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
http://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is currently unpublished.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 http://krona.sourceforge.net
Biogems.info
This Biogem is published at #bio-krona
Copyright
Copyright (c) 2012 Ben J. Woodcroft. See LICENSE.txt for further details.