Fedarko, M. W. | Search bioRxiv

bioRxiv2020

EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets

Standard workflows for analyzing microbiomes often include the creation and curation of phylogenetic trees. Here we present EMPress, an interactive tool for visualizing trees in the context of microbiome, metabolome, etc. community data scalable beyond modern large datasets like the Earth Microbiome Project. EMPress provides novel functionality--including ordination integration and animations--alongside many standard tree visualization features, and thus simplifies exploratory analyses of many forms of omic data.

bioinformatics↗

bioRxiv2019

Visualizing 'omic feature rankings and log-ratios using Qurro

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"). Qurros 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.

bioinformatics↗