Chapter 6 PERMANOVA + beta dispersion + Ordination
Loading packages
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
##
## 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
## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.3 (2022-03-10)
## os macOS Monterey 12.2.1
## system x86_64, darwin17.0
## 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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## 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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