mp_extract_tree-methods: extract the taxonomy tree in MPSE object

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

extract the taxonomy tree in MPSE object

Description

extract the taxonomy tree in MPSE object

Usage

mp_extract_tree(x, type = "taxatree", tip.level = "OTU", ...)

## S4 method for signature 'MPSE'
mp_extract_tree(x, type = "taxatree", tip.level = "OTU", ...)

## S4 method for signature 'tbl_mpse'
mp_extract_tree(x, type = "taxatree", tip.level = "OTU", ...)

## S4 method for signature 'grouped_df_mpse'
mp_extract_tree(x, type = "taxatree", tip.level = "OTU", ...)

mp_extract_taxatree(x, tip.level = "OTU", ...)

mp_extract_otutree(x, ...)

Arguments

x	MPSE object
type	character taxatree or otutree
tip.level	character This argument will keep the nodes belong to the tip.level as tip nodes when type is taxatree, default is OTU, which will return the taxa tree with OTU level as tips.
...	additional arguments

Value

taxatree treedata object

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.