Tools for visualising amplicon data

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:

install.packages("remotes")
remotes::install_github("kasperskytte/ampvis2")

Tip: For faster installation you can utilise multicore processors by setting the Ncpus argument, fx remotes::install_github("kasperskytte/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 \
  ghcr.io/kasperskytte/ampvis2:main

Access RStudio server through a browser at http://localhost:8787 with username rstudio. Ideally use a specific version tag, fx v2.7.31, instead of main to not just pull the latest image every time.

Blog posts about ampvis2

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

• ampvis2: The bread and butter of our amplicon analyses: amp_heatmap!
• ampvis2: A guide to ordination and how to use amp_ordinate in R
• Analysing amplicon data, how easy does it get?

Shiny app

An interactive Shiny app with some of the basic functionality of ampvis2 can be found at: https://kasperskytte.shinyapps.io/shinyampvis