Chapter 7 Microbial composition

Loading packages

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

A whole picture of the microbial composition.

7.1 Stacked barplot

  • XVIZ package
plot_stacked_bar_XIVZ(
        phyloseq = metaphlan2_ps_LOD_species,
        level = "Phylum",
        feature = "Group")
Microbial composition in XVIZ

Figure 7.1: Microbial composition in XVIZ

  • XMAS package
plot_StackBarPlot(
        ps = metaphlan2_ps_LOD_species,
        taxa_level = "Phylum",
        group = "Group",
        cluster = TRUE)
## [1] "This palatte have 20 colors!"
Microbial composition

Figure 7.2: Microbial composition

7.2 Core microbiota

prevalences <- seq(0.05, 1, 0.05)
detections <- 10^seq(log10(1e-3), log10(0.2), length = 10)

pl_core <- plot_core_taxa(metaphlan2_ps_LOD_species, 
                    plot.type = "heatmap", 
                    colours = gray(seq(0, 1, length=5)),
                    prevalences = prevalences, 
                    detections = detections, 
                    min.prevalence = 0.5)+
    xlab("Detection Threshold (Relative Abundance (%))")

pl_core
Core taxa

Figure 7.3: Core taxa

The degree of color indicates the size of abundance and prevalence.

  • Use core_members to obtain the core taxa. detection for abundance and prevalence for occurrence.
core_taxa_name <- core_members(metaphlan2_ps_LOD_species, 
                               detection = 0.01, 
                               prevalence = 0.5)
print(core_taxa_name)
## [1] "s__Bacteroides_uniformis"        "s__Bacteroides_vulgatus"         "s__Faecalibacterium_prausnitzii" "s__Ruminococcus_sp_5_1_39BFAA"

Result:

Only 4 genera (s__Bacteroides_uniformis, s__Bacteroides_vulgatus, s__Faecalibacterium_prausnitzii and s__Ruminococcus_sp_5_1_39BFAA) passed the threshold of detection and prevalence which we choose.

7.3 Systematic Information

devtools::session_info()
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##  language (EN)
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##  ctype    en_US.UTF-8
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##  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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