Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
Programmatic interface to krona visualisations
Ruby
Branch: master

update Gemfile to loosen

latest commit d06876f184
Ben J. Woodcroft authored
Failed to load latest commit information.
lib
spec
.document
.gitignore Initial commit to bio-krona.
.rspec Initial commit to bio-krona.
.travis.yml
Gemfile update Gemfile to loosen
LICENSE.txt
README.md README.md, up the version, fix dependency definitions
Rakefile
VERSION

README.md

bio-krona

Build Status

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bio-krona is currently unpublished.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.

Something went wrong with that request. Please try again.