It is common to advise against using 3D to visualize abstract data such as networks, however Ware and Mitchell's 2008 study showed that path tracing in a network is less error prone in 3D than in 2D. It is unclear, however, if 3D retains its advantage when the 2D presentation of a network is improved using edge-routing, and when simple interaction techniques for exploring the network are available. We address this with two studies of path tracing under new conditions. The first study was preregistered, involved 34 users, and compared 2D and 3D layouts that the user could rotate and move in virtual reality with a handheld controller. Error rates were lower in 3D than in 2D, despite the use of edge-routing in 2D and the use of mouse-driven interactive highlighting of edges. The second study involved 12 users and investigated data physicalization, comparing 3D layouts in virtual reality versus physical 3D printouts of networks augmented with a Microsoft HoloLens headset. No difference was found in error rate, but users performed a variety of actions with their fingers in the physical condition which can inform new interaction techniques.

BACKGROUND: Polygenic risk scores (PRS) describe the genomic contribution to complex phenotypes and consistently account for a larger proportion of variance in outcome than single nucleotide polymorphisms (SNPs) alone. However, there is little consensus on the optimal data input for generating PRS, and existing approaches largely preclude the use of imputed posterior probabilities and strand-ambiguous SNPs i.e., A/T or C/G polymorphisms. Our ability to predict complex traits that arise from the additive effects of a large number of SNPs would likely benefit from a more inclusive approach. RESULTS: We developed PRS-on-Spark (PRSoS), a software implemented in Apache Spark and Python that accommodates different data inputs and strand-ambiguous SNPs to calculate PRS. We compared performance between PRSoS and an existing software (PRSice v1.25) for generating PRS for major depressive disorder using a community cohort (N = 264). We found PRSoS to perform faster than PRSice v1.25 when PRS were generated for a large number of SNPs (~ 17 million SNPs; t = 42.865, p = 5.43E-04). We also show that the use of imputed posterior probabilities and the inclusion of strand-ambiguous SNPs increase the proportion of variance explained by a PRS for major depressive disorder (from 4.3% to 4.8%). CONCLUSIONS: PRSoS provides the user with the ability to generate PRS using an inclusive and efficient approach that considers a larger number of SNPs than conventional approaches. We show that a PRS for major depressive disorder that includes strand-ambiguous SNPs, calculated using PRSoS, accounts for the largest proportion of variance in symptoms of depression in a community cohort, demonstrating the utility of this approach. The availability of this software will help users develop more informative PRS for a variety of complex phenotypes.