plot_alpha_diversities: plot_alpha_diversities

In microsud/microbiomeutilities-shiny: microbiomeutilities: An R package with utility functions for the microbiome R 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 diversities (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

Useful for instances where user is interested only in some OTUs. For example OTUs reported to be significantly diferent.

Value

ggplot object. This can be further modified using ggpubr.

Examples

## Not run: 
  # Example data
    library(microbiome)
    library(microbiomeUtilities)
    data("biogeogut")
    p0 <- biogeogut
    p <- plot_alpha_diversities(p0, 
    type = "diversities", 
    index.val = "all", 
    plot.type = "stripchart", 
    variableA = "SampleType", 
    palette = "jco")
    
    print(p)
    
          
## End(Not run)

microsud/microbiomeutilities-shiny documentation built on May 7, 2019, 9:38 a.m.