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 0.002The 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 0.510726.3 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"))
Figure 6.1: PCoA
6.4 Systematic Information
devtools::session_info()## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.2 (2021-11-01)
## os macOS Monterey 12.2.1
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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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