plotTopAbundant: Plot Top Abundant Taxa

In RIVM-IIV-Microbiome/biomeViz: Data visualization for microbiome analytics

Plot Top Abundant Taxa

Description

Plot Top Abundant Taxa

Usage

plotTopAbundant(x, taxa_level = "Family", top = 10L, ...)

Arguments

x	phyloseq object
taxa_level	Taxonomic level at which features are selected. Abundances are summed up for each of the taxa at this level and then top are selected.
top	Numeric value, how many top taxa_level to return. Default top = 100
...	Options to pass ggplot2::geom_jitter()

Details

Plot the features with the highest abundance in all samples, at a user specific taxonomic level.

Value

A ggplot2 object.

Author(s)

Sudarshan A. Shetty

References

Shetty SA (2021). Data visualization for microbiome analytics. https://github.com/microsud/biomeUtils

Examples

library(biomeUtils)
library(biomeViz)
p <- plotTopAbundant(SprockettTHData,
                     taxa_level = "Family",
                     top=10L,
                     alpha = 0.25,
                     shape = 124,
                     color="black",
                     fill = "black",
                     size=3,
                     width = 0.02)
print(p)

RIVM-IIV-Microbiome/biomeViz documentation built on July 20, 2022, 3:52 a.m.