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bio-express_beta_diversity

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Ruby interface to express beta diversity things. Currently, functionality is limited to parsing the output distance matrices, and input "OTU table" format.

Note: this software is under active development!

Installation

gem install bio-express_beta_diversity

Usage

Parsing the distance matrix:

require 'bio-express_beta_diversity'

dists = Bio::EBD::DistanceMatrix.parse_from_file 'Bray-Curtis.cluster.diss'
dists.sample_names #=> ["sample1", "sample2", ... ]
dists.distance('sample1','sample2') #=> 0.251761
dists.distance('sample2','sample1') #=> 0.251761

Parsing the input OTU table:

otus = Bio::EBD::Format.parse_from_file 'my.ebd'
otus.sample_counts.keys #=> ['sample1','sample2', ..]
otus.sample_counts['sample1'] #=> [1.0,4.0,0.0,..]
otus.otu_names #=> ['otu1','otu2','otu3',..]

The otu_names correspond with the order of the sample_counts.values.

The API doc is online. For more code examples see the test files in the source tree.

Project home page

Information on the source tree, documentation, examples, issues and how to contribute, see

http://github.com/wwood/bioruby-express_beta_diversity

Cite

If you use this software, please cite one of

Biogems.info

This Biogem is published at (http://biogems.info/index.html#bio-express_beta_diversity)

Copyright

Copyright (c) 2013 Ben J. Woodcroft. See LICENSE.txt for further details.

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Ruby interface to the express beta diversity distance matrix

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