Extract Tree Link Metadata

Return the explicit mapping table between variable_id and nodes in otu_tree or taxa_tree.

Usage

extract_tree_link_data(object, tree = c("otu_tree", "taxa_tree"))

Arguments

object

A microbiome_dataset object.

tree

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

Value

A data frame or NULL.

Examples

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

x <- prune_taxa(global_patterns, variable_id = global_patterns@variable_info$variable_id[1:120])
x <- microbiomedataset::convert2microbiome_dataset(
  microbiomedataset::convert2phyloseq(x)
)
#> 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’
extract_tree_link_data(x, tree = "taxa_tree")[1:6, ]
#>   variable_id node                  node_label      tree link_rank
#> 1      549322  128             c__Thermoprotei taxa_tree     Class
#> 2      522457  128             c__Thermoprotei taxa_tree     Class
#> 3         951  197 s__Sulfolobusacidocaldarius taxa_tree   Species
#> 4      244423  126                    c__Sd-NA taxa_tree     Class
#> 5      586076  126                    c__Sd-NA taxa_tree     Class
#> 6      246140  126                    c__Sd-NA taxa_tree     Class