lorenzgerber / krakenSankey

a re-packaging of the sankey plot function for kraken reports taken from pavian and sankeyD3 from Florian Breitwieser

krakenSankey

Commandline

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

Rscript krakenSankey.R kraken.report

Functions in krakenSankey.R require the sankeyD3 package which itself has a number of dependencies.

Docker

The repository also contains a Dockerfile to build a Docker image that already contains all required R packages. The Docker image can also be obtained from the author's DockerHub.

The syntax for running dockerized:

docker run -v /host/path/to/krakenreport/:/data/ lorenzgerber/krakensankey kraken.report

The result file, kraken.html is written in the mounted directory.

References / Acknowledgments

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