Chapter 5 Diversity analysis
Loading packages
5.1 Alpha diveristy
- Calculate the alpha diversity
Notes: the otu table must be counts matrix (rarefied but not trim counts matrix) when you choose Observed etc measures.
dada_ps_rare_genus_alpha <- run_alpha_diversity(ps = dada2_ps_rare_genus,
measures = c("Shannon", "Chao1", "Observed"))
print(dada_ps_rare_genus_alpha)## TempRowNames Group Observed Chao1 se.chao1 Shannon
## 1 S6030 BB 74 74.00000 0.0000000 2.622800
## 2 S6032 BB 38 38.00000 0.0000000 1.711068
## 3 S6033 BB 80 80.16667 0.5431879 2.719495
## 4 S6035 AA 35 35.00000 0.1232013 1.953807
## 5 S6036 BB 95 95.00000 0.0000000 2.942657
## 6 S6037 AA 35 35.00000 0.0000000 1.933007
## 7 S6040 BB 58 58.00000 0.0000000 2.490198
## 8 S6043 AA 65 65.33333 0.9246628 2.098003
## 9 S6045 BB 60 60.00000 0.0000000 2.920363
## 10 S6046 BB 71 71.00000 0.1241166 2.264433
## 11 S6048 BB 66 66.00000 0.0000000 2.630421
## 12 S6049 AA 60 60.00000 0.0000000 2.506885
## 13 S6050 BB 53 53.00000 0.0000000 2.431334
## 14 S6054 BB 84 84.00000 0.0000000 2.769973
## 15 S6055 BB 75 75.00000 0.0000000 2.297388
## 16 S6058 BB 37 37.00000 0.2465985 2.262059
## 17 S6059 AA 71 71.00000 0.0000000 2.682960
## 18 S6060 AA 48 48.00000 0.0000000 1.883809
## 19 S6061 AA 80 80.00000 0.0000000 3.088651
## 20 S6063 BB 38 38.00000 0.0000000 1.543267
## 21 S6065 AA 77 77.00000 0.0000000 2.877568
## 22 S6066 AA 67 67.00000 0.0000000 2.638564
## 23 S6068 BB 40 40.00000 0.0000000 2.100363- visualization
plot_boxplot(data = dada_ps_rare_genus_alpha,
y_index = c("Shannon", "Chao1", "Observed"),
group = "Group",
group_names = c("AA", "BB"),
group_color = c("red", "blue"))
Figure 5.1: Alpha diversity (16s example)
5.2 Beta diversity
- beta dipersion
##
## 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
Figure 5.2: Beta diversity (16s example)
- beta distance
Figure 5.3: Beta distance
5.3 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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## umap 0.2.10.0 2023-02-01 [2] CRAN (R 4.1.2)
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## usethis * 2.2.2 2023-07-06 [2] CRAN (R 4.1.3)
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## 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)
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## Wrench 1.12.0 2021-10-26 [2] Bioconductor
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## 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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