diversity_beta_test {animalcules} | R Documentation |
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