ShinyAIM: Shiny-based application of interactive Manhattan plots for longitudinal genome-wide association studies
ShinyAIM: Shiny-based application of interactive Manhattan plots for longitudinal genome-wide association studies
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DOI：
10.1002/pld3.91
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发表时间：
2018-10-01
期刊：
影响因子：
3
通讯作者：
Morota, Gota
中科院分区：
文献类型：
--
作者：
Hussain, Waseem;Campbell, Malachy;Morota, Gota
由于基于传感器的非破坏性表型分析平台的进步，研究人员越来越多地收集具有更高时间分辨率的数据。在几个时间点收集的这些表型被归类为纵向性状，并用于全基因组关联研究（GWAS）。纵向GWAS通常会产生大量的输出文件，这对数据解释和可视化构成了重大挑战。高效，动态和综合的数据可视化工具是必不可少的纵向GWAS结果的生物学家的解释，但是，这些工具并没有广泛提供给社会。我们已经开发了一个灵活的和用户友好的基于Shiny的在线应用程序，ShinyAIM，动态查看和解释时间GWAS结果。该应用程序的主要功能包括（a）单个时间点的交互式曼哈顿图，（B）同时查看所有时间点的曼哈顿图的网格图，（c）p值过滤的选定标记物的动态散点图，以研究跨时间点的共定位基因组区域，（d）交互式表型数据可视化，以捕获表型的变化和趋势。该应用程序完全用R语言编写，可以在有限的编程经验下使用。ShinyAIM作为Shiny Web服务器应用程序在线部署在https：//chikudaisei.shinyapps.io/shinyaim/，用户无需安装即可轻松访问。应用程序也可以在RStudio中的本地机器上启动。
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.