plot_taxa_boxplot {microbiomeutilities}R Documentation

Taxonomic Composition Plot boxplot

Description

Plot taxon abundance for samples.

Usage

plot_taxa_boxplot(x, taxonomic.level, top.otu, VariableA, title,
  color = NULL)

Arguments

x

phyloseq-class object

taxonomic.level

Merge the OTUs (for phyloseq object) into a higher taxonomic level. This has to be one from colnames(tax_table(x)).

top.otu

Top number of taxa to plot.

VariableA

Specify main variable of interest. This should be one of the variables in sample_variables(x).

title

title for the plot

color

any of the palette supported by ggpubr/RColorBrewer packages or user specified as c("red", "blue").

Value

A ggplot plot object.

Examples

## Not run: 
# Example data
library(microbiomeutilities)
library(RColorBrewer)
data("zackular2014")
ps1 <- zackular2014
pn <- plot_taxa_boxplot(ps1,
  taxonomic.level = "Phylum",
  top.otu = 3, VariableA = "DiseaseState",
  title = "Rel plot", color = "Set2"
)
print(pn)

## End(Not run)


[Package microbiomeutilities version 0.99.02 Index]