A boxplot for user specified list of taxa

User specifed OTUs are plotted.

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.

Value

ggplot object. This can be further modified using ggpubr.

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.

Examples

if (FALSE) {
# 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)
}