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

Source: R/diversity_beta_test.R

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
)

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

#> Permutation test for adonis under reduced model
#> Terms added sequentially (first to last)
#> Permutation: free
#> Number of permutations: 999
#> 
#> vegan::adonis2(formula = dist.mat ~ condition, data = sam_table, permutations = input_num_permutation_permanova)
#>           Df SumOfSqs      R2      F Pr(>F)
#> condition  1   0.2286 0.01583 0.7722  0.619
#> Residual  48  14.2108 0.98417              
#> Total     49  14.4394 1.00000