Toydata: Toy data used for illustration

In chanw0/MTA: Microbial Trend Analysis for Common Dynamic Trend, Group Comparison, and Classification in Longitudinal Microbiome Study

Description

Toydata is a list with the length=3.

Usage

Toydata

Format

A list with the length=3 with names Case, Control, and phy.tree:

Case

A 15 * 35 * 4 Array of relative abundances for 15 Cases

Control

A 15 * 35 * 4 Array of relative abundances for 15 Controls

phy.tree

The phylogenetic tree (phylo-class) object for 35 taxa

Examples

####### Toy data for illustration
library(ggpubr)
library(toOrdinal)
library(reshape2)

Case=Toydata[[1]]
Control=Toydata[[2]]
phy.tree=Toydata[[3]]

### Group comparison

aa=MTA(list(Control,Case),phy.tree=phy.tree)$`Comparison between group 1 and group 2`


aa1=aa[[4]]
aa2=aa[[5]]

for(i in 1:nrow(aa2)) {

 bb1=aa1[i,-1];bb2=aa2[i,-1]
 bb=order(bb1^2/sum(bb1^2),decreasing =TRUE)
 bb1[-c(bb[1:which(cumsum(cumsum(sort(bb1^2/sum(bb1^2),decreasing =TRUE))>0.99)==1)])]=0

 bb1[((bb1+1.96*bb2)>=0 & (bb1-1.96*bb2)<=0)]=NA

 aa1[i,-1]=bb1
}
effect1=aa1
colnames(effect1)=c("trend",unlist(dimnames(Control)[2]))
effect1=data.frame(effect1,check.names =FALSE)
effect1=melt(effect1,id.vars = 1,variable.name = "taxa",value.name = "score")
effect1$trend=paste(sapply(effect1$trend, toOrdinal), "common trend")

effect1=na.omit(effect1)

pp1=ggbarplot(effect1, x = "taxa", y = "score",
             ylab = "Estimated factor score", xlab="", facet.by = "trend",
             add = "mean")+
 facet_wrap(~trend,scales="free")+theme(axis.text.x = element_text(angle = 90, hjust = 1))

######### trend figure

trend1=aa[[2]]

pp2=ggline(trend1, x = "time",y = "Escore",
          ylab = "Common trend", xlab="Week", facet.by = "trend",
          add = "mean")+
 facet_wrap(~trend,scales="free_y")


ggarrange(pp2,pp1,labels = c("(A)", "(B)"), ncol = 2)

#### Classification
aa=MTA(list(Control,Case),Case, phy.tree=phy.tree)

### Group label 1: the first group (Control); 2: the second group (Case)
print(aa)

chanw0/MTA documentation built on July 11, 2021, 7:49 a.m.