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Overview
Taxonomic diversity can be measured using a variety of statistical models. Alpha diversity represents the diversity (richness, evenness, compositional complexity) within a group (e.g. an experiment group) and beta diversity (next section) examines diversity between groups.
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Combined Shannon and Observed ASV. An additional plot combing both Shannon’s index and Observed ASV indices has been included, to compare similarities and differences between these results. As each index uses different units, results for both have been normalised between 0 and 1.
Kruskal-Wallis rank sum test is a rank-based nonparametric test that can be used to determine if there are statistically significant differences between two or more groups. This statistical analysis is provided for each plot, to estimate if there is a significant difference (q.value < 0.05) between all groups.
Pairwise Wilcoxon rank sum test (AKA: Mann-Whitney test is the same as the Kruskal-Wallis test, but applied pairwise to each group (technically, The Kruskal-Wallis test is the generalization of the Wilcoxon rank sum test).
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Preparing your data
The ampvis2 package requires a
Import the
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metadata table
When you ran your sequences through the ampliseq pipeline, you submitted the samples with a metadata file. This file contains information on your samples and variables. We need to import this metadata file to run our analysis on selected variables.
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