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. 2016 Jun 23;11(6):e0158261.
doi: 10.1371/journal.pone.0158261. eCollection 2016.

MetaTreeMap: An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees

Maxime Hebrard  1 , Todd D Taylor  1
Affiliations

MetaTreeMap: An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees

Maxime Hebrard et al. PLoS One. .

Abstract

Metagenomic samples can contain hundreds or thousands of different species. The most common method to identify these species is to sequence the samples and then classify the reads to nodes along a phylogenic tree. Linear representations of trees with so many nodes face legibility issues. In addition, such views are not optimal for appreciating the read quantity assigned to each node. The problem is exaggerated when comparison between multiple samples is needed. MetaTreeMap adapts a visualization method that addresses these weaknesses. The tree is represented by nested rectangles that illustrate the number or percentage of assigned reads. MetaTreeMap implements various options specific to phylogenic trees that allow for quick overview and investigation of the information. More generally, the goal of this software is to provide the user with the ability to easily display phylogenic trees based on various quantities assigned to the nodes, such as read number, percentage or other values. The tool can be used online at http://metasystems.riken.jp/visualization/treemap/.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Construction of the MetaTreeMap data structure.
(a) Trees representing the two datasets to be compared. (b) Merged tree constructed by the software. Circles are nodes, squares are assigned reads. From the initial datasets (black), MetaTreeMap creates a skeleton tree (blue) with leaves (green).
Fig 2
Fig 2. Visualization of Gammaproteobacteria present in two human gut samples.
(a) Menu bar. (b) Treemap view of Gammaproteobacteria from samples F1-S and F1-T [6]. All phylogenic ranks are displayed, nodes are colored by taxon name. (c) Synchronized table view of the same data.
Fig 3
Fig 3. Comparison of Gammaproteobacteria present in two human gut samples.
Treemap view of Gammaproteobacteria from samples F1-S and F1-T [6]. Phylogenic rank genus and above are displayed, nodes are colored by sample. The percentage of reads by sample is displayed inside square brackets.
See this image and copyright information in PMC

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