BACKGROUND: Recent advances in high-throughput sequencing allow for much deeper exploitation of natural and engineered microbial communities, and to unravel so-called "microbial dark matter" (microbes that until now have evaded cultivation). Metagenomic analyses result in a large number of genomic fragments (contigs) that need to be grouped (binned) in order to reconstruct draft microbial genomes. While several contig binning algorithms have been developed in the past 2 years, they often lack consensus. Furthermore, these software tools typically lack a provision for the visualization of data and bin characteristics. RESULTS: We present ICoVeR, the Interactive Contig-bin Verification and Refinement tool, which allows the visualization of genome bins. More specifically, ICoVeR allows curation of bin assignments based on multiple binning algorithms. Its visualization window is composed of two connected and interactive main views, including a parallel coordinates view and a dimensionality reduction plot. To demonstrate ICoVeR's utility, we used it to refine disparate genome bins automatically generated using MetaBAT, CONCOCT and MyCC for an anaerobic digestion metagenomic (AD microbiome) dataset. Out of 31 refined genome bins, 23 were characterized with higher completeness and lower contamination in comparison to their respective, automatically generated, genome bins. Additionally, to benchmark ICoVeR against a previously validated dataset, we used Sharon's dataset representing an infant gut metagenome. CONCLUSIONS: ICoVeR is an open source software package that allows curation of disparate genome bins generated with automatic binning algorithms. It is freely available under the GPLv3 license at https://git.list.lu/eScience/ICoVeR . The data management and analytical functions of ICoVeR are implemented in R, therefore the software can be easily installed on any system for which R is available. Installation and usage guide together with the example files ready to be visualized are also provided via the project wiki. ICoVeR running instance preloaded with AD microbiome and Sharon's datasets can be accessed via the website.

Abstract We present a set of interactive techniques for the visual analysis of multi‐dimensional categorical data. Our approach is based on multiple correspondence analysis (MCA), which allows one to analyse relationships, patterns, trends and outliers among dependent categorical variables. We use MCA as a dimensionality reduction technique to project both observations and their attributes in the same 2D space. We use a treeview to show attributes and their domains, a histogram of their representativity in the data set and as a compact overview of attribute‐related facts. A second view shows both attributes and observations. We use a Voronoi diagram whose cells can be interactively merged to discover salient attributes, cluster values and bin categories. Bar chart legends help assigning meaning to the 2D view axes and 2D point clusters. We illustrate our techniques with real‐world application data.

We present a visual analytics solution designed to address prevalent issues in the area of Operational Decision Management (ODM). In ODM, which has its roots in Artificial Intelligence (Expert Systems) and Management Science, it is increasingly important to align business decisions with business goals. In our work, we consider decision models (executable models of the business domain) as ontologies that describe the business domain, and production rules that describe the business logic of decisions to be made over this ontology. Executing a decision model produces an accumulation of decisions made over time for individual cases. We are interested, first, to get insight in the decision logic and the accumulated facts by themselves. Secondly and more importantly, we want to see how the accumulated facts reveal potential divergences between the reality as captured by the decision model, and the reality as captured by the executed decisions. We illustrate the motivation, added value for visual analytics, and our proposed solution and tooling through a business case from the car insurance industry.

We characterize the design space of the algorithms that sequentially tile a rectangular area with smaller, fixed-surface, rectangles. This space consist of five independent dimensions: Order, Size, Score, Recurse and Phrase. Each of these dimensions describe a particular aspect of such layout tasks. This class of layouts is interesting, because, beyond encompassing simple grids, tables and trees, it also includes all kinds of treemaps involving the placement of rectangles. For instance, Slice and dice, Squarified, Strip and Pivot layouts are various points in this five dimensional space. Many classic statistics visualizations, such as 100% stacked bar charts, mosaic plots and dimensional stacking, are also instances of this class. A few new and potentially interesting points in this space are introduced, such as spiral treemaps and variations on the strip layout. The core algorithm is implemented as a JavaScript prototype that can be used as a layout component in a variety of InfoViz toolkits.