alpha_sample_rare: Plotting sample rarefaction boxplot

In microbiota/amplicon: Statistics and visualization for microbiome data

Plotting sample rarefaction boxplot

Description

Input feature (OTU/ASV) table

Usage

alpha_sample_rare(otutab, length = 18, rep = 30, count_cutoff = 1)

Arguments

otutab	OTU table
length	Number of boxplot, recommend < 30 & sample number
rep	replicate sample times, is the dot number in boxplot, default 30, recommend < 30 & sample number
count_cutoff	cutoff of reads count , default is 1

Details

By default, returns ggplot2

Value

ggplot2 object.

Author(s)

Contact: 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

alpha_boxplot alpha_rare_curve alpha_rare_all

Examples

# feature table, all parameters in default. Length is sample size times(boxplot number), rep is sampling times (dots in boxplot), count_cutoff is minimum reads count as detectable feature
alpha_sample_rare(otutab, length=18, rep=30, count_cutoff=1)
# Change the number of boxplot
alpha_sample_rare(otutab, length=9)
# Cutoff apparently affect trends
alpha_sample_rare(otutab, count_cutoff=9)

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