring in your full phyloseq object WITH sequence information

physeq_Key <- readRDS(file = "C:\\Users\\angus\\OneDrive - UNBC\\Angus Ball\\Lab work\\Bioinformatics\\ULTRA\\physeq_Key_merged.rds")
#I can tell it has sequence information by this
physeq_Key

phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 48054 taxa and 52 samples ]
sample_data() Sample Data:       [ 52 samples by 4 sample variables ]
tax_table()   Taxonomy Table:    [ 48054 taxa by 7 taxonomic ranks ]
refseq()      DNAStringSet:      [ 48054 reference sequences ]

refseq is the sequence info

okay lets extract the otu table

OTU1 = as(otu_table(physeq_Key), "matrix")
OTUdf = as.data.frame(OTU1)

A taxa table

TAXA1 = as(tax_table(physeq_Key), "matrix")
TAXAdf = as.data.frame(TAXA1)

#Export sequences to .fna file
ShortRead::writeFasta(refseq(physeq_Key), "C:\\Users\\angus\\OneDrive - UNBC\\Angus Ball\\Lab work\\Bioinformatics\\ULTRA\\picrust\\rep-seqs.fna")

#Export metadata as .txt file 
write.table(data.frame("sampleid"=sample_names(physeq_Key),sample_data(physeq_Key)),"C:\\Users\\angus\\OneDrive - UNBC\\Angus Ball\\Lab work\\Bioinformatics\\ULTRA\\picrust\\sample-metadata.txt", sep="\t", row.names=FALSE, col.names=TRUE, quote=FALSE)

#export taxa table
write.table(TAXAdf, "C:\\Users\\angus\\OneDrive - UNBC\\Angus Ball\\Lab work\\Bioinformatics\\ULTRA\\picrust\\tax.txt", quote=FALSE, col.names=FALSE, sep="\t")


#bad news picrust can't handle names with spaces in them, uhhh thanks for telling me before hand???
spaceless <- function(x) {colnames(x) <- gsub(" ", "_", colnames(x));x}
OTUdf <- spaceless(OTUdf)

#also to avoid pain in the future (need a header name for the OTU labels which won't happen automatically within write.table)
OTUdf$OTU <- row.names(OTUdf) #make a column of row names
OTUdf<-relocate(OTUdf, OTU, .before = everything())#just moves the OTU column first


#export the OTU table
write.table(OTUdf, "C:\\Users\\angus\\OneDrive - UNBC\\Angus Ball\\Lab work\\Bioinformatics\\ULTRA\\picrust\\OTU.txt", quote=FALSE, col.names=TRUE, row.names = FALSE, sep="\t")

These documents should be ready for picrust!