PlotDendogram: Plotting a dendogram

In CoDaLoMic: Compositional Models to Longitudinal Microbiome Data

Plotting a dendogram

Description

Plots the dendogram obtained using the Ward’s method for obtaining the principal balances. The process follow in this function is explained in Section 3.1 of (Creus-Martí et al, 2022)

Usage

PlotDendogram(especie, names)

Arguments

especie	Matrix that contains at row i the bacterial taxa of bacteria i at all time points.
names	Vector with the names of the bacteria in the same order that are written in especie.

Value

Returns a list with: the dendogram.

• Num: List. The component i of the list has the number of the row of the matrix especie where the bacteria in the numerator of the principal balance i are placed.

• Dem: List. The component i of the list has the number of the row of the matrix especie where the bacteria in the denominator of the principal balance i are placed.

• dendogram: Plots the dendogram.

References

Creus-Martí, I., Moya, A., Santonja, F. J. (2022). Bayesian hierarchical compositional models for analysing longitudinal abundance data from microbiome studies. Complexity, 2022.

Examples

names2=c("Bact1","Bact2","Bact3","Bact4","Bact5")
set.seed(314)
esp2=t(gtools::rdirichlet(n=6, c(1,1,5,1,1)))


PlotDendogram(esp2,names2)

CoDaLoMic documentation built on April 12, 2025, 2:18 a.m.