prep_tern_otu: Create table for ternary plot OTU

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

Create table for ternary plot OTU

Description

Create a table for ternary plot ggtern package.

Usage

prep_tern_otu(x, abund.thres = 1e-04, prev.thres = 0.1, group = NULL)

Arguments

x	phyloseq-class object.
abund.thres	= 0.0001 check microbiome package core function. remove taxa that are detected at 0.0001 in less than prev.thres of samples.
prev.thres	= 0.1 check microbiome package core function.
group	Grouping variable to compare, for this plot there has to be three groups in the data

Details

Plots the mean relative abundance of taxa in 3 groups being compared.

Value

tibble object.

Examples

# library(microbiome)
# library(microbiomeutilities)
# library(dplyr)
# data("zackular2014")
# p0 <- zackular2014
# prep_tern_otu(p0, group="DiseaseState",
# abund.thres=0.0001, prev.thres=0.25)

microsud/microbiomeutilities documentation built on Nov. 29, 2022, 12:18 a.m.