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
}