A tutorial for constructing a GMD-biplot

Introduction

In this vignette, we illustrate how to construct the GMD-biplot and screeplot using the tobacco data set from (Satten et al. 2017). This data set includes 15 smokeless tobacco products: 6 dry snuffs, 7 moist snuffs, and 2 toombak samples from Sudan. Three separate (replicate) observations (starting with sample preparation) were made of each product, so that in total 45 observations are available. Each observation has a 271 × 1 vector of taxon counts. To make the measurements comparable, we consider the centered log ratio (CLR) transformation of the data set. Additionally, the squared weighted UniFrac distance, denoted \(\Delta\), is used to measure the distance between samples. The corresponding similarity kernel \(H\) is derived from \(\Delta\) using the Gower’s centering matrix.

Step 1: Loading the tobacco data set

We first load our R package GMDecomp.

library(GMDecomp)

The data object tobacco_clr in the package include

• data: the CLR transformed out table, with rows for samples and columns for OTU.
• \(H\): the similarity kernel derived from the squared weighted UniFrac distance.
• sample.col: the color for plotting each sample point.
• sample.pch: the shape for plotting each sample point.
• out.names: the taxonomic name of each OTU.

Step 2: Generalized Matrix Decomposition

To construct the GMD-biplot and screeplot, we need to first perform the generalized matrix decomposition (Allen, Grosenick, and Taylor 2014) of the data with respect to \(H\). This can be easily achieved using the following line:

tobacco.gmd <- GMD(X = tobacco_clr$data, H = tobacco_clr$H, Q = diag(1, dim(tobacco_clr$data)[2]), K = 10)

Note that here we don’t have a similarity kernel for the OTUs, so \(Q\) is set to be an identity matrix. One can set \(Q\) to be any informative positive semi-definite matrix, if such information is available. Also, here we set \(K = 10\), since we want to display the screeplot the top 10 GMD components. If only the GMD-biplot is needed, one can set \(K = 2\), which may save computational time.

tabacco.gmd is a list of class gmd, which consists of the following variables.

• U: the left GMD components with 45 rows and 10 columns.
• S: the top 10 GMD values.
• V: the right GMD components with 271 rows and 10 columns.
• H: the similarity matrix for samples.
• Q: the similarity matrix for OTUs.

Step 3: The GMD-biplot and screeplot

Once the GMD outputs are obtained, the screeplot can by easily constructed as follows.

screeplot(tobacco.gmd) #the screeplot of the top 10 GMD components 

Note that one can select specific OTUs to display in the GMD-biplot. For this analysis, we display the top 3 OTUs that have the longest arrows.

gmd.order = order(rowSums(tobacco.gmd$V[,1:2]^2), decreasing = T)
plot.index = gmd.order[1:3]
plot.names = tobacco_clr$otu.names[plot.index]
biplot(fit = tobacco.gmd, index = plot.index, names = plot.names, sample.col = tobacco_clr$sample.color, sample.pch = tobacco_clr$sample.pch, arrow.col = 'grey50')