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Plant Direct. 2018 Oct 24;2(10):e00091. doi: 10.1002/pld3.91. eCollection 2018 Oct.

ShinyAIM: Shiny-based application of interactive Manhattan plots for longitudinal genome-wide association studies.

Author information

1
Department of Animal Science University of Nebraska-Lincoln Lincoln Nebraska.
2
Department of Agronomy and Horticulture University of Nebraska-Lincoln Lincoln Nebraska.
3
Department of Animal and Poultry Sciences Virginia Polytechnic Institute and State University Blacksburg Virginia.

Abstract

Owning to advancements in sensor-based, non-destructive phenotyping platforms, researchers are increasingly collecting data with higher temporal resolution. These phenotypes collected over several time points are cataloged as longitudinal traits and used for genome-wide association studies (GWAS). Longitudinal GWAS typically yield a large number of output files, posing a significant challenge to data interpretation and visualization. Efficient, dynamic, and integrative data visualization tools are essential for the interpretation of longitudinal GWAS results for biologists; however, these tools are not widely available to the community. We have developed a flexible and user-friendly Shiny-based online application, ShinyAIM, to dynamically view and interpret temporal GWAS results. The main features of the application include (a) interactive Manhattan plots for single time points, (b) a grid plot to view Manhattan plots for all time points simultaneously, (c) dynamic scatter plots for p-value-filtered selected markers to investigate co-localized genomic regions across time points, (d) and interactive phenotypic data visualization to capture variation and trends in phenotypes. The application is written entirely in the R language and can be used with limited programming experience. ShinyAIM is deployed online as a Shiny web server application at https://chikudaisei.shinyapps.io/shinyaim/, enabling easy access for users without installation. The application can also be launched on a local machine in RStudio.

KEYWORDS:

ShinyAIM; genome‐wide association studies; interactive visualization; longitudinal traits

Conflict of interest statement

The authors declare there are no competing interests.

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