erictleung · March 16, 2018 22:46 · kediza · Oct 26, 2018 · LinaMaMar · Jan 21, 2019
diff --git a/1_qiime_part.sh b/1_qiime_part.sh
 # ---
 # title: Export QIIME2 OTU table to compatible file for phyloseq
 # description: |
 #   Three main steps to get to compatible file to import to phyloseq
 #
 #   Outline:
 #   1. Export OTU table
 #   2. Export taxonomy table
 #   3. Export phylogenetic tree
 # ---

 # 1 Export OTU table
 # - table-no-mitochondria-no-chloroplast.qza replace with your file
 # - phyloseq => replace with where you'd like to output directory
 qiime tools export \
  table-no-mitochondria-no-chloroplast.qza \
  --output-dir phyloseq

 # OTU tables exports as feature-table.biom so convert to .tsv
 # - Change -i and -o paths accordingly
 biom convert \
  -i phyloseq/feature-table.biom \
  -o phyloseq/otu_table.txt \
  --to-tsv
  
 # Manually change #OTUID to OTUID

 # 2 Export taxonomy table
 qiime tools export \
  taxonomy.qza \
  --output-dir phyloseq
  
 # Manually change "feature ID" to "OTUID"

 # 3 Export phylogenetic tree
 qiime tools export \
  unrooted-tree.qza \
  --output-dir phyloseq
  
 # 4 Merge files
 # Filtered sequences will make taxonomy and OTU tables have different lengths
diff --git a/2_format_in_R.R b/2_format_in_R.R
 # ---
 # title: Manipulate QIIME2 output in R
 # description: |
 #   Take in output from 1_qiime_part.sh and manipulate files in R
 # ---

 # Setup environment
 library(here)

 # Read in OTU table
 in_path <- here("phyloseq", "otu_table.txt")
 otu <- read.table(file = in_path, header = TRUE)
 head(otu)

 #	Read in taxonomy table
 tax	<- read.table(Sile = "taxonomy.tsv", sep = '\t', header = TRUE)
 head(tax)

 # Merge files
 merged_file <- merge(otu, tax, by.x = c("OTUID"), by.y = c("OTUID"))
 head(merged_file)

 # Note: the number of rows should equal your shortest file length, drops taxonomy
 # for OTUs that don't exist in your OTU table

 # Output merged .txt file
 out_path <- here("phyloseq", "combined_otu_tax.tsv")
 write.table(merged_file, file = out_path, sep = "\t", col.names = TRUE, row.names = FALSE)
diff --git a/3_import_to_phyloseq.R b/3_import_to_phyloseq.R
 # Setup environment
 library(phyloseq)
 library(ggplot2)
 library(ape)

 # Read in OTU table
 otu_table_in <- read.csv("otu_matrix.csv", sep = ",", row.names = 1)
 otu_table_in <- as.matrix(otu_table_in)

 # Read in taxonomy
 # Separated by kingdom, phylum, class, order, family, genus, species
 taxonomy <- read.csv("taxonomy.csv", sep = ",", row.names = 1)
 taxonomy <- as.matrix(taxonomy)

 # Read in metadata
 metadata <- read.table("metadata.txt", row.names = 1)

 # Read in tree
 phy_tree <- read_tree("tree.nwk")

 # Import all as phyloseq objects
 OTU <- otu_table(otu_table_in, taxa_are_rows = TRUE)
 TAX <- tax_table(taxonomy)
 META <- sample_data(metadata)

 # Sanity checks for consistent OTU names
 taxa_names(TAX)
 taxa_names(OTU)
 taxa_names(phy_tree)

 # Same sample names
 sample_names(OTU)
 sample_names(META)

 # Finally merge!
 ps <- phyloseq(OTU, TAX, META, phy_tree)
 ps
	# ---
	# title: Export QIIME2 OTU table to compatible file for phyloseq
	# description: \|
	# Three main steps to get to compatible file to import to phyloseq
	#
	# Outline:
	# 1. Export OTU table
	# 2. Export taxonomy table
	# 3. Export phylogenetic tree
	# ---

	# 1 Export OTU table
	# - table-no-mitochondria-no-chloroplast.qza replace with your file
	# - phyloseq => replace with where you'd like to output directory
	qiime tools export \
	table-no-mitochondria-no-chloroplast.qza \
	--output-dir phyloseq

	# OTU tables exports as feature-table.biom so convert to .tsv
	# - Change -i and -o paths accordingly
	biom convert \
	-i phyloseq/feature-table.biom \
	-o phyloseq/otu_table.txt \
	--to-tsv

	# Manually change #OTUID to OTUID

	# 2 Export taxonomy table
	qiime tools export \
	taxonomy.qza \
	--output-dir phyloseq

	# Manually change "feature ID" to "OTUID"

	# 3 Export phylogenetic tree
	qiime tools export \
	unrooted-tree.qza \
	--output-dir phyloseq

	# 4 Merge files
	# Filtered sequences will make taxonomy and OTU tables have different lengths
	# ---
	# title: Manipulate QIIME2 output in R
	# description: \|
	# Take in output from 1_qiime_part.sh and manipulate files in R
	# ---

	# Setup environment
	library(here)

	# Read in OTU table
	in_path <- here("phyloseq", "otu_table.txt")
	otu <- read.table(file = in_path, header = TRUE)
	head(otu)

	# Read in taxonomy table
	tax <- read.table(Sile = "taxonomy.tsv", sep = '\t', header = TRUE)
	head(tax)

	# Merge files
	merged_file <- merge(otu, tax, by.x = c("OTUID"), by.y = c("OTUID"))
	head(merged_file)

	# Note: the number of rows should equal your shortest file length, drops taxonomy
	# for OTUs that don't exist in your OTU table

	# Output merged .txt file
	out_path <- here("phyloseq", "combined_otu_tax.tsv")
	write.table(merged_file, file = out_path, sep = "\t", col.names = TRUE, row.names = FALSE)
	# Setup environment
	library(phyloseq)
	library(ggplot2)
	library(ape)

	# Read in OTU table
	otu_table_in <- read.csv("otu_matrix.csv", sep = ",", row.names = 1)
	otu_table_in <- as.matrix(otu_table_in)

	# Read in taxonomy
	# Separated by kingdom, phylum, class, order, family, genus, species
	taxonomy <- read.csv("taxonomy.csv", sep = ",", row.names = 1)
	taxonomy <- as.matrix(taxonomy)

	# Read in metadata
	metadata <- read.table("metadata.txt", row.names = 1)

	# Read in tree
	phy_tree <- read_tree("tree.nwk")

	# Import all as phyloseq objects
	OTU <- otu_table(otu_table_in, taxa_are_rows = TRUE)
	TAX <- tax_table(taxonomy)
	META <- sample_data(metadata)

	# Sanity checks for consistent OTU names
	taxa_names(TAX)
	taxa_names(OTU)
	taxa_names(phy_tree)

	# Same sample names
	sample_names(OTU)
	sample_names(META)

	# Finally merge!
	ps <- phyloseq(OTU, TAX, META, phy_tree)
	ps