Microbial taxa present in diseased and healthy Southern Green Stink Bugs

Load libraries

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

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

path="/Users/rivers/Documents/collaboratorProjects/nosema-stinkbugs/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)

Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.

names(comp)<-data[,1]

Format data for plotting

compdf<-as.data.frame(comp)
compdf$tissue<-c("FatBody","Ovary","Spermatheca","Egg","FatBody","Ovary","Spermatheca","Egg")
compdf$infection<-c(TRUE,TRUE,TRUE,TRUE,FALSE,FALSE,FALSE,FALSE)
longcomp<- melt(compdf, value.name="clr")

Using tissue, infection as id variables

ggplot(longcomp[longcomp$variable=="OTU_6",], aes(x=tissue, y=clr, fill=infection)) + geom_bar(stat="identity", position="dodge") + ggtitle("Presence of Microsporidian Nosema OTU in Nezara viridula") +     ylab("Centered Log Ratio") + xlab("Tissue")

 ggplot(longcomp[longcomp$variable=="OTU_5",], aes(x=tissue, y=clr, fill=infection)) + geom_bar(stat="identity", position="dodge") + ggtitle("Presence of Salmonella OTU in Nezara viridula") + ylab("Centered Log Ratio") + xlab("Tissue")

Export the data

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