Moving samples to Qiime2

By Angus

So you want to move your phyloseq object to qiime2 eh? well its a pain in the ass but so are all things in life i suppose.

Load the packages you need

library(phyloseq)
library(tidyr)
library(dplyr)
library(ggplot2)

Load your phyloseq object, make sure it has 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:         [ 48050 taxa and 52 samples ]
sample_data() Sample Data:       [ 52 samples by 4 sample variables ]
tax_table()   Taxonomy Table:    [ 48050 taxa by 7 taxonomic ranks ]
refseq()      DNAStringSet:      [ 48050 reference sequences ]

Remove taxa that have zero counts in all of samples summed (why would you have this? well I removed some samples from this analysis and merged tables so there might be some hold over taxa)

physeq_Key <- prune_taxa(taxa_sums(physeq_Key) >0, physeq_Key)
physeq_Key

phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 29865 taxa and 52 samples ]
sample_data() Sample Data:       [ 52 samples by 4 sample variables ]
tax_table()   Taxonomy Table:    [ 29865 taxa by 7 taxonomic ranks ]
refseq()      DNAStringSet:      [ 29865 reference sequences ]

Take the OTU and taxa tables from the phyloseq object

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

TAXA1 = as(phyloseq::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\\gemelli\\rep-seqs.fna")

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

#for the boim command it needs a row of OTU names, and since the write table function wont automatically add the row names we will add them as a seperate column
OTUdf$OTU <- row.names(OTUdf) #make a column of row names
OTUdf<-relocate(OTUdf, OTU, .before = everything())#just moves the OTU column first

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