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ShinyAIM: Shiny-based Application of Interactive Manhattan Plots for Longitudinal Genome-Wide Association Studies

View ORCID ProfileWaseem Hussain, View ORCID ProfileMalachy Campbell, Harkamal Walia, View ORCID ProfileGota Morota
doi: https://doi.org/10.1101/383026
Waseem Hussain
1Department of Animal Science, University of Nebraska-Lincoln
2Department of Agronomy and Horticulture, University of Nebraska-Lincoln
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Malachy Campbell
1Department of Animal Science, University of Nebraska-Lincoln
2Department of Agronomy and Horticulture, University of Nebraska-Lincoln
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Harkamal Walia
2Department of Agronomy and Horticulture, University of Nebraska-Lincoln
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Gota Morota
1Department of Animal Science, University of Nebraska-Lincoln
3Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University
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Abstract

Due 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 for data interpretation and visualization. Efficient, dynamic, and integrative data visualization tools are essential for the interpretation of longitudinal GWAS results for biologists but 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 (i) an interactive Manhattan plots for single time points, (ii) a grid plot to view Manhattan plots for all time points simultaneously, (iii) dynamic scatter plots for p-value-filtered selected markers to investigate co-localized genomic regions across time points, (iv) 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 the local machine in RStudio.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 06, 2018.
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ShinyAIM: Shiny-based Application of Interactive Manhattan Plots for Longitudinal Genome-Wide Association Studies
Waseem Hussain, Malachy Campbell, Harkamal Walia, Gota Morota
bioRxiv 383026; doi: https://doi.org/10.1101/383026
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ShinyAIM: Shiny-based Application of Interactive Manhattan Plots for Longitudinal Genome-Wide Association Studies
Waseem Hussain, Malachy Campbell, Harkamal Walia, Gota Morota
bioRxiv 383026; doi: https://doi.org/10.1101/383026

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