CytoSimplex: visualizing single-cell fates and transitions on a simplex

Abstract

Summary: Cells differentiate to their final fates along unique trajectories, often involving multi-potent progenitors that can produce multiple terminally differentiated cell types. Recent developments in single-cell transcriptomic and epigenomic measurement provide tremendous opportunities for mapping these trajectories. The visualization of single-cell data often relies on dimension reduction methods such as UMAP to simplify high-dimensional single-cell data down to an understandable 2D form. However, these dimension reduction methods are not constructed to allow direct interpretation of the reduced dimensions in terms of cell differentiation. To address these limitations, we developed a new approach that places each cell from a single-cell dataset within a simplex whose vertices correspond to terminally differentiated cell types. Our approach can quantify and visualize current cell fate commitment and future cell potential. We developed CytoSimplex, a standalone open-source package implemented in R and Python that provides simple and intuitive visualizations of cell differentiation in 2D ternary and 3D quaternary plots. We believe that CytoSimplex can help researchers gain a better understanding of cell type transitions in specific tissues and characterize developmental processes.

Availability and implementation: The R version of CytoSimplex is available on Github at https://github.com/welch-lab/CytoSimplex. The Python version of CytoSimplex is available on Github at https://github.com/welch-lab/pyCytoSimplex.

Figure 1.

CytoSimplex shows multi-lineage differentiation potential of progenitor cells in different organs. (A) Input and output of CytoSimplex. CytoSimplex takes a gene-by-cell RNA and/or ATAC count matrix, RNA velocity transition matrix, and cluster annotations as input, and generates ternary or quaternary plots. The coordinates of each cell within the simplex analysis indicate the cell’s differentiation potential toward each terminal fate. The color coding of both the arrows and vertices corresponds to the final fates selected. Together, these simplexes and arrows provide an intuitive visualization of cellular trajectories. (B) RNA velocity of major cell types in mouse bone marrow. The velocity streamline plot is generated by scVelo. The streamlines connect cells on a differentiation path together and arrows indicate path directions. Corresponding to panel (B) and (C), RNA dynamic vectors originate from OCT-stem cells and point to other differentiated cell types, suggesting OCT-stem cells as the cell-of-origin cluster. (C, D) Ternary plots of representative cell types in embryonic mouse bone marrow generated from scRNA and snATAC data. OCT stem cells demonstrate transcriptomic potential toward all three terminal fates, while also showing epigenomic potential toward Reticular and chondrocyte cells. Red arrow and axis: Reticular cluster (RE). Blue: Osteoblast cluster (OS). Green: Chondrocyte cluster (CH). (E) RNA velocity of major cell types in HSPC data. HSC and MEP, functioning as progenitor cell types, serve as two distinct cell-of-origin clusters. (F, G) Ternary and quaternary plots of human hematopoietic stem and progenitor cells (HSPC). Corresponding to their locations on the UMAP plots in (E), progenitor cell types including HSC and MEP show distinct transcriptomic similarities to all terminal fates, while showing identical differentiation potential toward all vertices, regardless of in the ternary or quaternary plot. HSC: Human hematopoietic stem, MEP: Megakaryocyte-erythrocyte progenitor. Blue arrow and axis: Erythrocyte cluster (ER). Yellow: Progenitor Megakaryocyte cluster (PMK). Light blue: Progenitor Dendritic cluster (PDC). Green: Granulocyte cluster (GR). (H) RNA velocity of major cell types in mouse brain atlas. Neural tube and neural crest cell serve as root cells of distinct differentiation trajectories while also sharing a similar location in UMAP plot. (I, J) Ternary and quaternary plots of major cell types in mouse brain atlas. Neural tube and neural crest cell, as two topologically close stem cell types, share similar transcriptomic similarities and differentiation potential toward all fates in ternary and quaternary plots. Green arrow and axis: Glioblast (GL). Orange: Fibroblasts (FI). Gray: Neurons (NE). Blue: Ependymal cells (EP).