Chapter 6 PERMANOVA + beta dispersion + Ordination

Loading packages

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

6.1 PERMANOVA

dada2_ps_per <- run_permanova(ps = dada2_ps_rare_genus, 
                              method = "bray", 
                              columns = "Group")
print(dada2_ps_per)
##       SumsOfSample Df SumsOfSqs   MeanSqs  F.Model         R2 Pr(>F) AdjustedPvalue
## Group           23  1 0.2014665 0.2014665 1.132006 0.05114792  0.328          0.328

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 = dada2_ps_rare_genus, 
                              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 0.017526 0.0175257 2.7119    999  0.109
## Residuals 21 0.135711 0.0064624                     
## 
## Pairwise comparisons:
## (Observed p-value below diagonal, permuted p-value above diagonal)
##         AA    BB
## AA         0.116
## BB 0.11449

6.3 Ordination

We performed ordination by using Principal Coordinate Analysis (PCoA). If you want to try other methods please go to see Chapter 8 for more details.

dada2_ps_ordination <- run_ordination(
                           ps = dada2_ps_rare_genus,
                           group = "Group",
                           method = "PCoA")

plot_Ordination(ResultList = dada2_ps_ordination, 
                group = "Group", 
                group_names = c("AA", "BB"),
                group_color = c("blue", "red"))
PCoA (16s example)

Figure 6.1: PCoA (16s example)

6.4 Systematic Information

devtools::session_info()
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##  ui       RStudio
##  language (EN)
##  collate  en_US.UTF-8
##  ctype    en_US.UTF-8
##  tz       Asia/Shanghai
##  date     2023-10-27
##  rstudio  2023.09.0+463 Desert Sunflower (desktop)
##  pandoc   3.1.1 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
## 
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##  sjmisc                 2.8.9     2021-12-03 [2] CRAN (R 4.1.0)
##  snow                   0.4-4     2021-10-27 [2] CRAN (R 4.1.0)
##  SpiecEasi            * 1.1.2     2022-07-14 [2] Github (zdk123/SpiecEasi@c463727)
##  SPRING                 1.0.4     2022-08-03 [2] Github (GraceYoon/SPRING@3d641a4)
##  stringi                1.7.12    2023-01-11 [2] CRAN (R 4.1.2)
##  stringr                1.5.0     2022-12-02 [2] CRAN (R 4.1.2)
##  SummarizedExperiment * 1.24.0    2021-10-26 [2] Bioconductor
##  survival               3.5-5     2023-03-12 [2] CRAN (R 4.1.2)
##  svglite                2.1.1     2023-01-10 [2] CRAN (R 4.1.2)
##  systemfonts            1.0.4     2022-02-11 [2] CRAN (R 4.1.2)
##  tensorA                0.36.2    2020-11-19 [2] CRAN (R 4.1.0)
##  TH.data                1.1-2     2023-04-17 [2] CRAN (R 4.1.2)
##  tibble               * 3.2.1     2023-03-20 [2] CRAN (R 4.1.2)
##  tidyr                * 1.3.0     2023-01-24 [2] CRAN (R 4.1.2)
##  tidyselect             1.2.0     2022-10-10 [2] CRAN (R 4.1.2)
##  timechange             0.2.0     2023-01-11 [2] CRAN (R 4.1.2)
##  truncnorm              1.0-9     2023-03-20 [2] CRAN (R 4.1.2)
##  tzdb                   0.4.0     2023-05-12 [2] CRAN (R 4.1.3)
##  umap                   0.2.10.0  2023-02-01 [2] CRAN (R 4.1.2)
##  units                  0.8-2     2023-04-27 [2] CRAN (R 4.1.2)
##  urlchecker             1.0.1     2021-11-30 [2] CRAN (R 4.1.0)
##  usethis              * 2.2.2     2023-07-06 [2] CRAN (R 4.1.3)
##  utf8                   1.2.3     2023-01-31 [2] CRAN (R 4.1.2)
##  uuid                   1.1-0     2022-04-19 [2] CRAN (R 4.1.2)
##  vctrs                  0.6.3     2023-06-14 [1] CRAN (R 4.1.3)
##  vegan                * 2.6-4     2022-10-11 [2] CRAN (R 4.1.2)
##  VennDiagram          * 1.7.3     2022-04-12 [2] CRAN (R 4.1.2)
##  VGAM                   1.1-8     2023-03-09 [2] CRAN (R 4.1.2)
##  viridis              * 0.6.3     2023-05-03 [2] CRAN (R 4.1.2)
##  viridisLite          * 0.4.2     2023-05-02 [2] CRAN (R 4.1.2)
##  vroom                  1.6.3     2023-04-28 [2] CRAN (R 4.1.2)
##  webshot                0.5.5     2023-06-26 [2] CRAN (R 4.1.3)
##  WGCNA                  1.72-1    2023-01-18 [2] CRAN (R 4.1.2)
##  withr                  2.5.0     2022-03-03 [2] CRAN (R 4.1.2)
##  Wrench                 1.12.0    2021-10-26 [2] Bioconductor
##  xfun                   0.40      2023-08-09 [1] CRAN (R 4.1.3)
##  XMAS2                * 2.2.0     2023-10-27 [1] local
##  XML                    3.99-0.14 2023-03-19 [2] CRAN (R 4.1.2)
##  xml2                   1.3.5     2023-07-06 [2] CRAN (R 4.1.3)
##  xtable                 1.8-4     2019-04-21 [2] CRAN (R 4.1.0)
##  XVector                0.34.0    2021-10-26 [2] Bioconductor
##  yaml                   2.3.7     2023-01-23 [2] CRAN (R 4.1.2)
##  zCompositions          1.4.0-1   2022-03-26 [2] CRAN (R 4.1.2)
##  zlibbioc               1.40.0    2021-10-26 [2] Bioconductor
##  zoo                    1.8-12    2023-04-13 [2] CRAN (R 4.1.2)
## 
##  [1] /Users/zouhua/Library/R/x86_64/4.1/library
##  [2] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
## 
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