Taxonomic tree — taxtree • yatah

Compute taxonomic tree from taxonomic table.

Usage

taxtree(table, collapse = TRUE, lineage_length = 1, root = "")

Arguments

table: dataframe.
collapse: logical. Should node with one child be vanished? Default to TRUE.
lineage_length: double. Lineage length from the root to the leaves. Default to 1.
root: character. Name of the root if there is no natural root.

Value

A phylo object.

Examples

lineage1 <- "k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae"
lineage2 <- "k__Bacteria|p__Firmicutes|c__Clostridia"
lineage3 <- "k__Bacteria|p__Firmicutes|c__Bacilli"
table <- taxtable(c(lineage1, lineage2, lineage3))
taxtree(table)
#> 
#> Phylogenetic tree with 3 tips and 2 internal nodes.
#> 
#> Tip labels:
#>   Verrucomicrobiae, Clostridia, Bacilli
#> Node labels:
#>   Bacteria, Firmicutes
#> 
#> Rooted; includes branch lengths.