Alpha Diversity Plot

Plot the alpha diversity using a violin plot. alpha_diversity_plots generates plots for all alpha diversity measures.

alpha_diversity_plot(obj, measure = "Shannon",
  group = "TreatmentGroup", select_otu_table = NULL, title = NULL)

alpha_diversity_plots(obj, measures = c("Shannon", "GiniSimpson",
  "InverseSimpson"), group = "TreatmentGroup")

Arguments

obj	An object to be converted to a Taxmap object with create_taxmap.
measure	Select an alpha diversity measure such as Shannon, Fisher, Coverage, GiniSimpson, and InverseSimpson, Default: 'Shannon'
group	The "TreatmentGroup" or similar grouping or column from your metadata to denote sample groups, Default: 'TreatmentGroup'
select_otu_table	DEPRECATED. Choose an otu table to analyze, Default: 'otu_proportions'
title	The title of the plot, Default: NULL
measures	A list of alpha diversity measures such as Shannon, Fisher, Coverage, GiniSimpson, and InverseSimpson, Default: 'c("Shannon", "GiniSimpson", "InverseSimpson")'

Value

Returns an alpha diversity plot.

Returns a melted dataframe.

Details

Alpha diversity helps to determine the species richness (the number of different species in a sample) or evenness (similar abundance level). We prefer to use Shannon as it is better for data generated using the QIIME pipeline.

See also

alpha_diversity_measures, diversity, ggviolin

Other Visualizations: correlation_data, correlation_plots, correlation_plot, heat_tree_parameters, heat_tree_plots, ordination_plots, ordination_plot, plot_limits, save_alpha_diversity_plots, save_correlation_plots, save_heat_tree_plots, save_ordination_plots, save_stacked_barplots, stacked_barplots, stacked_barplot, top_coefficients_barplot

Other Visualizations: correlation_data, correlation_plots, correlation_plot, heat_tree_parameters, heat_tree_plots, ordination_plots, ordination_plot, plot_limits, save_alpha_diversity_plots, save_correlation_plots, save_heat_tree_plots, save_ordination_plots, save_stacked_barplots, stacked_barplots, stacked_barplot, top_coefficients_barplot

Examples

# NOT RUN {
if (interactive()) {
  library(MicrobiomeR)
  data <- analyzed_silva
  plot <- alpha_diversity_plot(obj = data,
                               measure = "Shannon")
  plot
}
# }