alpha_rare_curve: Plotting rarefaction curve for each group

In microbiota/amplicon: Statistics and visualization for microbiome data

Plotting rarefaction curve for each group

Description

Input alpha rare and metadata, and manual set metadata column names. ggplot2 show line plot, and standard error

Usage

alpha_rare_curve(alpha_rare, metadata, groupID = "Group")

Arguments

alpha_rare	alpha rarefaction matrix, typical output of usearch -alpha_div_rare;
metadata	matrix or dataframe, including sampleID and groupID;
groupID	column name for groupID.

Details

By default, returns grouped curve, sample parameter to be continued

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

Examples

# usearch -alpha_div_rare result(alpha_rare), metadata and groupID
alpha_rare_curve(alpha_rare, metadata, "Group")
# alpha_rare, metadata, and groupID using site
alpha_rare_curve(alpha_rare, metadata, groupID="Site")

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