Only 2 ranks present in data importend from biom table to R

[dsan...@uic.edu]

Hi All, 

For some reason only 2 ranks are recognized whenever I run my code. Any ideas on how to fix this?

otubiom="table.from_txt_json.biom"

NMR_otu_table <- import_biom(otubiom, parseFunction = parse_taxonomy_greengenes)

NMR_mapping_file="SampleMappingFile-NMR.txt"

Mytree <- read.tree("correct_rep_set_tree.tree")

NMR_data <- merge_phyloseq(NMR_otu_table,NMR_mapping_file,Mytree)

print(NMR_data)

rank_names(NMR_data)

 print(NMR_data)

phyloseq-class experiment-level object

otu_table()   OTU Table:         [ 725 taxa and 77 samples ]

tax_table()   Taxonomy Table:    [ 725 taxa by 2 taxonomic ranks ]

phy_tree()    Phylogenetic Tree: [ 725 tips and 724 internal nodes ]

> rank_names(NMR_data)

[1] "Kingdom" "Rank1"