plot_alpha_diversities: Creat a plot for alpha diversities calculated using the...

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

Creat a plot for alpha diversities calculated using the microbiome package

Description

Utility plot function for diversity measures calcualted by microbiome package.

Usage

plot_alpha_diversities(
  x,
  type,
  index.val = "all",
  plot.type,
  variableA,
  palette
)

Arguments

x	phyloseq-class object.
type	Either alpha (Diversity Index) or dominance (Dominance Index) or evenness (Evenness Index)
index.val	see global function in microbiome package
plot.type	Three optons c("stripchart", "boxplot", "violin")
variableA	Variable of interested to be checked. This will also be used to color the plot
palette	Any of the RColorBrewer plettes

Details

Uses the microbiome package global function to calculate diversities and then returns a plot.

Value

ggplot object. This can be further modified using ggpubr

Examples

library(microbiome)
library(microbiomeutilities)
data("zackular2014")
p0 <- zackular2014
p <- plot_alpha_diversities(p0,
  type = "dominance",
  index.val = "all",
  plot.type = "stripchart",
  variableA = "DiseaseState",
  palette = "jco"
)

print(p)

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