Visualizing'omic feature rankings and log-ratios using Qurro.
Visualizing'omic feature rankings and log-ratios using Qurro.
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DOI：
10.1093/nargab/lqaa023
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发表时间：
2020-06-01
影响因子：
4.6
通讯作者：
Knight, Rob
中科院分区：
文献类型：
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作者：
Fedarko, Marcus W;Martino, Cameron;Knight, Rob
许多用于处理组合“组学”数据的工具都会产生特征值，这些值可以进行排名，以描述特征与某种变化的关联。这些值包括微分（描述特征与指定协变量的关联）和特征载荷（描述特征与沿双标图中给定轴沿着变化的关联）。虽然先前的工作已经讨论了使用这些“排名”作为探索特别高或低排名的功能的对数比的起点，这样的探索性分析以前已经使用自定义代码来可视化功能排名和感兴趣的对数比。这种方法很费力，容易出错，并引发有关可重复性的问题。为了解决这些问题，我们引入了Qurro，这是一种交互式可视化特征排名图（“排名图”）以及样本内选定特征对数比图（“样本图”）的工具。Qurro的界面包括各种控件，允许用户从秩图中沿着选择特征以计算对数比;此操作更新秩图（通过突出显示所选特征）和样本图（通过显示样本的当前对数比）。在这里，我们展示了这个独特的界面如何帮助用户简单有效地探索功能排名和对数比。
Many tools for dealing with compositional ''omics' data produce feature-wise values that can be ranked in order to describe features' associations with some sort of variation. These values include differentials (which describe features' associations with specified covariates) and feature loadings (which describe features' associations with variation along a given axis in a biplot). Although prior work has discussed the use of these 'rankings' as a starting point for exploring the log-ratios of particularly high- or low-ranked features, such exploratory analyses have previously been done using custom code to visualize feature rankings and the log-ratios of interest. This approach is laborious, prone to errors and raises questions about reproducibility. To address these problems we introduce Qurro, a tool that interactively visualizes a plot of feature rankings (a 'rank plot') alongside a plot of selected features' log-ratios within samples (a 'sample plot'). Qurro's interface includes various controls that allow users to select features from along the rank plot to compute a log-ratio; this action updates both the rank plot (through highlighting selected features) and the sample plot (through displaying the current log-ratios of samples). Here, we demonstrate how this unique interface helps users explore feature rankings and log-ratios simply and effectively.