FROGS Phyloseq: Visualize Data Composition

Phyloseq 1.24.2

Bar plot


Composition plot

R code

Loading packages & data

library(plotly)
source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R")
#if in new session 
#data <- path to Rdata file 
#load(data)

Bar plot

p <- plot_bar(data,fill="Phylum") + facet_wrap(~EnvType, scales = "free_x", nrow = 1) + ggtitle("Bar plot colored by Phylum ")+ theme(plot.title = element_text(hjust = 0.5))
plot(p)

Composition plot

taxaSet1 <- unlist(strsplit(Bacteria, " "))
p <- plot_composition(data,"Kingdom" ,taxaSet1 , "Phylum" ,9, fill="Phylum") + eval(facet_wrap(~EnvType, scales = "free_x", nrow = 1)) + theme(plot.title = element_text(hjust = 0.5)) 
ggplotly(p, tooltip = c("x", "y", "fill"))