Chapter 6 PERMANOVA + beta dispersion + Ordination

Loading packages

library(XMAS2)
library(dplyr)
library(tibble)
library(phyloseq)
library(ggplot2)
library(ggpubr)

6.1 PERMANOVA

metaphlan2_ps_LOD_species_per <- run_permanova(ps = metaphlan2_ps_LOD_species, 
                                               method = "bray", 
                                               columns = "Group")
print(metaphlan2_ps_LOD_species_per)
##       SumsOfSample Df SumsOfSqs   MeanSqs  F.Model        R2 Pr(>F) AdjustedPvalue
## Group           22  1 0.8017593 0.8017593 2.564587 0.1136554  0.002          0.002

The PERMANOVA result of the Group (AdjustedPvalue > 0.05) revealed that the two groups had not the distinct patterns of microbial community.

6.2 beta dispersion

beta_df <- run_beta_diversity(ps = metaphlan2_ps_LOD_species, 
                              method = "bray", 
                              group = "Group")
## 
## Permutation test for homogeneity of multivariate dispersions
## Permutation: free
## Number of permutations: 999
## 
## Response: Distances
##           Df   Sum Sq   Mean Sq      F N.Perm Pr(>F)
## Groups     1 0.003162 0.0031624 0.4485    999  0.514
## Residuals 20 0.141034 0.0070517                     
## 
## Pairwise comparisons:
## (Observed p-value below diagonal, permuted p-value above diagonal)
##         AA    BB
## AA         0.512
## BB 0.51072

6.3 Ordination

We performed ordination by using Principal Coordinate Analysis (PCoA).

metaphlan2_ps_species_ordination <- run_ordination(
                                       ps = metaphlan2_ps_LOD_species,
                                       group = "Group",
                                       method = "PCoA")

# plot_Ordination(ResultList = metaphlan2_ps_species_ordination, 
#                 group = "Group", 
#                 group_names = c("AA", "BB"),
#                 group_color = c("blue", "red"),
#                 circle_type = "ellipse_groups",
#                 sidelinechart = FALSE,
#                 sideboxplot = TRUE)

plot_Ordination(ResultList = metaphlan2_ps_species_ordination, 
                group = "Group", 
                group_names = c("AA", "BB"),
                group_color = c("blue", "red"))
PCoA

Figure 6.1: PCoA

6.4 Systematic Information

devtools::session_info()
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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##  ui       RStudio
##  language (EN)
##  collate  en_US.UTF-8
##  ctype    en_US.UTF-8
##  tz       Asia/Shanghai
##  date     2023-04-12
##  rstudio  2022.07.2+576 Spotted Wakerobin (desktop)
##  pandoc   2.19.2 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
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