ahderojas/ampvis2

Tools for visualising amplicon data

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("MadsAlbertsen/ampvis2")

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.

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

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

Releases

To install a specific (older) release of ampvis2 use "@release" as suffix, fx remotes::install_github("madsalbertsen/[email protected]") to install the first release (2.0) of ampvis2. The latest stable release can be installed with remotes::install_github("madsalbertsen/ampvis2@*release").