bio-krona¶ ↑
This biogem is built around Krona, a flashy way of representing hierarchical data.
Usage¶ ↑
bio-krona
is a pretty simple gem, at this stage, and only implements two useful methods. The first, the static method Bio::Krona#html
is to call the krona software itself (specifically, ktImportText
) to generate the visualisation in HTML form.
require 'bio-krona' html = Bio::Krona.html({ ['Sponge','Amphimedon']=>3, ['Sponge','Calciums']=>4, })
It takes as input a hash, where the keys are arrays representing the metadata, and the values are the weightings. In the example above, the data has two levels of hierarchy - first Sponge, second Ampphimedon/Calciums.
The second method collapse
implements a pre-processing step that might be of use when the data is overly complex. It collapses the data so that only a limited number of hierarchy levels are accounted for. The weightings are preseverd by adding up the individual abundances.
Bio::Krona.collapse({ ['Sponge','Amphimedon']=>3, ['Sponge','Calciums']=>4, }, 1) #=> {['Sponge'] => 7}
Installation¶ ↑
gem install bio-krona
Project home page¶ ↑
Information on the source tree, documentation, examples, issues and how to contribute, see
github.com/wwood/bioruby-krona
The BioRuby community is on IRC server: irc.freenode.org, channel: bioruby.
Cite¶ ↑
bio-krona
is currently unpublished. However Krona itself is - see krona.sourceforge.net
Biogems.info¶ ↑
This Biogem is published at #bio-krona
Copyright¶ ↑
Copyright © 2012 Ben J. Woodcroft. See LICENSE.txt for further details.