diversity_beta_test: Beta diversity test (by default we use bray-curtis distance)
In hiplot/animalcules: Interactive microbiome analysis toolkit

Description Usage Arguments Value Examples

Beta diversity test (by default we use bray-curtis distance)

diversity_beta_test(
  MAE,
  tax_level,
  input_beta_method,
  input_select_beta_condition,
  input_select_beta_stat_method,
  input_num_permutation_permanova = 999
)

`MAE`	A multi-assay experiment object
`tax_level`	The taxon level used for organisms
`input_beta_method`	bray, jaccard
`input_select_beta_condition`	Which condition to group samples
`input_select_beta_stat_method`	PERMANOVA,Kruskal-Wallis,Wilcoxon test
`input_num_permutation_permanova`	number of permutations

A plotly object

data_dir = system.file('extdata/MAE.rds', package = 'animalcules')
toy_data <- readRDS(data_dir)
p <- diversity_beta_test(toy_data,
                         tax_level = 'genus',
                         input_beta_method = 'bray',
                         input_select_beta_condition = 'DISEASE',
                         input_select_beta_stat_method = 'PERMANOVA',
                         input_num_permutation_permanova = 999)
p