Install

devtools::install_github("trevorjgould/dada2analysis")

You need the following files

1. seqtab output file from dada2
2. metadata with sample names matching seqtab output PROVIDED BY USER
3. taxonomy file with sequences matching seqtab output and taxa output from IDtaxa in R

library(dada2analysis)
# LOAD TABLES
# samples as rows, ASVs as headers
inputtable <- readRDS("seqtab_nochim.rds")
# ASV sequences as rows, taxonomy levels as headers
taxa <- readRDS("taxa.rds")
# samples as rows, metadata variables as headers
metadata <- read.table("metadata.txt", header= TRUE, row.names = 1)

outtab <- Create_Tables(inputtable,metadata,taxa)
brayWmeta <- diversity(outtab$newmap,outtab$newtable)
outlist <- rarefyTable(outtab$newtable)

# list object to single objects
PCOA <- outlist$PCOA
brayWmeta <- outlist$brayWmeta
ds.mes <- outlist$ds.mes
combined_taxa <-  outtab$combined_taxa

# diversity plots
Diversity_Plots(brayWmeta, outtab$newmap)

# taxonomy tables
taxaout <- Make_Taxa_Tables(combined_taxa)

#taxonomy plots
Create_Taxonomy_Plot(taxaout$Phylum,2,outtab$newmap)
Create_Taxonomy_Plot(taxaout$Class,10,outtab$newmap)
Create_Taxonomy_Plot(taxaout$Order,10,outtab$newmap)
Create_Taxonomy_Plot(taxaout$Family,10,outtab$newmap)
Create_Taxonomy_Plot(taxaout$Genus,10,outtab$newmap)
Create_Taxonomy_Plot(taxaout$Species,10,outtab$newmap)

Create_Taxonomy_Plot_Facet(taxaout$Phylum,10,outtab$newmap)
Create_Taxonomy_Plot_Facet(taxaout$Class,10,outtab$newmap)
Create_Taxonomy_Plot_Facet(taxaout$Order,10,outtab$newmap)
Create_Taxonomy_Plot_Facet(taxaout$Family,10,outtab$newmap)
Create_Taxonomy_Plot_Facet(taxaout$Genus,10,outtab$newmap)
Create_Taxonomy_Plot_Facet(taxaout$Species,10,outtab$newmap)

The output from this pipeline is:

1. combined tables for use in analysis
2. plots

• alpha diversity
• beta diversity
• taxonomy plots

3. statistical analysis
4. summary plots