Interactive metagenomic visualization in a Web browser

Abstract

Background: A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their hierarchical contexts and their prediction confidence. The current tools for visualizing metagenomic data, however, omit or distort quantitative hierarchical relationships and lack the facility for displaying secondary variables.

Results: Here we present Krona, a new visualization tool that allows intuitive exploration of relative abundances and confidences within the complex hierarchies of metagenomic classifications. Krona combines a variant of radial, space-filling displays with parametric coloring and interactive polar-coordinate zooming. The HTML5 and JavaScript implementation enables fully interactive charts that can be explored with any modern Web browser, without the need for installed software or plug-ins. This Web-based architecture also allows each chart to be an independent document, making them easy to share via e-mail or post to a standard Web server. To illustrate Krona's utility, we describe its application to various metagenomic data sets and its compatibility with popular metagenomic analysis tools.

Conclusions: Krona is both a powerful metagenomic visualization tool and a demonstration of the potential of HTML5 for highly accessible bioinformatic visualizations. Its rich and interactive displays facilitate more informed interpretations of metagenomic analyses, while its implementation as a browser-based application makes it extremely portable and easily adopted into existing analysis packages. Both the Krona rendering code and conversion tools are freely available under a BSD open-source license, and available from: http://krona.sourceforge.net.

Figure 1

The Krona architecture. XML within an XHTML document is used to store chart data within a web page. XML tag nesting is used to describe the hierarchy, while attributes are used to store magnitude and other information about each node. Krona displays these attributes as HTML elements, allowing hyperlinks to supplemental pages for each node. These could be either pages created with the Krona chart, such as BLAST results, or existing web pages, such as NCBI taxonomy pages for the taxonomy IDs of the nodes. The Krona interface JavaScript is linked into the chart either via the Web or locally.

Figure 2

The Krona RSF display. The bacterioplankton metagenome from a vertical profiling of the North Pacific Subtropical Gyre [19] was imported from METAREP and displayed using Krona. Taxonomy nodes are shown as nested sectors arranged from the top level of the hierarchy at the center and progressing outward. Navigational controls are at the top left, and details of the selected node are at the top right. The chart is zoomed to place the domain "Bacteria" at the root and the taxon "Gammaproteobacteria" is shown selected. An interactive version of this chart is available on the Krona website.

Figure 3

Coloring by classification confidence. Human gut sample MH0072 from the MetaHIT project [23] was classified using PhymmBL and displayed using Krona. Abundance can be simultaneously visualized with an accessory attribute by linking it to hue. In this example, hue is used to display classification confidence as reported by PhymmBL. The average confidence value for each node is colored from low (red) to high (green), distinguishing uncertain from certain classifications. An interactive version of this chart is available on the Krona website.

Figure 4

Comparison of three hierarchical display strategies. The acid mine drainage metagenome [21] was classified using MG-RAST and displayed using MG-RAST, MEGAN, and Krona. MG-RAST and MEGAN augment hierarchical node-link diagrams with log-scaled, quantitative charts. Krona displays abundance and hierarchy simultaneously using a radial space-filling display. The Krona chart features a red-green color gradient signifying average e-values of BLAST hits within each taxon, with red being the highest observed e-value (least significant) and green being the lowest (most significant). An interactive version of this chart and a second chart displaying the functional classifications of the same dataset are available on the Krona website.