gmteunisse
commented
2 years ago Hi pauGaus,
Thanks for using fantaxtic.
The get_top_taxa function outputs a phyloseq object with that information if relative = T. This does have the non-top taxa collapsed into "Other". To access this table, run the following:
# Get the top 10 taxa and collapse all otehr into "Other". Make abundances relative.
ps_tmp <- get_top_taxa(physeq_obj = physeq_obj, n = 10, relative = TRUE,
discard_other = FALSE, other_label = "Other")
rel_abun <- phyloseq::otu_table(ps_tmp)
# The taxon names are stored in the tax table
tax_names <- tax_table(ps_tmp)
# Bind the two together
final_table <- cbind(tax_names, rel_abun)If you don't want to collapse the taxa into "Other" and want information for all taxa instead, you'll need to calculate relative abundances yourself. Use the following code in base R:
#Get the tax and OTU tables
otu_tbl <- as.data.frame(phyloseq::otu_table(physeq_obj))
#Check the orientation of the otu_tbl and change if required
if (!taxa_are_rows(phyloseq::otu_table(physeq_obj))){
otu_tbl <- as.data.frame(t(otu_tbl))
}
#Transform absolute taxon counts to relative values
otu_tbl <- apply(otu_tbl, 2, function(x){
x / sum (x)
})
# The taxon names are stored in the tax table
tax_names <- tax_table(physeq_obj)
# Bind the two together
final_table <- cbind(tax_names, rel_abun)You are correct that "Other" just means all the taxa that weren't in the top most abundant.
Hope this helps you.
pauGuas
Hi, I need a table showing the relative abundance of each taxon in each sample. Is there a way to extract that data from the fantaxtic bar plot?
I also want to double check.... "Other" just means taxa that weren't in the top most abundant, right? And not that it's just a taxon that isn't identified?
Thank you!