Stat: Beta Diversity Visualisation(phyloseq_beta_diversity.py v5.1.0)

## Import packages
library(phyloseq)
library(ggplot2)
library(gridExtra)
library(reshape2)
source(file.path(params$libdir, "graphical_methods.R"))
## Alternative to source all extra function from a github repo
## source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R")

## Setting variables
  ## The Phyloseq object (format rdata)
  # phyloseq <- ""

  ## The experiment variable that you want to analyse
  # varExp <- ""

  ## The methods of beta diversity you want to compute
  ## to see all available distance methods, type distanceMethodList
  ## The most common one are : cc for Jaccard, bray for Bray-Curtis, unifrac and wunifrac for Unifrac and weighted Unifrac
  ## N.B. if the tree is not available in your RData, you cannot choose Unifrac or Weighted Unifrac
  ## You may precise multiple distance by separating them by a comma
  # methods <- ""

## Create input and parameters dataframe
  # params <- data.frame( "phyloseq" = phylose, "varExp" = varExp, "methods" = methods)

## Load data
  ## the phyloseq object
load(params$phyloseq) 

## store methods in list
methods <- as.list(strsplit(params$methods, ",")[[1]])

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

Switch theme Default Coral Gold Steel

Distance as heatmap plot(s)

for (method in methods){
  dist.a <- distance(data, method = method)
  a <- as.matrix(dist.a)
  write.table(a, paste(sep="", method, ".tsv"), sep="\t", quote=FALSE, col.names=NA)
  pa <- plot_dist_as_heatmap(dist.a, order = sampleOrder, title = paste("Heatmap plot of the beta distance :",method)) + 
    theme(plot.title = element_text(hjust = 0.5))
  plot(pa)
}

Reproducibility token

sessioninfo::session_info()

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.1.2 (2021-11-01)
 os       Ubuntu 24.04.2 LTS
 system   x86_64, linux-gnu
 ui       X11
 language fr_FR:en
 collate  en_US.utf8
 ctype    en_US.utf8
 tz       Europe/Paris
 date     2026-01-14
 pandoc   2.19.2 @ /home/maria/miniforge3/envs/frogs@5.1.0/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package          * version   date (UTC) lib source
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 ape                5.7-1     2023-03-13 [1] CRAN (R 4.1.3)
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 permute            0.9-7     2022-01-27 [1] CRAN (R 4.1.3)
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 [1] /home/maria/miniforge3/envs/frogs@5.1.0/lib/R/library

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