boxplot_alpha: Alpha Boxplot

In microbiome/microbiome: Microbiome Analytics

Alpha Boxplot

Description

Plot alpha index.

Usage

boxplot_alpha(
  x,
  x_var = NULL,
  index = NULL,
  violin = FALSE,
  na.rm = FALSE,
  show.points = TRUE,
  zeroes = TRUE,
  element.alpha = 0.5,
  element.width = 0.2,
  fill.colors = NA,
  outlier.fill = "grey50"
)

Arguments

x	phyloseq-class object
x_var	Metadata variable to map to the horizontal axis.
index	Alpha index to plot. See function alpha.
violin	Use violin version of the boxplot
na.rm	Remove NAs
show.points	Include data points in the figure
zeroes	Include zero counts in diversity estimation. Default is TRUE
element.alpha	Alpha value for plot elements. Controls the transparency of plots elements.
element.width	Width value for plot elements. Controls the transparency of plots elements.
fill.colors	Specify a list of colors passed on to ggplot2 scale_fill_manual
outlier.fill	If using boxplot and and points together how to deal with outliers. See ggplot2 outlier.fill argument in geom_ elements.

Details

A simple wrapper to visualize alpha diversity index.

Value

A ggplot plot object

Examples

data("dietswap")
p <- boxplot_alpha(dietswap, x_var = "sex", index="observed", violin=FALSE, 
                   na.rm=FALSE, show.points=TRUE, zeroes=TRUE, 
                   element.alpha=0.5, element.width=0.2, 
                   fill.colors= c("steelblue", "firebrick"),
                   outlier.fill="white")
p

microbiome/microbiome documentation built on Dec. 12, 2024, 2:45 p.m.