alpha_rare_all: Plotting rarefaction curve for each sample or group
In microbiota/amplicon: Statistics and visualization for microbiome data

alpha_rare_all

R Documentation

Plotting rarefaction curve for each sample or group

Description

Input otutab and metadata, and manual set metadata column names. ggplot2 show line plot, and/or standard error

Usage

alpha_rare_all(
  otu = otutab,
  map = metadata,
  ps = NULL,
  method = "Richness",
  group = "Group",
  start = 100,
  step = 100
)

Arguments

`method`	method for calculate alpha diversity,including "observed", "chao1", "diversity_shannon", "diversity_inverse_simpson", "diversity_gini_simpson", "diversity_fisher", "diversity_coverage", "evenness_camargo", "evenness_pielou", "evenness_simpson", "evenness_evar", "evenness_bulla", "dominance_dbp", "dominance_dmn", "dominance_absolute","dominance_relative", "dominance_simpson", "dominance_core_abundance" , "dominance_gini", "rarity_log_modulo_skewness", "rarity_low_abundance", "rarity_noncore_abundance", "rarity_rare_abundance"
`start`	sampling OTU/ASV table with the start number sequence count;
`step`	number of intervals for sampling
`otutab`	OTU/ASV table;
`metadata`	matrix or data frame, including sampleID and groupID;
`groupID`	column name for groupID, such as "Group".

Value

ggplot2 object.

Author(s)

Contact: Tao Wen 2018203048@njau.edu.cn, Yong-Xin Liu yxliu@genetics.ac.cn

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

Examples

# rare plot with otutab and metadata
result = alpha_rare_all(otu = otutab, map = metadata, group = "Group", method = "chao1", start = 200, step = 200)
result[[1]]# output sample curve plot
result[[2]]# data table
result[[3]]# output group curve plot
result[[4]]# output group curve with CI plot
# rare plot with phyloseq Object
library(phyloseq)
ps = phyloseq(otu_table(otutab, taxa_are_rows=TRUE), sample_data(metadata))
result = alpha_rare_all(ps = ps, group = "Group", method = "chao1", start = 1000, step = 1000)
result[[4]]# output group curve with CI plot

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