2.2.5.4 vAMPirus Analyze reports
The final process within the Analyze pipeline generates HTML reports using R Markdown (v2.3; (Xie et al., 2018). By default, an individual summary report containing community composition/diversity, taxonomy and phylogeny results is generated for ASVs, aminotypes, and cASVs. Users provide a metadata file that includes the sample name and category used to group the samples (i.e., sample treatment, location) for alpha and beta diversity analyses. vAMPirus summary reports are interactive and include: 1. Pre- and post-processing read statistics in tables and plots, 2. Rarefaction curves, 3. Shannon’s diversity (H ), Simpson’s diversity (reported as 1-D ), richness and distance to centroid box plots with statistical tests (Shapiro-Wilk normality test, Bartlett test of variance homogeneity, Kruskal-Wallis rank sum test, Wilcox test, ANOVA and Tukey HSD, as appropriate), 4. Two- and three-dimensional NMDS plots (if no convergence, then PCoA plots), 5. Relative abundance bar plots, and 6. Taxonomy and phylogenetic results. An example vAMPirus Analyze summary report can be downloaded and reviewed at github.com/Aveglia/vAMPirusExamples.