ampvis2: an R package to analyse and visualise 16S rRNA amplicon data

Key results

1. Claimedamp_load checks and merges a required OTU table (with Kingdom-to-Species taxonomy) and sample metadata, plus optional OTU sequences and a phylogenetic tree, into a single ampvis2 object, so subsetting and filtering act on all components at once.

   Minimum input is two row-by-column files (an OTU table with taxonomy; sample metadata as CSV or Excel); FASTA sequences and a tree are optional; QIIME, mothur and UPARSE outputs can be imported directly; two dedicated functions subset and filter; Fig. 1 outlines the workflow. No usability data are reported. · 2 Implementation and features; Figure legends

2. ClaimedHeatmaps show the most abundant taxa with both colour gradients and exact abundance values, can aggregate OTUs to any taxonomic level by summing their read counts, and can average relative abundances over sample groups defined by metadata variables.

   Taxa built from combined OTU read counts at the chosen rank occupy the second axis, while the first axis shows mean relative abundance for groups set by one or more metadata variables. Authors highlight this as a key feature; no example values or comparison with other heatmap tools are given. · Abstract; 2.1 Flexible heatmaps

3. ClaimedA single function call chains low-abundance OTU filtering, data transformation, distance-matrix calculation, site and species scores, fitting of metadata environmental variables, and ggplot2 plotting, notably via vegan functions, for seven ordination methods common in microbial ecology.

   Seven methods are supported; the output is a 2-dimensional ggplot2 plot that can be rendered interactive through the Plotly JavaScript library. The text does not name the seven methods, the distance measures, or default filtering thresholds. · Abstract; 2.2 Simplified ordination

4. ClaimedBecause all plots are generated with ggplot2, figures are presented as publication-ready and customisable through the wider ggplot2 framework, and interactive rendering with zoom and hover information is provided where possible to help explore larger, more complex datasets.

   Abstract and Introduction assert publication-ready, easily customised figures and interactive zooming and hovering for growing next-generation sequencing datasets; ordination plots are the stated Plotly example. No assessment of figure quality, interactive performance, or dataset-size limits is presented. · Abstract; 1 Introduction; 2.2 Simplified ordination

5. ClaimedFurther functions cover diversity analyses (rarefaction curves, alpha diversity), core-community and co-occurrence network analysis, boxplots and time-series plots, and data subsetting and export, with detailed documentation stated to be available online.

   Functions are only listed; the manuscript gives no worked examples, parameter descriptions, or validation of these analyses and refers readers to the online documentation. · 2.3 Additional functionality