Visualizing hierarchies in scRNA-seq data using a density tree-biased autoencoder

MOTIVATION: Single-cell RNA sequencing (scRNA-seq) allows studying the development of cells in unprecedented detail. Given that many cellular differentiation processes are hierarchical, their scRNA-seq data are expected to be approximately tree-shaped in gene expression space. Inference and representation of this tree structure in two dimensions is highly desirable for biological interpretation and exploratory analysis. RESULTS: Our two contributions are an approach for identifying a meaningful tree structure from high-dimensional scRNA-seq data, and a visualization method respecting the tree structure. We extract the tree structure by means of a density-based maximum spanning tree on a vector quantization of the data and show that it captures biological information well. We then introduce density-tree biased autoencoder (DTAE), a tree-biased autoencoder that emphasizes the tree structure of the data in low dimensional space. We compare to other dimension reduction methods and demonstrate the success of our method both qualitatively and quantitatively on real and toy data. AVAILABILITY AND IMPLEMENTATION: Our implementation relying on PyTorch and Higra is available at github.com/hci-unihd/DTAE. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.