Replace a Tree Slot in a Microbiome Dataset

Set otu_tree or taxa_tree on a microbiome_dataset and optionally align it with the current dataset.

Usage

replace_tree(
  object,
  tree = c("otu_tree", "taxa_tree"),
  value = NULL,
  align = TRUE
)

Arguments

object

A microbiome_dataset object.

tree

Tree slot to replace, either "otu_tree" or "taxa_tree".

value

A treedata object or NULL.

align

Should the tree be aligned after replacement? Defaults to TRUE.

Value

A microbiome_dataset object.

Examples

data("global_patterns", package = "microbiomedataset")

x0 <- prune_taxa(global_patterns, variable_id = global_patterns@variable_info$variable_id[1:80])
x <- microbiomedataset::convert2microbiome_dataset(
  microbiomedataset::convert2phyloseq(x0)
)
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
#> Found more than one class "phylo" in cache; using the first, from namespace 'phyloseq'
#> Also defined by ‘tidytree’
otu_phylo <- ape::rtree(
  n = nrow(x@variable_info),
  tip.label = x@variable_info$variable_id
)
x <- replace_tree(
  x,
  tree = "otu_tree",
  value = tidytree::treedata(
    phylo = otu_phylo,
    data = tibble::tibble(node = seq_len(length(otu_phylo$tip.label) + otu_phylo$Nnode))
  )
)
class(x@otu_tree)
#> [1] "treedata"
#> attr(,"package")
#> [1] "tidytree"