Conference Poster Year : 2016

SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Abstract

Flow and mass cytometry are experimental techniques used for the characterization of cell phenotypes. With the increase of usable cell markers (up to 50 markers), the identification of cell populations through manual gating is impossible. These high-dimensional data require new computational algorithms to automatically identify cell clusters. The SPADE algorithm has been proposed as a new way to analysis and explore mass-cytometry data. This algorithm performs a density-based down-sampling combined with an agglomerative hierarchical clustering. While SPADE offers new opportunities for identifying cell populations, complementary approaches are needed to improve the characterization of identified cell populations. We present here SPADEVizR, an R package to better visualize and analyze SPADE clustering results. We extended the original SPADE outputs with techniques such as parallel coordinates, heatmaps, multidimensional scaling, volcano plots or streamgraph representations. Moreover, the proposed statistical methods allow the identification of SPADE clusters with relevant biological behaviors. For instance, significantly abundant clusters or differentially enriched clusters can be identified using SPADEVizR. In addition, the integration of cell cluster behaviors with additional phenotypical variables can be performed. We illustrate the capabilities of our R package using a dataset of 15 cytometry profiles with 27 markers each, obtained in the context of a MVA macaque vaccine study. SPADEVizR has been designed in a way that it can be easily used by non bioinformatician experts, but can also be easily customizable by users with more expertise in bioinformatics. Through the multiple visualization and analysis features, SPADEVizR is also a powerful analysis pipeline for high-dimensional cytometry data.
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hal-04862508 , version 1 (03-01-2025)

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Guillaume Gautreau, David Pejoski, Roger Le Grand, Antonio Cosma, Anne-Sophie Beignon, et al.. SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) 2016, Jun 2016, Lyon, France. ⟨10.7490/f1000research.1112446.1⟩. ⟨hal-04862508⟩
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