Extract taxonomic names from a phyloseq object
Source:R/taxonomic_rank_to_taxnames.R
taxonomic_rank_to_taxnames.Rd<a href="https://adrientaudiere.github.io/MiscMetabar/articles/Rules.html#lifecycle"> <img src="https://img.shields.io/badge/lifecycle-experimental-orange" alt="lifecycle-experimental"></a>
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.
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"
if (FALSE) { # \dontrun{
taxonomic_rank_to_taxnames(gna_verifier_pq(data_fungi_mini), taxonomic_rank="currentCanonicalSimple")
taxonomic_rank_to_taxnames(gna_verifier_pq(data_fungi_mini), taxonomic_rank="genusEpithet")
} # }
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"