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OpenCyto: An Open Source Infrastructure for Scalable, Robust, Reproducible, and Automated, End-to-End Flow Cytometry Data Analysis

Figure 3

Comparison of OpenCyto automated gating and manual gating (performed with FlowJo and imported and reproduced in R using OpenCyto) for HVTN 080.

A) Box-plots of the paired differences (post-vaccination – baseline) in proportions of cytokine-producing cells from significant cell subsets identified by the linear model (see Supplementary Methods) for each stimulation condition, gating method, and vaccine regimen. Differences between baseline and post-vaccination are background-corrected (stimulated – non-stimulated). There were no significant differences between the observed distributions for manual or OpenCyto gating (paired Wilcoxon test). B) Scatter plots comparing manual gating vs. OpenCyto gating. The per-subject, background-corrected difference between vaccine and baseline is plotted for OpenCyto and manual gating, with concordance correlation coefficients shown for all stimulations.

Figure 3