I can easily generate the chart from properly formatted input (generated from Kraken) like this:
zcat file.fastq.gz | head -4000 | kraken --fastq-input /dev/fd/0 | cut -f2,3 > krona.input ktImportTaxonomy krona.input -o krona.out.html
However I would like to also be able to automatically (programmatically) save this rendered chart as a static PNG, PDF, or similar image format. There does not seem to be any easy way to do this from within the program itself. Any ideas? Here is what I have tried; none of them render correctly, as you can see. Ideally there would be a solution that can be used in a script, running on a headless server.
phantomjs rasterize.js krona.out.html krona_snap.png