Original title: CytoSimplex: Visualizing Single-cell Fates and Transitions on a Simplex
Authors: Jialin Liu,Yichen Wang,Chen Li,Yichen Gu,Noriaki Ono,Joshua D Welch
In this article, the authors discuss the challenges and limitations of current methods for visualizing cell differentiation trajectories using single-cell data. They introduce a new approach called CytoSimplex, which offers improved visualization of cell fate commitment and future cell potential. The authors explain that traditional methods like UMAP can be misleading and inadequately represent the direction of cell differentiation. To address these issues, CytoSimplex places each cell from a single-cell dataset within a simplex, where the vertices correspond to terminally differentiated cell types. They have developed a standalone open-source package in R and Python that provides simple and intuitive visualizations of cell differentiation in both two-dimensional ternary plots and three-dimensional quaternary plots. The authors believe that CytoSimplex will be a valuable tool for researchers to gain a better understanding of cell type transitions in specific tissues and characterize developmental processes.
Original article: https://www.biorxiv.org/content/10.1101/2023.12.07.570655v1