BetaDiv: Beta diversity plotting and statistics

In microbiota/amplicon: Statistics and visualization for microbiome data

Beta diversity plotting and statistics

Description

Input otutab, metadata and tree or phyloseq object; support 47 distance types (bray, unifrac, wunifrac ...), 8 ordination method (PCoA, NMDS, ...); output ggplot2 figure, data and statistical test result.

Usage

BetaDiv(
  otu = otutab,
  map = metadata,
  tree = tree,
  ps = NULL,
  group = "Group",
  dist = "bray",
  method = "NMDS",
  Micromet = "adonis",
  pvalue.cutoff = 0.05
)

Arguments

otu	OTU/ASV table;
map	Sample metadata;
tree	tree/nwk file;
group	group ID;
dist	distance type, including "unifrac" "wunifrac" "dpcoa" "jsd" "manhattan" "euclidean" "canberra" "bray" "kulczynski" "jaccard" "gower" "altGower" "morisita" "horn" "mountford" "raup" "binomial" "chao" "cao" "w" "-1" "c" "wb" "r" "I" "e" "t" "me" "j" "sor" "m" "-2" "co";
method	DCA, CCA, RDA, NMDS, MDS, PCoA, PCA, LDA;
Micromet	statistics by adonis/anosim/MRPP;
pvalue.cutoff	Pvalue threshold;

Details

By default, input phyloseq object include metadata, otutab and tree The available diversity indices include the following:

• most used indices: bray, unifrac, wunifrac

• other used indices: manhattan, euclidean, jaccard ...

Value

list object including plot, stat table

Author(s)

Contact: Tao Wen [e-mail], Yong-Xin Liu [e-mail]

References

Yong-Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo & Yang Bai. A practical guide to amplicon and metagenomic analysis of microbiome data. Protein Cell, 2020(41), 1-16, DOI: https://doi.org/10.1007/s13238-020-00724-8

Jingying Zhang, Yong-Xin Liu, Na Zhang, Bin Hu, Tao Jin, Haoran Xu, Yuan Qin, Pengxu Yan, Xiaoning Zhang, Xiaoxuan Guo, Jing Hui, Shouyun Cao, Xin Wang, Chao Wang, Hui Wang, Baoyuan Qu, Guangyi Fan, Lixing Yuan, Ruben Garrido-Oter, Chengcai Chu & Yang Bai. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nature Biotechnology, 2019(37), 6:676-684, DOI: https://doi.org/10.1038/s41587-019-0104-4

See Also

beta_pcoa beta_cpcoa

Examples

BetaDiv(otu=otutab_rare, map=metadata, tree=tree, group="Group", dist="bray", method="NMDS", Micromet="adonis", pvalue.cutoff=0.05)

microbiota/amplicon documentation built on April 30, 2023, 1:48 p.m.