Chapter 7 Microbial composition
Loading packages
A whole picture of the microbial composition.
7.1 Stacked barplot
- XVIZ package
Figure 7.1: Microbial composition (16s example) XVIZ
- XMAS package
## [1] "This palatte have 20 colors!"
Figure 7.2: Microbial composition (16s example)
7.2 Core microbiota
- convert absolute abundance into relative abundance
## phyloseq-class experiment-level object
## otu_table() OTU Table: [ 891 taxa and 23 samples ]
## sample_data() Sample Data: [ 23 samples by 1 sample variables ]
## tax_table() Taxonomy Table: [ 891 taxa by 7 taxonomic ranks ]
## phy_tree() Phylogenetic Tree: [ 891 tips and 888 internal nodes ]
## refseq() DNAStringSet: [ 891 reference sequences ]- visualization
prevalences <- seq(0.05, 1, 0.05)
detections <- 10^seq(log10(1e-3), log10(0.2), length = 10)
pl_core <- plot_core_taxa(dada2_ps_rare_rb,
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
Figure 7.3: Core taxa (16s example)
The degree of color indicates the size of abundance and prevalence.
- Use
core_membersto obtain the core taxa. detection for abundance and prevalence for occurrence.
core_taxa_name <- core_members(dada2_ps_rare_rb, detection = 0.01, prevalence = 0.8)
print(core_taxa_name)## [1] "ASV_1"Result:
Only 2 genera (g__Bifidobacterium and g__Blautia) passed the threshold of detection and prevalence which we choose.
7.3 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)
##
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
## package * version date (UTC) lib source
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## ade4 1.7-22 2023-02-06 [2] CRAN (R 4.1.2)
## ALDEx2 1.30.0 2022-11-01 [2] Bioconductor
## annotate 1.72.0 2021-10-26 [2] Bioconductor
## AnnotationDbi 1.60.2 2023-03-10 [2] Bioconductor
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## Biobase * 2.54.0 2021-10-26 [2] Bioconductor
## BiocGenerics * 0.40.0 2021-10-26 [2] Bioconductor
## BiocParallel 1.28.3 2021-12-09 [2] Bioconductor
## biomformat 1.22.0 2021-10-26 [2] Bioconductor
## Biostrings 2.62.0 2021-10-26 [2] Bioconductor
## bit 4.0.5 2022-11-15 [2] CRAN (R 4.1.2)
## bit64 4.0.5 2020-08-30 [2] CRAN (R 4.1.0)
## bitops 1.0-7 2021-04-24 [2] CRAN (R 4.1.0)
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## car 3.1-2 2023-03-30 [2] CRAN (R 4.1.2)
## carData 3.0-5 2022-01-06 [2] CRAN (R 4.1.2)
## caTools 1.18.2 2021-03-28 [2] CRAN (R 4.1.0)
## cccd 1.6 2022-04-08 [2] CRAN (R 4.1.2)
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## compositions 2.0-6 2023-04-13 [2] CRAN (R 4.1.2)
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## GenomicRanges * 1.46.1 2021-11-18 [2] Bioconductor
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## memoise 2.0.1 2021-11-26 [2] CRAN (R 4.1.0)
## metagenomeSeq 1.36.0 2021-10-26 [2] Bioconductor
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## microbiome 1.16.0 2021-10-26 [2] Bioconductor
## mime 0.12 2021-09-28 [2] CRAN (R 4.1.0)
## miniUI 0.1.1.1 2018-05-18 [2] CRAN (R 4.1.0)
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## NetCoMi * 1.0.3 2022-07-14 [2] Github (stefpeschel/NetCoMi@d4d80d3)
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## purrr * 1.0.1 2023-01-10 [2] CRAN (R 4.1.2)
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## 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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