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. 2018 Apr 1;34(7):1246-1248.
doi: 10.1093/bioinformatics/btx792.

SPRING: a kinetic interface for visualizing high dimensional single-cell expression data

Caleb Weinreb  1 , Samuel Wolock  1 , Allon M Klein  1
Affiliations

SPRING: a kinetic interface for visualizing high dimensional single-cell expression data

Caleb Weinreb et al. Bioinformatics. .

Abstract

Motivation: Single-cell gene expression profiling technologies can map the cell states in a tissue or organism. As these technologies become more common, there is a need for computational tools to explore the data they produce. In particular, visualizing continuous gene expression topologies can be improved, since current tools tend to fragment gene expression continua or capture only limited features of complex population topologies.

Results: Force-directed layouts of k-nearest-neighbor graphs can visualize continuous gene expression topologies in a manner that preserves high-dimensional relationships and captures complex population topologies. We describe SPRING, a pipeline for data filtering, normalization and visualization using force-directed layouts and show that it reveals more detailed biological relationships than existing approaches when applied to branching gene expression trajectories from hematopoietic progenitor cells and cells of the upper airway epithelium. Visualizations from SPRING are also more reproducible than those of stochastic visualization methods such as tSNE, a state-of-the-art tool. We provide SPRING as an interactive web-tool with an easy to use GUI.

Availability and implementation: https://kleintools.hms.harvard.edu/tools/spring.html, https://github.com/AllonKleinLab/SPRING/.

Contact: calebsw@gmail.com or allon_klein@hms.harvard.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
(A) SPRING depicts the dynamic trajectories of hematopoietic progenitor cells as they differentiate from stem cells (HSCs; black circle) into each of seven lineages (colored arms; lineage identities are described in a separate publication, in submission). In contrast, tSNE (B) and diffusion map (C) visualizations of the same data show disconnected clusters of cells or do not capture the full complexity of the data in two dimensions. (D) SPRING and tSNE plots of upper airway epithelium cells from three human donors highlight the reproducibility of SPING visualizations. Cells in (A–D) are colored by marker gene scores. Detailed methodology for producing all plots is available in the Supplementary Material
See this image and copyright information in PMC

References

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