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