Bipartite Graphs for Visualization Analysis of Microbiome Data

Bipartite Graphs for Visualization Analysis of Microbiome Data

WoS Article

Visualization analysis plays an important role in metagenomics research. Proper and clear visualization can help researchers get their first insights into data and by selecting different features, also revealing and highlighting hidden relationships and drawing conclusions. To prevent the resulting presentations from becoming chaotic, visualization techniques have to properly tackle the high dimensionality of microbiome data. Although a number of different methods based on dimensionality reduction, correlations, Venn diagrams, and network representations have already been published, there is still room for further improvement, especially in the techniques that allow visual comparison of several environments or developmental stages in one environment. In this article, we represent microbiome data by bipartite graphs, where one partition stands for taxa and the other stands for samples. We demonstrated that community detection is independent of taxonomical level. Moreover, focusing on higher taxonomical levels and the appropriate merging of samples greatly helps improving graph organization and makes our presentations clearer than other graph and network visualizations. Capturing labels in the vertices also brings the possibility of clearly comparing two or more microbial communities by showing their common and unique parts.

Visualization analysis plays an important role in metagenomics research. Proper and clear visualization can help researchers get their first insights into data and by selecting different features, also revealing and highlighting hidden relationships and drawing conclusions. To prevent the resulting presentations from becoming chaotic, visualization techniques have to properly tackle the high dimensionality of microbiome data. Although a number of different methods based on dimensionality reduction, correlations, Venn diagrams, and network representations have already been published, there is still room for further improvement, especially in the techniques that allow visual comparison of several environments or developmental stages in one environment. In this article, we represent microbiome data by bipartite graphs, where one partition stands for taxa and the other stands for samples. We demonstrated that community detection is independent of taxonomical level. Moreover, focusing on higher taxonomical levels and the appropriate merging of samples greatly helps improving graph organization and makes our presentations clearer than other graph and network visualizations. Capturing labels in the vertices also brings the possibility of clearly comparing two or more microbial communities by showing their common and unique parts.

metagenomics; OTU table; 16S rRNA; bipartite graph; visualization analysis; graph modularity

metagenomics; OTU table; 16S rRNA; bipartite graph; visualization analysis; graph modularity

SEDLÁŘ, K.; VÍDEŇSKÁ, P.; ŠKUTKOVÁ, H.; RYCHLÍK, I.; PROVAZNÍK, I.

2017

31.05.2016

Libertas Academica

1176-9343

Evolutionary Bioinformatics

12

S1

United Kingdom of Great Britain and Northern Ireland

17

23

7

https://doi.org/10.4137/EBO.S38546

http://hdl.handle.net/11012/60591

f_5661-EBO-Bipartite-Graphs-for-Visualization-Analysis-of-Microbiome-Data.pdf_7539