Visualizing 'omic feature rankings and log-ratios using Qurro

被引:99
作者
Fedarko, Marcus W. [1 ,2 ]
Martino, Cameron [2 ,3 ]
Morton, James T. [4 ]
Gonzalez, Antonio [5 ]
Rahman, Gibraan [3 ]
Marotz, Clarisse A. [6 ]
Minich, Jeremiah J. [7 ]
Allen, Eric E. [2 ,7 ,8 ]
Knight, Rob [1 ,2 ,5 ,9 ]
机构
[1] Univ Calif San Diego, Dept Comp Sci & Engn, 9500 Gilman Dr, La Jolla, CA 92093 USA
[2] Univ Calif San Diego, Ctr Microbiome Innovat, 9500 Gilman Dr, La Jolla, CA 92093 USA
[3] Univ Calif San Diego, Bioinformat & Syst Biol Program, 9500 Gilman Dr, La Jolla, CA 92093 USA
[4] Flatiron Inst Simons Fdn, 162 Fifth Ave, New York, NY 10010 USA
[5] Univ Calif San Diego, Dept Pediat, 9500 Gilman Dr, La Jolla, CA 92093 USA
[6] Univ Calif San Diego, Dept Biomed Sci, 9500 Gilman Dr, La Jolla, CA 92093 USA
[7] Univ Calif San Diego, Marine Biol Res Div, Scripps Inst Oceanog, 9500 Gilman Dr, La Jolla, CA 92093 USA
[8] Univ Calif San Diego, Dept Biol Sci, 9500 Gilman Dr, La Jolla, CA 92093 USA
[9] Univ Calif San Diego, Dept Bioengn, 9500 Gilman Dr, La Jolla, CA 92093 USA
基金
美国国家科学基金会;
关键词
VEGA;
D O I
10.1093/nargab/lqaa023
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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.
引用
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页数:7
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