Chapter 7 Microbial composition
Loading packages
library(XMAS2)
library(dplyr)
library(tibble)
library(phyloseq)
library(ggplot2)A whole picture of the microbial composition.
7.1 Stacked barplot
- XVIZ package
plot_stacked_bar_XIVZ(
phyloseq = dada2_ps_rare,
level = "Phylum",
feature = "Group")
Figure 7.1: Microbial composition (16s example) XVIZ
- XMAS package
plot_StackBarPlot(
ps = dada2_ps_rare,
taxa_level = "Phylum",
group = "Group",
cluster = TRUE)
Figure 7.2: Microbial composition (16s example)
7.2 Core microbiota
- convert absolute abundance into relative abundance
dada2_ps_rare_rb <- XMAS2::normalize(object = dada2_ps_rare,
method = "TSS")
dada2_ps_rare_rb## 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
devtools::session_info()## ─ Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────
## setting value
## version R version 4.1.2 (2021-11-01)
## 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 2022-08-09
## rstudio 2022.07.1+554 Spotted Wakerobin (desktop)
## pandoc 2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
##
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