plot_taxa_boxplot: Taxonomic Composition Plot boxplot

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

Taxonomic Composition Plot boxplot

Description

Plot taxon abundance for samples.

Usage

plot_taxa_boxplot(
  x,
  taxonomic.level,
  top.otu,
  keep.other = FALSE,
  group,
  title,
  group.colors = NULL,
  group.order = NULL,
  add.violin = TRUE,
  violin.opacity = 0.25,
  box.opacity = 0.25,
  dot.opacity = 0.25,
  dot.size = 2
)

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.
keep.other	TRUE or FALSE. Default is FALSE. This will not plot taxa group as Other
group	Specify main variable of interest. This should be one of the variables in sample_variables(x).
title	title for the plot
group.colors	Colors for plotting groups
group.order	Default is NULL. a list specifing order of x-axis. E.g. c("H","CRC","nonCRC")
add.violin	Loical. If half violoin to the added. Default=TRUE
violin.opacity	If add.violin=TRUE, opacity for violin.
box.opacity	For ggplot alpha to determine opacity for box
dot.opacity	For ggplot alpha to determine opacity for points
dot.size	For ggplot alpha to determine size for points

Value

A ggplot plot object.

Examples

## Not run: 
# Example data
library(microbiomeutilities)
library(RColorBrewer)
data("zackular2014")
ps0 <- zackular2014
mycols <- c("brown3", "steelblue", "grey50")
pn <- plot_taxa_boxplot(ps0,
  taxonomic.level = "Phylum",
  top.otu = 6,
  group = "DiseaseState",
  title = "Relative abudance plot",
  keep.other = FALSE,
  group.order = c("H", "CRC", "nonCRC"),
  group.colors = mycols
)
print(pn + theme_biome_utils())

## End(Not run)

microsud/microbiomeutilities documentation built on Nov. 29, 2022, 12:18 a.m.