taxtree: Taxonomic tree

In abichat/yatah: Yet Another TAxonomy Handler

Taxonomic tree

Description

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)

abichat/yatah documentation built on April 14, 2024, 7:25 a.m.