Extract taxonomic names from a phyloseq object

Mainly a internal function for function [gna_verifier_pq()], [tax_oa_pq()], [gbif_occur_pq()], [tax_iucn_code_pq()], [tax_globi_pq()], [plot_tax_gbif_pq()], ...

Usage

taxonomic_rank_to_taxnames(
  physeq,
  taxonomic_rank = c("Genus", "Species"),
  discard_genus_alone = FALSE,
  discard_NA = TRUE,
  distinct_names = TRUE
)

Arguments

physeq

A phyloseq object

taxonomic_rank

(Character) The column(s) present in the @tax_table slot of the phyloseq object. Can be a vector of two columns (e.g. the default c("Genus", "Species")).

discard_genus_alone

(logical default FALSE). If TRUE genus without information at the species level are discarded.

discard_NA

(logical default TRUE). If TRUE, taxa with NA in the taxonomic_rank are discarded.

distinct_names

(logical default TRUE). If TRUE, return only unique taxonomic names.

Value

A vector of unique taxonomic names

Author

Adrien Taudiere

Examples

taxonomic_rank_to_taxnames(data_fungi_mini)
#>  [1] "Stereum ostrea"             "Xylodon raduloides"        
#>  [3] "Ossicaulis lachnopus"       "Stereum hirsutum"          
#>  [5] "Antrodiella brasiliensis"   "Basidiodendron eyrei"      
#>  [7] "Sistotrema oblongisporum"   "Entocybe"                  
#>  [9] "Fomes fomentarius"          "Mycena renati"             
#> [11] "Helicogloea pellucida"      "Radulomyces molaris"       
#> [13] "Elmerina caryae"            "Phanerochaete livescens"   
#> [15] "Gloeohypochnicium analogum" "Auricularia"               
#> [17] "Hyphoderma roseocremeum"    "Hyphoderma setigerum"      
#> [19] "Trametes versicolor"        "Peniophora versiformis"    
#> [21] "Exidia glandulosa"          "Peniophorella pubera"      
#> [23] "Auricularia mesenterica"    "Marchandiomyces buckii"    
#> [25] "Hericium coralloides"       "Xylodon flaviporus"        
taxonomic_rank_to_taxnames(data_fungi_mini, discard_genus_alone = TRUE)
#>  [1] "Stereum ostrea"             "Xylodon raduloides"        
#>  [3] "Ossicaulis lachnopus"       "Stereum hirsutum"          
#>  [5] "Antrodiella brasiliensis"   "Basidiodendron eyrei"      
#>  [7] "Sistotrema oblongisporum"   "Fomes fomentarius"         
#>  [9] "Mycena renati"              "Helicogloea pellucida"     
#> [11] "Radulomyces molaris"        "Elmerina caryae"           
#> [13] "Phanerochaete livescens"    "Gloeohypochnicium analogum"
#> [15] "Hyphoderma roseocremeum"    "Hyphoderma setigerum"      
#> [17] "Trametes versicolor"        "Peniophora versiformis"    
#> [19] "Exidia glandulosa"          "Peniophorella pubera"      
#> [21] "Auricularia mesenterica"    "Marchandiomyces buckii"    
#> [23] "Hericium coralloides"       "Xylodon flaviporus"        
taxonomic_rank_to_taxnames(data_fungi_mini, discard_NA = TRUE)
#>  [1] "Stereum ostrea"             "Xylodon raduloides"        
#>  [3] "Ossicaulis lachnopus"       "Stereum hirsutum"          
#>  [5] "Antrodiella brasiliensis"   "Basidiodendron eyrei"      
#>  [7] "Sistotrema oblongisporum"   "Entocybe"                  
#>  [9] "Fomes fomentarius"          "Mycena renati"             
#> [11] "Helicogloea pellucida"      "Radulomyces molaris"       
#> [13] "Elmerina caryae"            "Phanerochaete livescens"   
#> [15] "Gloeohypochnicium analogum" "Auricularia"               
#> [17] "Hyphoderma roseocremeum"    "Hyphoderma setigerum"      
#> [19] "Trametes versicolor"        "Peniophora versiformis"    
#> [21] "Exidia glandulosa"          "Peniophorella pubera"      
#> [23] "Auricularia mesenterica"    "Marchandiomyces buckii"    
#> [25] "Hericium coralloides"       "Xylodon flaviporus"        
taxonomic_rank_to_taxnames(data_fungi_mini,
  discard_NA = TRUE, discard_genus_alone = TRUE
)
#>  [1] "Stereum ostrea"             "Xylodon raduloides"        
#>  [3] "Ossicaulis lachnopus"       "Stereum hirsutum"          
#>  [5] "Antrodiella brasiliensis"   "Basidiodendron eyrei"      
#>  [7] "Sistotrema oblongisporum"   "Fomes fomentarius"         
#>  [9] "Mycena renati"              "Helicogloea pellucida"     
#> [11] "Radulomyces molaris"        "Elmerina caryae"           
#> [13] "Phanerochaete livescens"    "Gloeohypochnicium analogum"
#> [15] "Hyphoderma roseocremeum"    "Hyphoderma setigerum"      
#> [17] "Trametes versicolor"        "Peniophora versiformis"    
#> [19] "Exidia glandulosa"          "Peniophorella pubera"      
#> [21] "Auricularia mesenterica"    "Marchandiomyces buckii"    
#> [23] "Hericium coralloides"       "Xylodon flaviporus"        

taxonomic_rank_to_taxnames(gna_verifier_pq(data_fungi_mini), taxonomic_rank="currentCanonicalSimple")
#> ✔ GNA verification summary:
#> • Total taxa in phyloseq: 45
#> • Taxa submitted for verification: 37
#> • Genus-level only taxa: 2
#> • Total matches found: 25
#> • Synonyms: 2 (including 2 at genus level)
#> • Accepted names: 23 (including 21 at genus level)
#>  [1] "NA"                         "Stereum ostrea"            
#>  [3] "Xylodon raduloides"         ""                          
#>  [5] "Stereum hirsutum"           "Trametopsis brasiliensis"  
#>  [7] "Basidiodendron eyrei"       "Sistotrema oblongisporum"  
#>  [9] "Entocybe"                   "Fomes fomentarius"         
#> [11] "Mycena renati"              "Helicogloea pellucida"     
#> [13] "Radulomyces molaris"        "Elmerina caryae"           
#> [15] "Phanerochaete livescens"    "Gloeohypochnicium analogum"
#> [17] "Auricularia"                "Hyphoderma roseocremeum"   
#> [19] "Hyphoderma setigerum"       "Trametes versicolor"       
#> [21] "Peniophora versiformis"     "Exidia glandulosa"         
#> [23] "Peniophorella pubera"       "Auricularia mesenterica"   
#> [25] "Laetisaria buckii"          "Hericium coralloides"      
#> [27] "Xylodon flaviporus"        
taxonomic_rank_to_taxnames(gna_verifier_pq(data_fungi_mini), taxonomic_rank="genusEpithet")
#> ✔ GNA verification summary:
#> • Total taxa in phyloseq: 45
#> • Taxa submitted for verification: 37
#> • Genus-level only taxa: 2
#> • Total matches found: 25
#> • Synonyms: 2 (including 2 at genus level)
#> • Accepted names: 23 (including 21 at genus level)
#>  [1] "NA"                "Stereum"           "Xylodon"          
#>  [4] ""                  "Trametopsis"       "Basidiodendron"   
#>  [7] "Sistotrema"        "Entocybe"          "Fomes"            
#> [10] "Mycena"            "Helicogloea"       "Radulomyces"      
#> [13] "Elmerina"          "Phanerochaete"     "Gloeohypochnicium"
#> [16] "Auricularia"       "Hyphoderma"        "Trametes"         
#> [19] "Peniophora"        "Exidia"            "Peniophorella"    
#> [22] "Laetisaria"        "Hericium"         
taxonomic_rank_to_taxnames(data_fungi_mini, taxonomic_rank="Class")
#> [1] "Agaricomycetes"     "Atractiellomycetes" "Tremellomycetes"   
#> [4] "NA"                
taxonomic_rank_to_taxnames(data_fungi_mini, taxonomic_rank="Class",
 distinct_names = FALSE,
 discard_NA = TRUE
)
#>  [1] "Agaricomycetes"     "Agaricomycetes"     "Agaricomycetes"    
#>  [4] "Agaricomycetes"     "Agaricomycetes"     "Agaricomycetes"    
#>  [7] "Agaricomycetes"     "Agaricomycetes"     "Agaricomycetes"    
#> [10] "Agaricomycetes"     "Agaricomycetes"     "Agaricomycetes"    
#> [13] "Agaricomycetes"     "Atractiellomycetes" "Agaricomycetes"    
#> [16] "Agaricomycetes"     "Agaricomycetes"     "Agaricomycetes"    
#> [19] "Agaricomycetes"     "Agaricomycetes"     "Agaricomycetes"    
#> [22] "Agaricomycetes"     "Agaricomycetes"     "Agaricomycetes"    
#> [25] "Agaricomycetes"     "Agaricomycetes"     "Agaricomycetes"    
#> [28] "Agaricomycetes"     "Tremellomycetes"    "Agaricomycetes"    
#> [31] "Agaricomycetes"     "Agaricomycetes"     "Agaricomycetes"    
#> [34] "Tremellomycetes"    "Agaricomycetes"     "Agaricomycetes"    
#> [37] "Agaricomycetes"     "Agaricomycetes"     "Agaricomycetes"    
#> [40] "NA"                 "Agaricomycetes"     "Agaricomycetes"    
#> [43] "Agaricomycetes"     "Agaricomycetes"     "Agaricomycetes"