FROGS Phyloseq: Multivariate Analysis of Variance

Phyloseq 1.24.2

Multivariate ANOVA performed with adonis


Call:
adonis(formula = dist ~ EnvType, data = metadata, permutations = 9999) 

Permutation: free
Number of permutations: 9999

Terms added sequentially (first to last)

          Df SumsOfSqs MeanSqs F.Model      R2 Pr(>F)    
EnvType    7    7.6565 1.09379  13.699 0.63132  1e-04 ***
Residuals 56    4.4713 0.07984         0.36868           
Total     63   12.1278                 1.00000           
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

R code

Loading packages & data

library(vegan)
## if in new session
# library(phyloseq)
#
## load phyloseq object
# data <- path to Rdata file
# load(data)
# extract sample metadata in a dataframe
metadata <- as(sample_data(data), "data.frame")

## load beta distance matrix
beta_file <- # path to Beta diversity tsv file
A <- read.table(file=beta_file, row.names=1)
beta_dist <- as.dist(A)

With adonis

## change experiment variable (currently EnvType )if you wish
## Multivariate ANOVA performed with adonis
adonis(beta_dist ~ EnvType, data = metadata, perm = 9999)