Convert a taxonomic table to an ape phylo object. — taxonomy_to

Creates a phylo from a taxonomic tree, skipping over any NA assignments. Assumes that the columns are sorted from coarsest to finest taxonomic resolution.

Usage

taxonomy_to_tree(taxa)

Arguments

taxa: A data.frame or matrix with columns representing taxonomic ranks (sorted coarsest to finest) and rows representing taxa. NA or empty values are skipped.

Value

An object of class 'phylo' representing the taxonomic tree.

Examples

taxa <- matrix(
  c("Firmicutes", "Bacilli", "Lactobacillales",
    "Proteobacteria", "Gammaproteobacteria", "Enterobacterales"),
  ncol = 3, byrow = TRUE,
  dimnames = list(NULL, c("Phylum", "Class", "Order"))
)
tree <- taxonomy_to_tree(taxa)
str(tree)
#> List of 4
#>  $ edge      : int [1:4, 1:2] 3 4 5 6 4 1 6 2
#>   ..- attr(*, "dimnames")=List of 2
#>   .. ..$ : chr [1:4] "Firmicutes" "Bacilli" "Proteobacteria" "Gammaproteobacteria"
#>   .. ..$ : NULL
#>  $ tip.label : chr [1:2] "Lactobacillales" "Enterobacterales"
#>  $ node.label: chr [1:4] "Firmicutes" "Bacilli" "Proteobacteria" "Gammaproteobacteria"
#>  $ Nnode     : int 4
#>  - attr(*, "class")= chr "phylo"

# A more involved example with missing values
taxa <- matrix(
  c("Firmicutes", "Bacilli", "Lactobacillales", "ASV1",
    "Proteobacteria", "Gammaproteobacteria", "Enterobacterales", "ASV2",
    "Firmicutes", "Bacilli", NA, "ASV3"),
  ncol = 4, byrow = TRUE,
  dimnames = list(NULL, c("Phylum", "Class", "Order", "ASV"))
)
taxmat <- add_prefix(taxa)
tree <- taxonomy_to_tree(taxmat)
str(tree)
#> List of 4
#>  $ edge      : int [1:7, 1:2] 4 5 6 7 8 9 5 5 6 1 ...
#>   ..- attr(*, "dimnames")=List of 2
#>   .. ..$ : chr [1:7] "P_Firmicutes" "C_Bacilli" "O_Lactobacillales" "P_Proteobacteria" ...
#>   .. ..$ : NULL
#>  $ tip.label : chr [1:3] "ASV1" "ASV2" "ASV3"
#>  $ node.label: chr [1:6] "P_Firmicutes" "C_Bacilli" "O_Lactobacillales" "P_Proteobacteria" ...
#>  $ Nnode     : int 6
#>  - attr(*, "class")= chr "phylo"