#export data into R. This code uses qiime2020.8 and R version 3.6.3

#in qiime2
#step 1: export OTU table
qiime tools export \
--input-path table-phyla-no-mt-no-infrequent.qza \
--output-path phyloseq

#step1b: convert to tsv
biom convert \
-i phyloseq/feature-table.biom \
-o phyloseq/feature-table.txt \
--to-tsv

#Step2: export taxonomy table
qiime tools export \
--input-path taxonomy_16S.qza \
--output-path phyloseq

#Step3: export tree
qiime tools export \
--input-path unrooted-tree.qza \
--output-path phyloseq

#in R

#install packages we need for the session
library(tidyverse)
library(ggplot2)
library(phyloseq)
library(ape)
library(xlsx)
library(dplyr)
library(vegan)
library(RColorBrewer)
#set working directory
setwd("~/directory name")
#read files generated in qiime 
otu <- read.table(file = "filepath/feature-table.txt",header = TRUE,fill = TRUE)
head(otu)
tax <- read.table(file = "filepath/taxonomy.tsv",header = TRUE, sep = '\t')
head(tax)
#merge them to make one file
merged_file <- merge(otu,tax,by.x=c("OTUID"),by.y=c("OTUID"))
head(merged_file)
#output merged text file
write.table(merged_file,	file	=	"combined_otu_tax.txt",	sep	=	'\t',	col.names	=	
              TRUE,	row.names	=	FALSE)
#splitting the merged file as two separate documents - done in excel
#and saved as csv
otu_table	=	read.csv("otu_matrix.csv",	sep=",",	row.names=1)
otu_table	=	as.matrix(otu_table)
head(otu_table)
taxonomy	=	read.csv("taxonomy.csv",	sep=",",	row.names=1)
taxonomy	=	as.matrix(taxonomy)
head(taxonomy)
#import metadata and the tree
#metadata = read.table("sample-metadata.tsv", row.names=1, fill = TRUE)
#metadata
metadata <- read.xlsx("sample-metadata.xlsx",sheetName = "sample-metadata", row.names=1)
phy_tree = read_tree("tree.nwk")
#convert otu,tax and metadata to phyloseq objects
OTU = otu_table(otu_table,taxa_are_rows=TRUE)
TAX = tax_table(taxonomy)
META = sample_data(metadata)
taxa_names(TAX)
taxa_names(OTU)
taxa_names(phy_tree)
#now combine them in phyloseq
physeq = phyloseq(OTU,TAX,META,phy_tree)
physeq