Rename columns in tax_table

Rename columns (taxonomic ranks) in tax_table using tidyselect semantics.

Usage

rename_taxa_pq(physeq, ...)

Arguments

physeq

(phyloseq, required) A phyloseq object.

...

Name-value pairs where the name is the new name and the value is the old name. Use new_name = old_name syntax.

Value

A phyloseq object with renamed tax_table columns.

Author

Adrien Taudière

Examples

library(MiscMetabar)
# Rename a single rank
rename_taxa_pq(data_fungi, tax_domain = Domain)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1420 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1420 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1420 reference sequences ]

# Rename multiple ranks
rename_taxa_pq(data_fungi, tax_phylum = Phylum, tax_class = Class)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1420 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1420 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1420 reference sequences ]