plot_taxa_boxplot: Taxonomic Composition Plot boxplot

In microsud/microbiomeutilities-shiny: microbiomeutilities: An R package with utility functions for the microbiome R package

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("biogeogut")
    ps1 <- biogeogut
    pn <- plot_taxa_boxplot(ps1,
    taxonomic.level = "Phylum",
    top.otu = 3, VariableA = "SampleType",
    title = "Rel plot", color = "Set2")
    print(pn)

          
## End(Not run)

microsud/microbiomeutilities-shiny documentation built on May 7, 2019, 9:38 a.m.