plot_paired_abundances: A paired-boxplot for user specified list of taxa

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

A paired-boxplot for user specified list of taxa

Description

User specified taxa are plotted.

Usage

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.

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.

Value

ggplot object. This can be further modified using ggpubr.

Examples

## Not run: 
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

## End(Not run)

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