FourHquaternary: Plot bootstrapped 4H-indices

In HybridMicrobiomes: Analysis of Host-Associated Microbiomes from Hybrid Organisms

Plot bootstrapped 4H-indices

Description

Draws bootstrapped values of the 4H-index on a quaternary (four dimensional barycentric, Aitchison Simplex) plot with an additional option to draw the centroid of the bootstrapped samples as well.

Usage

FourHquaternary(boots,col='red',addplot=FALSE,plotcentroid=TRUE,
               plotgrid=TRUE, size_bootstrap=1,size_centroid=15,size_font=2)

Arguments

boots	(Required) Output matrix from the FourHbootstrap function
col	The color of the points in the quaternary plot. The default is RED
addplot	Whether or not to add the data to an existing plot. The default is FALSE
plotcentroid	Whether or not to plot the centroid of the bootstrap samples. The default is TRUE.
plotgrid	Whether or not to plot gridlines on the quaternary plot. The default is TRUE
size_bootstrap	The size of each point representing a single bootstrap sample. The default is 1.
size_centroid	The size of the point representing the centroid of the bootstrap samples. The default is 15.
size_font	The size of the font used to label the four vertices. The default is 2.

Details

FourHquaternary allows for visualization of bootstrapped 4H-indices within the framework of a 4-dimensional Aitchison Simplex, also known as a 4-dimensional barycentric plot or quaternary plot. Commonly used for compositional data, the Aitchison Simplex is convenient for the 4H-index, because \mathcal{U} + \mathcal{I} + \mathcal{G} + \mathcal{L} = 1, reflecting the fact that each of the four different conceptual models - Union, Intersection, Gain and Loss - comprise one part of the whole, where the whole is the total microbial diversity across the entire hybrid host complex. FourHquaternary uses functions from the compositions R package to transform the four coordinates of the 4H-index, such that they can be drawn on a quaternary plot.

Value

This function plots bootstrapped 4H-indices on quaternary plot (Aitchison Simplex, 4-dimensional barycentric plot).

References

Henry, L., Wickham H., et al. "rlang: Functions for Base Types and Core R and 'Tidyverse' Features" https://CRAN.R-project.org/package=rlang

Van den Boogaart, K. Gerald, and Raimon Tolosana-Delgado. "“Compositions”: a unified R package to analyze compositional data." Computers & Geosciences 34.4 (2008): 320-338.

van den Boogaart, K. Gerald, et al. "Package ‘compositions’." Compositional data analysis Ver (2013): 1-40.

van den Boogaart, K. Gerald, Tolosana-Delgado, R., Bren, M. "compositions: Compositional Data Analysis" https://CRAN.R-project.org/package=compositions

Adler, Daniel, Oleg Nenadic, and Walter Zucchini. "Rgl: A r-library for 3d visualization with opengl." Proceedings of the 35th symposium of the interface: computing science and statistics, Salt Lake City. Vol. 35. 2003.

Adler, D., Murdoch, M. D., Suggests, M. A. S. S., WebGL, P. L. Y., OBJ, S., & OpenGL, S. (2019). Package ‘rgl’.

Murdoch, Duncan, Daniel Adler, and Oleg Nenadic. "Package ‘rgl’." R Package (2023).

Examples

#Test with enterotype dataset
library(phyloseq)
data(enterotype)
#Covert the OTU table to reads, rather than fractional abundances
otu_table(enterotype)<-round(10000*otu_table(enterotype))

#Randomly assign host classes (these should be known in a real hybrid microbiome dataset)
#The two parent species are assigned '1' and '3' respectively, the hybrid is assigned '2'
hybrid_status<-sample(1:3,280, replace=TRUE)

#Bootstrap the dataset
boot_samples<-FourHbootstrap(enterotype,hybrid_status,0.5,5,10)

#Plot the bootstrapped samples as a new quaternary plot including the centroid
FourHquaternary(boot_samples,col='red')

#Plot the bootstrapped samples on an existing quaternary plot without including the centroid
#An existing quaternary plot should already be open
FourHquaternary(boot_samples,col='red',addplot=TRUE, plotcentroid=FALSE)

HybridMicrobiomes documentation built on May 29, 2024, 2:15 a.m.