plot_density: Plot Density

In microbiome/microbiome: Microbiome Analytics

Plot Density

Description

Plot abundance density across samples for a given taxon.

Usage

plot_density(
  x,
  variable = NULL,
  log10 = FALSE,
  adjust = 1,
  kernel = "gaussian",
  trim = FALSE,
  na.rm = FALSE,
  fill = "gray",
  tipping.point = NULL,
  xlim = NULL
)

Arguments

x	phyloseq-class object or an OTU matrix (samples x phylotypes)
variable	OTU or metadata variable to visualize
log10	Logical. Show log10 abundances or not.
adjust	see stat_density
kernel	see stat_density
trim	see stat_density
na.rm	see stat_density
fill	Fill color
tipping.point	Optional. Indicate critical point for abundance variations to be highlighted.
xlim	X axis limits

Value

A ggplot plot object.

Examples

# Load gut microbiota data on 1006 western adults
# (see help(atlas1006) for references and details)
data(dietswap)
# Use compositional abundances instead of absolute signal
pseq.rel <- transform(dietswap, 'compositional')
# Population density for Dialister spp.; with log10 on the abundance (X)
# axis
library(ggplot2)
p <- plot_density(pseq.rel, variable='Dialister') + scale_x_log10()

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.