ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways.
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.
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:
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.
Check out the blog posts at http://albertsenlab.org/ about selected ampvis2 plotting functions. The posts include details as well as example code:
An interactive Shiny app with some of the basic functionality of ampvis2 can be found at: https://kasperskytte.shinyapps.io/shinyampvis