Bipartite Graphs for Visualization Analysis of Microbiome Data.
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.
Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic.
Karel
K
Sedlar
Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic.
Petra
P
Videnska
Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic.
Helena
H
Skutkova
Veterinary Research Institute, Brno, Czech Republic.
Ivan
I
Rychlik
Department of Biomedical Engineering, Brno University of Technology, Brno, Czech Republic.
Ivo
I
Provaznik
16S rRNA; OTU table; bipartite graph; graph modularity; metagenomics; visualization analysis