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

13 views
Skip to first unread message

dsan...@uic.edu

unread,
Mar 19, 2018, 4:20:07 PM3/19/18
to Qiime 1 Forum

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" 
Reply all
Reply to author
Forward
0 new messages