OTU Table Extraction from Phyloseq Object

Question

[safiq713]

I want to extract otu table from the phyloseq object:

> physeq_N

phyloseq-class experiment-level object
otu_table()   OTU Table:         [ 1581 taxa and 4 samples ]
sample_data() Sample Data:       [ 4 samples by 1 sample variables ]
tax_table()   Taxonomy Table:    [ 1581 taxa by 8 taxonomic ranks ]

PTU Table is like this

 >otu_table(physeq_N)*

OTU Table:          [1581 taxa and 4 samples]
                     taxa are columns
           e37dba1608aafb21f6c51dd721e39455 6e1a4303bd0c4c67e4b19b18c09221de e18fe870915e68610993c7a077ee6b79 ec4edc4bc6abe7f1978e69c4e0acea7c 7df2cd8fd4882b411c8cf03224a9a77c
           9ef92be0c5a2879062904cf0d17544ff 1f7727dd435fe7255c5eba63d6b033de d424237f7a32df5ff6912973b09183bd 557730296c9ff8394732518bcee9cae1 f983978ebf8ee1da64bb98a3e742eb95

> tax_table(physeq_N)

Taxonomy Table:     [1581 taxa by 8 taxonomic ranks]:
                                 Kingdom    Phylum             Class                 Order                                 Family                             
e37dba1608aafb21f6c51dd721e39455 "Bacteria" "Bacteroidota"     "Bacteroidia"         "Bacteroidales"                       "Bacteroidaceae"                   
6e1a4303bd0c4c67e4b19b18c09221de "Bacteria" "Bacteroidota"     "Bacteroidia"         "Bacteroidales"                       "Bacteroidaceae"                   
e18fe870915e68610993c7a077ee6b79 "Bacteria" "Bacteroidota"     "Bacteroidia"         "Bacteroidales"                       "Bacteroidaceae" 

How can Extract a OTU Table like this:

   Species.ID   Sample 1    sample2 sample 3    sample 4    Domain  Phylum  Class   Order   Family  Genus   Species
    EQAS.001    10  11105   125 524774  Animalia    xxx xx  xxx xxx xxx xxx

Thanks a lot

Answer 1

[Asaf]

cbind(data.frame(otu_table(physeq_N)), data.frame(tax_table(physeq_N)))

[safiq713]

thanks a lot for your kind reply, Exactly I want to get the file this but problem is sample information is missing

I want include samples information as well.

[Asaf]

You mean the count matrix? You didn't include both tables in the cbind, only the first one (the otu_table) so you got two table instead of one.

[safiq713]

Thanks a lot for your reply. a. What I want, first column as it it is, OTU Name. b. from second to n Column Samples names c. then taxonomy

<OTU name ><samples name><Kingdom><Phylum>

[Asaf]

This is really weird, the otu_table should have 1581 rows and 4 columns, unless you changed it somehow. The OTU names are the rownames, when you write the data.frame as csv with write.csv() it will be printed as first column.