Alpha Diversity

Users can visualize alpha diversity with a boxplot comparing different levels within a selected condition by selecting taxonomy levels and target condition. Users can also choose different alpha diversity metrics including Shannon, Inverse Simpson and Gini Simpson.

The statistical test will be performed between levels in the selected target condition. Appropriate statistical test methods will be applied automatically, which may include T-test, Kruskal-Wallis rank sum test, or Wilcoxon rank sum test. Test p-values will be shown in the result table.

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Beta Diversity Heatmap

Users can visualize the beta diversity with a heatmap by selecting the "Beta Diversity" tab within "Diversity" tab. Users should select the taxonomy level they wish to view, as well as the beta diversity metric of interest (including Bray-curtis or Jaccard), and which sample conditions they wish the heatmap to display. Samples can also be sorted by the selected condition.

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Beta Diversity Statistical Test

To check if there is significant beta diversity difference existing between two communities, users can also perform statistical test like PERMANOVA test, Kruskal-Wallis rank sum test, and Wilcoxon rank sum test. Note that the left panel options apply to both beta diversity heatmap and statistical test. Test p-value will be showed in the "Pr(>F)" column from the result table.

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Beta Diversity NMDS Plot

Users may wish to display beta diversity information in an NMDS plot. This can be accomplished using the NMDS tab.

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compbiomed/animalcules documentation built on Feb. 7, 2024, 12:13 p.m.