Entering edit mode
4.0 years ago
Bioinfonext
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460
Hi,
I do have relative abundance in phyloseq object, could you please let me know how I can plot biplot with taxonomy at phylum level after getting relative abundance in phyloseq.
physeq <- phyloseq(OTU, TAX, samples)
colnames(tax_table(physeq))= c("Kingdom","Phylum","Class","Order","Family","Genus", "Species")
rank_names(physeq)
nsamples(physeq)
ntaxa(physeq)
physeq2Phylum=tax_glom(physeqN2,"Phylum",NArm=TRUE)
physeq2PhylumR = transform_sample_counts(physeq2Phylum, function(x) x / sum(x))
Many thanks Bioinfonext