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.