alpha_div_plot: Alpha diversity plot

In ericjcgalvez/MicrobiomeWrangler:

Alpha diversity plot

Description

Plots boxplot of alpha-diversity distance together with jitter plot.

Usage

alpha_div_plot(
  phylo,
  x_axis,
  color_var,
  alpha_dist,
  jitter_params = list(),
  boxplot_params = list(),
  ...
)

Arguments

phylo	phyloseq object with alpha-diversity distances in the sample data
x_axis	Determines x variable in plots. Column name in sample data from phyloseq object as character
color_var	Variable in sample data from phyloseq object for color aesthetics
jitter_params	Additional parameters for ggplot2 geom_jitter
boxplot_params	Additional parameters for ggplot2 geom_boxplot
...	More Paremeters
measure	Alpha-diversity distance. Character string of column name of sample data from the phyloseq object. Normally calculated with alpha_div_calc(). Examples: "Observed"; "Simpson"; "Shannon"; "BF_ratio"

Examples

data("mice_B6_N")
phylo <- phyloseq::subset_samples(mice_B6_N, Description == "IN")
phylo <- phyloseq::prune_taxa(phyloseq::taxa_sums(mice_B6_N) > 0, phylo)
phylo_a_dist <- alpha_div_calc(phylo, 2000)
alpha_div_plot(phylo_a_dist, "Vendor", "Vendor", "Simpson")

ericjcgalvez/MicrobiomeWrangler documentation built on April 14, 2022, 6:33 p.m.