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

In animalcules: Interactive microbiome analysis toolkit

Description

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

Usage

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

Arguments

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

Value

A plotly object

Examples

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

animalcules documentation built on Nov. 8, 2020, 6:47 p.m.