Get taxonomic table

Function to extract taxonomic information from a data frame and prepare it for phyloseq.

Usage

get_taxa_table(
  df,
  taxa_lvl = NULL,
  taxa_are_rows = FALSE,
  use_taxa_names = FALSE
)

Arguments

df

The input data frame.

taxa_lvl

The taxonomic level to extract ('kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species' or 't' (SGB)). First letter abbreviations (e.g., 's') are also accepted. Is deactivated with NULL by default.

taxa_are_rows

Logical; if TRUE, taxa information is in the row names of the data frame, otherwise it is assumed to be in the 'clade_name' column.

use_taxa_names

Logical; if TRUE, assign taxa names as row names, otherwise assign Otu as row names.

Value

A taxonomic matrix.

Note

Will work with unfiltered as well as filtered to a specific taxonomic level input data frames.

Author

Jérémy Rotzetter

Examples

taxmat <- get_taxa_table(species_only, taxa_lvl = "s")
head(taxmat)
#>      Kingdom    Phylum           Class                 Order              
#> Otu1 "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Moraxellales"     
#> Otu2 "Bacteria" "Actinobacteria" "Actinomycetia"       "Corynebacteriales"
#> Otu3 "Bacteria" "Firmicutes"     "Negativicutes"       "Veillonellales"   
#> Otu4 "Bacteria" "Bacteroidota"   "Bacteroidia"         "Bacteroidales"    
#> Otu5 "Bacteria" "Firmicutes"     "Bacilli"             "Lactobacillales"  
#> Otu6 "Bacteria" "Proteobacteria" "Gammaproteobacteria" "Pasteurellales"   
#>      Family               Genus            
#> Otu1 "Moraxellaceae"      "Moraxella"      
#> Otu2 "Corynebacteriaceae" "Corynebacterium"
#> Otu3 "Veillonellaceae"    "Veillonella"    
#> Otu4 "Prevotellaceae"     "Prevotella"     
#> Otu5 "Streptococcaceae"   "Streptococcus"  
#> Otu6 "Pasteurellaceae"    "Haemophilus"    
#>      Species                               
#> Otu1 "Moraxella_nonliquefaciens"           
#> Otu2 "Corynebacterium_pseudodiphtheriticum"
#> Otu3 "Veillonella_dispar"                  
#> Otu4 "Prevotella_histicola"                
#> Otu5 "Streptococcus_mitis"                 
#> Otu6 "Haemophilus_haemolyticus"