4.0 Article

Visualizing 'omic feature rankings and log-ratios using Qurro

Journal

NAR GENOMICS AND BIOINFORMATICS
Volume 2, Issue 2, Pages -

Publisher

OXFORD UNIV PRESS
DOI: 10.1093/nargab/lqaa023

Keywords

-

Funding

  1. IBM Research AI through the AI Horizons Network
  2. UC San Diego Center for Microbiome Innovation
  3. Joint University Microelectronics Program (JUMP)'s Center for Research on Intelligent Storage and Processing-inmemory (CRISP) [GI18518]
  4. University of California San Diego Computer Science and Engineering Department
  5. University of California San Diego Frontiers of Innovation Scholars Program
  6. National Science Foundation [GRFP DGE1144086]
  7. National Institute of Dental and Craniofacial Research through F31 Fellowship [1F31DE028478]
  8. University of California San Diego Center for Microbiome Innovation through Microbial Sciences Graduate Research Fellowship

Ask authors/readers for more resources

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.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.0
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available