ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.

Installing ampvis2

First, install R (3.5.x or later) and RStudio. Windows users should also install RTools. Then open RStudio as administrator (!) and run the commands below to install ampvis2 from the console:


Tip: For faster installation you can utilise multicore processors by setting the Ncpus argument, fx remotes::install_github("madsalbertsen/ampvis2", Ncpus = 6). Most CPU’s today can run 8 processes simultaneously, so setting it to 6 is a good starting point unless you know you have a CPU with more (logical) cores than 8.

Get started

For a quick guide on how to use ampvis2 go to the Get Started page. Detailed documentation of all ampvis2 functions can be found at the Functions page.

RStudio Docker container

A Docker container based on the rocker/rstudio image is also provided with ampvis2 preinstalled. This is ideal for complete reproducibility and portability. All you need to do is install Docker and then run:

docker run -d \
  -e "PASSWORD=supersafepassword" \
  -v "local/folder/to/mount":/home/rstudio \
  -p 8787:8787 \

Access RStudio server through a browser at http://localhost:8787 with username rstudio. Ideally use a specific version tag, fx v2.7.12, instead of main to not just pull the latest image every time.

Blog posts about ampvis2

Check out the blog posts at about selected ampvis2 plotting functions. The posts include details as well as example code:

Shiny app

An interactive Shiny app with some of the basic functionality of ampvis2 can be found at: