plot_diversity_stats: Diversity plot with stats

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

Diversity plot with stats

Description

Diversity plot with stats

Usage

plot_diversity_stats(
  x,
  index,
  group = NULL,
  group.colors = c("brown3", "steelblue"),
  dot.opacity = 0.25,
  box.opacity = 0.25,
  violin.opacity = 0.5,
  group.order = NULL,
  stats = TRUE,
  label.format = "p.format",
  ...
)

Arguments

x	phyloseq-class object
index	diversity index. Calculated using microbiome::alpha
group	Grouping variable to compare
group.colors	Colors for plotting groups
dot.opacity	for ggplot alpha to determine opacity for points
box.opacity	for ggplot alpha to determine opacity for box
violin.opacity	for ggplot alpha to determine opacity for violin
group.order	Default is NULL. a list specifing order of x-axis.
stats	Logical TRUE or FALSE. Calls ggpubr::stat_compare_means.
label.format	For ggpubr::stat_compare_means "p.signif" E.g. c("H","CRC","nonCRC")
...	params for ggpubr::stat_compare_means

Examples

## Not run: 
library(microbiomeutilities)
library(ggpubr)
data("zackular2014")
p0 <- zackular2014
mycols <- c("brown3", "steelblue", "grey50")
p.m <- plot_diversity_stats(p0,
  group = "DiseaseState",
  index = "diversity_shannon",
  group.order = c("H", "CRC", "nonCRC"),
  group.colors = mycols
)
print(p.m)

## End(Not run)

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