FROGS Phyloseq: Beta Diversity Visualization

Phyloseq 1.24.2

Dist as heatmap plot

R code

Loading packages & data

library(phyloseq)
library(ggplot2)
library(gridExtra)
library(reshape2)
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) 
varExp <- #Experiment variable to split plot
method <- #Beta diversity method name  #To show all available distances: distanceMethodList
fileBeta <- "beta_diversity.tsv"  # output file path

Dist as heatmap plot

## Order samples according to grouping variable
sampleOrder <- levels(reorder(sample_names(data), as.numeric(get_variable(data, varExp)))) 

dist.a <- distance(data, method = method)

pa <- plot_dist_as_heatmap(dist.a, order = sampleOrder, title = method) + 
  theme(plot.title = element_text(hjust = 0.5))
plot(pa)

Save distance matrix

a <- as.matrix(dist.a)
write.table(a, fileBeta, sep="\t", quote=FALSE, col.names=NA)