COLT-Viz: Interactive Visualization of Antibody Lineage Trees

Abstract

Many tools have been developed to visualize phylogenetic trees, which is a traditional technique for evolutionary tree analysis. However, due to the unique characteristics of antibody lineage trees, the phylogenetic method cannot adequately construct proper tree structures for antibody lineages, and many other tools have been developed to address this problem. However, there still lacks of an adequate tool to visualize the resulted antibody lineage structures that are more complicated than phylogenetic trees. In addition, high-throughput sequencing-based antibody repertoire profiling enables the counting of the number of transcripts associated with individual antibody sequences, thus more dimensions need to be encoded in the tree structure visualization. Further, users may wish to manually adjust the tree structure for a special context. When doing so, they may wish to maintain some biological constraints that are applicable in antibody lineage tree structure, such as isotype switching constraints or different sampling constraints. Here, we report an interactive visualization tool (COLT-Viz) designed to display the number of RNA copies, number of somatic hypermutations, and sample collection time associated with each antibody sequence as well as the distance to neighboring sequences for each antibody sequence in the lineage. COLT-Viz also allows users to interactively visualize and edit antibody lineage structures while giving users the option to automatically check biological constraints on the edited structures to ensure accuracy. COLT-Viz takes JSON text format as input files and can easily be used to visualize networks with or without the biological constraints. We believe the amount of information that can be displayed for complex antibody lineages, the interactive interface, and the option of checking for biological constraints make COLT-Viz a versatile tool for antibody lineage tree visualization that will guide further biological discoveries.