AUTHOR=Baldi Benedetta F. , Vuong Jenny , O’Donoghue Seán I.
TITLE=Assessing 2D visual encoding of 3D spatial connectivity
JOURNAL=Frontiers in Bioinformatics
VOLUME=3
YEAR=2024
URL=https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2023.1232671
DOI=10.3389/fbinf.2023.1232671
ISSN=2673-7647
ABSTRACT=Introduction: When visualizing complex data, the layout method chosen can greatly affect the ability to identify outliers, spot incorrect modeling assumptions, or recognize unexpected patterns. Additionally, visual layout can play a crucial role in communicating results to peers.
Methods: In this paper, we compared the effectiveness of three visual layouts—the adjacency matrix, a half-matrix layout, and a circular layout—for visualizing spatial connectivity data, e.g., contacts derived from chromatin conformation capture experiments. To assess these visual layouts, we conducted a study comprising 150 participants from Amazon’s Mechanical Turk, as well as a second expert study comprising 30 biomedical research scientists.
Results: The Mechanical Turk study found that the circular layout was the most accurate and intuitive, while the expert study found that the circular and half-matrix layouts were more accurate than the matrix layout.
Discussion: We concluded that the circular layout may be a good default choice for visualizing smaller datasets with relatively few spatial contacts, while, for larger datasets, the half- matrix layout may be a better choice. Our results also demonstrated how crowdsourcing methods could be used to determine which visual layouts are best for addressing specific data challenges in bioinformatics.