MetaTreeMap

MetaTreeMap (MTM) is a module developed to visualize phylogenic trees where each species (node) has a number of reads (quantity) that map on the reference genome of this species. Each species is represented by a rectangle and its area is proportional to the number of assigned reads. The final figure is nested rectangles representing tree branches.

Citation

Hebrard M, Taylor TD. MetaTreeMap: an alternative visualization method for displaying metagenomic phylogenic trees. PLOS One 11(6):e0158261. (June 23, 2016) PMID 27336370

Web service

MTM can be use online at this address. For more information see the user guide.

Javascript Library

MTM can be use as a javascript library and include in your own webpage.

Download the minify version here. And include the library in your web page like this:

<script type="text/javascript" src="./mtm.min.js"></script>

Or You can use our CDN, and including the latest version.

<script type="text/javascript" src="http://metasystems.riken.jp/visualization/cdn/mtm.min.js"></script>

Add classes to HTML elements that will contain the different views

<div class="mtm-menu"><!--option bar--></div>
<div class="mtm-treemap"><!--treemap view--></div>
<div class="mtm-table"><!--table view--></div>

Call the script with a list of default datafile(s)

<script type="text/javascript">mtm.load(["path/to/file1","path/to/file2"]);</script>

In addition you can pass a config file in second argument (see Documentation for more information).

<script type="text/javascript">mtm.load(["path/to/file1"],"my_config.json");</script>

Exposed functions:

• mtm.version: return the version number

Repository

• data: example data files used as input for MTM. Sequensing data from Kurokawa et al, taxonomic assignation computed with MetaBin. In addition taxonomy.tsv is the list of NCBI taxa with ID and phylogenic rank information (file needed for convertor module).

Kurokawa,K. et al. (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res., 14(4), 169-181.

• html: Documentation and feedback form.
• img: images for documentation.
• js: javascript libraries and sources.
• LICENCE: full licence file.
• README: current abstract
• index.htm: The frontpage of the web interface.
• mtm.min.js: the minify version of MTM (used by the web interface)