Creat a plot for alpha diversities calculated using the microbiome package

Utility plot function for diversity measures calcualted by microbiome package.

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

Value

ggplot object. This can be further modified using ggpubr

Details

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

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"
)
#> Using sam_rep_nw as id variables
#> Using investigation_type, project_name, DiseaseState, body_product, FOBT.result, material, sam_rep_nw as id variables

print(p)