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bioRxiv · 10.1101/337485

Continuous visualization of differences between biological conditions in single-cell data

Burns, T. J.·Nolan, G. P.·Samusik, N.
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Abstract

In high-dimensional single cell data, comparing changes in functional markers between conditions is typically done across manual or algorithm-derived partitions based on population-defining markers. Visualizations of these partitions is commonly done on low-dimensional embeddings (eg. t-SNE), colored by per-partition changes. Here, we provide an analysis and visualization tool that performs these comparisons across overlapping k-nearest neighbor (KNN) groupings. This allows one to color low-dimensional embeddings by marker changes without hard boundaries imposed by partitioning. We devised an objective optimization of k based on minimizing functional marker KNN imputation error. Proof-of-concept work visualized the exact location of an IL-7 responsive subset in a B cell developmental trajectory on a t-SNE map independent of clustering. Per-condition cell frequency analysis revealed that KNN is sensitive to detecting artifacts due to marker shift, and therefore can also be valuable in a quality control pipeline. Overall, we found that KNN groupings lead to useful multiple condition visualizations and efficiently extract a large amount of information from mass cytometry data. Our software is publicly available through the Bioconductor package Sconify.

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Burns, T. J., Nolan, G. P., Samusik, N.. 2018-06-02. Continuous visualization of differences between biological conditions in single-cell data. https://doi.org/10.1101/337485

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