Load libraries

library(compositions)
library(ggplot2)
library(reshape2)
library(tibble)

Load microbiome OTU table of the V4 region of the SSU rRNA sequences using 515F and 806R primers

path="041918BEillcus515F-pr.fasta.otus.fa.OTU.clean.txt"
data <- read.table(path, header=T, sep="\t")
data2 <-data[,6:13]

#Create a count compositional dataset and perform a clr transformation

dc = ccomp(t(data2))
comp = clr(dc)
names(comp)<-data[,1]

Format the data for plotting

compdf<-as.data.frame(comp)
compdf$tissue<-c("Fat Body","Ovary","Spermatheca","Egg","Fat Body","Ovary","Spermatheca","Egg")
compdf$spotted<-c(TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE)
longcomp<- melt(compdf, value.name="clr")
Using tissue, spotted as id variables
ggplot(longcomp[longcomp$variable=="OTU_6",], aes(x=tissue, y=clr, fill=spotted)) + geom_bar(stat="identity", position="dodge") + ggtitle("Presence of Nosema maddoxi OTU in Nezara viridula") +     ylab("Centered Log Ratio") + xlab("Tissue")

ggplot(data = longcomp[longcomp$variable=="OTU_6",], aes(x = spotted, y = clr, group = tissue)) + geom_boxplot(width=0.3, aes(group=spotted), fill='#A4A4A4') +
  geom_line(aes(color = tissue), size = 1) +
  geom_point(aes(color = tissue), size = 2) +
   ylab("Centered Log Ratio") + xlab("Spotted") + ggtitle("Presence of Nosema maddoxi OTU in Nezara viridula") +
   guides(color=guide_legend("Tissue"))

Examine the CLR values

longcomp[longcomp$variable=="OTU_6",]

Examine the raw counts

t(data[6,])
                                        6                                                                                                                                                                                                    
otu.name                                "OTU_6"                                                                                                                                                                                              
Taxonomy                                "___af327408.1__gi:33340569_  ;k__fungi;p__microsporidia;c__microsporidia;o__microsporidia;f__burenellidae;g__vairimorpha;s__vairimorpha cheracis;superkingdom__eukaryota;suborder__pansporoblastina"
Percent.Homology                        "96.26168"                                                                                                                                                                                           
evalue                                  "6.11e-94"                                                                                                                                                                                           
bitscore                                "347.533"                                                                                                                                                                                            
X1.Nezara.viridula.Infected.Fat.Body    "4014"                                                                                                                                                                                               
X2.Nezara.viridula.Infected.Ovary       "4692"                                                                                                                                                                                               
X3.Nezara.viridula.Infected.Spermatheca "199"                                                                                                                                                                                                
X4.Nezara.viridula.Infected.Egg         "132"                                                                                                                                                                                                
X5.Nezara.viridula.Clean.Fat.Body       "22"                                                                                                                                                                                                 
X6.Nezara.viridula.Clean.Ovary          "24"                                                                                                                                                                                                 
X7.Nezara.viridula.Clean.Spermatheca    "20"                                                                                                                                                                                                 
X8.Nezara.viridula.Clean.Egg            "13"

Export the data

tempdf <-as.data.frame(t(compdf[,1:392]))
tempdf$taxa <-data$Taxonomy
write.table(tempdf, file="clrOTU.txt", sep="\t")
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