| plot_alpha_diversities {microbiomeutilities} | R Documentation |
microbiome packageUtility plot function for diversity measures calcualted by microbiome package.
plot_alpha_diversities(x, type, index.val = "all", plot.type, variableA, palette)
x |
|
type |
Either alpha (Diversity Index) or dominance (Dominance Index) or evenness (Evenness Index). |
index.val |
see global function in |
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 |
Uses the microbiome package global function to calcualte diversities and then returns
a plot.
ggplot object. This can be further modified using ggpubr.
library(microbiome)
library(microbiomeutilities)
data("zackular2014")
p0 <- zackular2014
p <- plot_alpha_diversities(p0,
type = "diversities",
index.val = "all",
plot.type = "stripchart",
variableA = "DiseaseState",
palette = "jco"
)
print(p)