CytoMelodics Files

Overview

VOLARE (Visualization Of LineAr Regression Elements) is a visual analysis environment designed for multi-omic biological studies. It was specifically developed to highlight microbiome:immune system interplay. It consists of two main parts: (1) R scripts that generate all possible pair-wise regressions of microbes and immune readouts (e.g. CyTOF immunophenotyping, multiplex cytokines), and (2) a JavaScript web application that enhances the traditional “top table” of promising results, providing search, an “mPlot” glyph of the fitted regression model, detailed plots on demand, a network summarizing the relationships in the top table, and the ability to synchronize the network with the top table and vice versa.

The R scripts for data preparation in in volareDataPreparation (zip or tar). There is a hosted version of VOLARE at http://aasix.cytoanalytics.com/volare/

The files needed to host the web application are in volareWepApplication (zip or tar).

Usage highlights

Perform regressions: Given a csv file (each row is a sample or person, each column an analyte) that contains (a) a sample or person identifier, (b) group or cohort for that person (e.g. HIV+ or HIV-), (c) microbiome relative abundance data, and (d) immune readout data, VolarePerformRegressions.R generates regression results for all possible pairs of microbes and immune responses. These can be filtered for statistical significance using an FDR adjustment or permutation testing, resulting in a “best of show” file.

Formatting regression details for web presentation: Given the original csv file and the “best of show” file, VolareFormatRegressionDetails.R gathers more details on the regression results, and marshals these results into a json file. Details include sample level data for the analytes that are included in the “best of show” top table (needed for the detailed regression plots), the end points of the fitted regression lines (needed to plot the fitted lines in both the mPlot and the detailed plot), and configuration data including the names of the cohorts and the colors associated with each cohort in the plots.

The resulting json file can be analyzed using the hosted version of VOLARE at http://aasix.cytoanalytics.com/volare/

Documentation

We provide user guides for data preparation, testing of the data preparation process, and customizing figures for publication. The user guides are pdf files that include narrative, R code, and selected results. The associated R code is also provided in separate files.

Other considerations

Performance: In our hands, we’ve dealt with ~50 microbes and ~100 immune cell populations, which yield ~70 – 150 rows in the top table. We are able to generate both the full regression results and the detailed json file in less than 30 seconds per file.

Web deployment: Should you choose to deploy VOLARE on your own web server, volare.html, logger.js and the two css files should be deployed in the same directory. The lowRes file adjusts the sizing of certain page elements for better visibility on a projected display. logger.js is a wrapper for server-side logging with your tool of choice.