A paired-boxplot for user specified list of taxa — plot_paired

User specified taxa are plotted.

plot_paired_abundances(
  x,
  select.taxa = NULL,
  group = NULL,
  group.colors = NULL,
  dot.opacity = 0.25,
  dot.size = 2,
  add.box = FALSE,
  box.opacity = 0.25,
  group.order = NULL,
  add.violin = TRUE,
  violin.opacity = 0.25,
  ncol = NULL,
  nrow = NULL,
  line = NULL,
  line.down = "#7209b7",
  line.stable = "#8d99ae",
  line.up = "#14213d",
  line.na.value = "grey50",
  line.guide = "legend",
  line.opacity = 0.25,
  line.size = 1,
  jitter.width = 0
)

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. x axis, eg. before-after, t1-t2.
group.colors: Colors for plotting groups.
dot.opacity: For ggplot alpha to determine opacity for points.
dot.size: For ggplot point size.
add.box: Logical. If boxplot to the added. Default=TRUE
box.opacity: For ggplot alpha to determine opacity for box.
group.order: Default is NULL. a list specifying order of x-axis.
add.violin: Logical. If half violin to the added. Default=TRUE
violin.opacity: If add.violin=TRUE, opacity for violin.
ncol: If 2 or more taxa to plot, specify number of columns.
nrow: If 2 or more taxa to plot, specify number of rows.
line: Variable to use for lines. E.g. "subject" before-after
line.down: Line Color for change when negative. Decreased abundance.
line.stable: Line Color for no change.
line.up: Line Color for change when positive. Increased abundance.
line.na.value: "grey50" for no/missing observations.
line.guide: "none" to plot guide for line.
line.opacity: Line opacity.
line.size: Size of line to plot.
jitter.width: Value to avoid over plotting by moving points.

Value

ggplot object. This can be further modified using ggpubr.

Details

Useful for instances where user is interested only in some taxa and thier change after an intervention. This can also be used at higher taxonomic levels, output from phyloseq::tax_glom or microbiome::aggregate_taxa.

Examples

if (FALSE) {
library(microbiome)
library(microbiomeutilities)
library(gghalves)
library(tidyr)
data(peerj32) # Source: https://peerj.com/articles/32/
pseq <- peerj32$phyloseq # Ren
pseq.rel <- microbiome::transform(pseq, "compositional")
select.taxa <- c("Akkermansia", "Dialister")
group.colors <- c("brown3", "steelblue", "grey70")
p <- plot_paired_abundances(pseq.rel,
  select.taxa = select.taxa,
  group = "time",
  group.colors = group.colors,
  dot.opacity = 0.25,
  dot.size = 2,
  group.order = NULL,
  line = "subject"
)
p
}