alpha_boxplot: Plotting alpha diversity boxplot for each group with ANOVA...

In microbiota/amplicon: Statistics and visualization for microbiome data

Plotting alpha diversity boxplot for each group with ANOVA statistics

Description

Input alpha index and metadata, and manual set alpha index and metadata column name ANOVA+TukeyHSD/agricolae::LSD.test calculate p-value, and dplyr summary each group max for p-value groups position. ggplot2 show boxplot, jitter and stat groups.

Usage

alpha_boxplot(alpha_div, metadata, index = "richness", groupID = "Group")

Arguments

alpha_div	alpha diversity matrix, typical output of usearch(-alpha_div)/QIIME/vegan rowname is sample ID, colname is index of alpha diversity;
metadata	matrix or data frame, including sample ID and group ID;
index	index type of alpha diversity;
groupID	column name for group ID.

Details

By default, returns richness diversity index The available diversity indices include the following:

• most used indices: richness, simpson, shannon_2

• other used indices: berger_parker, buzas_gibson, dominance, equitability, jost, jost1, reads, robbins, simpson, shannon_2, shannon_10

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

See Also

alpha_barplot

Examples

# Input alpha index (alpha_div) and metadata, select richness (index type) and Group (catagory)
alpha_boxplot(alpha_div, metadata, "richness", "Group")
# Select shannon_2 (index type) and Site (catagory)
alpha_boxplot(alpha_div = alpha_div, metadata = metadata, index = "shannon_2", groupID = "Site")

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