bio-express_beta_diversity¶ ↑
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
github.com/wwood/bioruby-express_beta_diversity
Cite¶ ↑
If you use this software, please cite one of
Biogems.info¶ ↑
This Biogem is published at (biogems.info/index.html#bio-express_beta_diversity)
Copyright¶ ↑
Copyright © 2013 Ben J. Woodcroft. See LICENSE.txt for further details.