taxtree: Taxonomic tree

Description Usage Arguments Value Examples

View source: R/taxtree.R

Description

Compute taxonomic tree from taxonomic table.

Usage

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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

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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)

yatah documentation built on March 1, 2020, 5:08 p.m.