This repository contains an R file that can be run with Rscript from the cli to create sankey html plots from kraken report files.

Use conda to install R and other dependencies using the environment.yml file.

# Create environment
conda create env -f environment.yml

# Activate environment
conda activate krakenSankey

# Create sankey plot from kraken report
Rscript krakenSankey.R kraken.report sankey_plot.html

Functions in krakenSankey.R requires several packages and attempts to install them for you if they are missing. If an error occurs, please try to install the packages manually.

Most of the code in this repo is 1:1 extracted from Florian Breitwieser's repo pavian.