plot_listed_taxa: A boxplot for user specified list of taxa

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

A boxplot for user specified list of taxa

Description

User specifed OTUs are plotted.

Usage

plot_listed_taxa(
  x,
  select.taxa,
  group,
  group.colors,
  dot.opacity = 0.25,
  box.opacity = 0.25,
  group.order = NULL,
  add.violin = TRUE,
  violin.opacity = 0.25,
  panel.arrange = "grid",
  ncol = NULL,
  nrow = NULL
)

Arguments

x	phyloseq-class object.
select.taxa	a character list of taxa to be plotted. eg. select.taxa <- c("OTU-370251", "OTU-311173", "OTU-341024").
group	Grouping variable to compare
group.colors	Colors for plotting groups
dot.opacity	For ggplot alpha to determine opacity for points
box.opacity	For ggplot alpha to determine opacity for box
group.order	Default is NULL. a list specifing order of x-axis.
add.violin	Loical. If half violoin to the added. Default=TRUE
violin.opacity	If add.violin=TRUE, opacity for violin.
panel.arrange	panels "grid" or "wrap" ggplot's facet_XXX
ncol	if wrap, specify number of columns.
nrow	if wrap, specify number of rows.

Details

Useful for instances where user is interested only in some OTUs. For example OTUs reported to be significantly diferent. This can also be used at higher taxonomic levels, output from phyloseq::tax_glom or microbiome::aggregate_taxa.

Value

ggplot object. This can be further modified using ggpubr.

Examples

## Not run: 
# Example data
library(microbiome)
library(microbiomeutilities)
data("zackular2014")
p0 <- zackular2014
p0.f <- format_to_besthit(p0)
select.taxa <- c("OTU-d__denovo31:Dorea", "OTU-d__denovo24:Blautia")
mycols <- c("brown3", "steelblue", "grey50")
p <- plot_listed_taxa(p0.f, select.taxa,
  group = "DiseaseState",
  add.violin = TRUE,
  group.colors = mycols
)
print(p)

## End(Not run)

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