6.1 EMP_alpha_analysis

Alpha diversity analysis is one of the most commonly used downstream microbial analysis methods, mainly used to assess the richness of species. The module EMP_alpha_analysis is based on relative abundance data and has built-in six common alpha diversity analysis methods (including: the Shannon index, Simpson index, Invsimpson index, observd_index, chao1, and ACE), and provides conventional statistical analysis and visualization functions.

6.1.1 Use absolute abundance for diversity analysis

🏷️Example：

MAE |>
  EMP_assay_extract(experiment='taxonomy') |> 
  EMP_alpha_analysis()

6.1.2 Use relative abundance for diversity analysis

Note：
When relative abundance is used, some alpha indices (e.g. ACE, chao1) will not be calculated.

🏷️Example：

MAE |>
  EMP_assay_extract(experiment='taxonomy') |> 
  EMP_decostand(method = 'relative') |>
  EMP_alpha_analysis()

6.1.3 Visualization of difference analysis result

Note：
The module EMP_boxplot can filter the required alpha diversity indicators by specifying the parameter select_metrics.

🏷️Example1：

MAE |>
  EMP_assay_extract(experiment='taxonomy') |> 
  EMP_alpha_analysis() |>
  EMP_boxplot(estimate_group='Group',method='t.test')

🏷️Example2：

MAE |>
  EMP_assay_extract(experiment='taxonomy') |> 
  EMP_alpha_analysis() |>
  EMP_boxplot(estimate_group='Group',method='t.test',
              plot_category='violin',dot_size=4)

6.1 EMP_alpha_analysis