Diversity Analysis

Create phyloseq Object

library(phyloseq)
library(vegan)
library(ggplot2)

seqtab <- readRDS('seqtab_nochim.rds')
taxa <- readRDS('taxa.rds')
metadata <- read.csv('sample_metadata.csv', row.names = 1)

ps <- phyloseq(otu_table(seqtab, taxa_are_rows = FALSE),
               tax_table(taxa),
               sample_data(metadata))
taxa_names(ps) <- paste0('ASV', seq(ntaxa(ps)))