Simplex Visualization of Cell Fate Similarity in Single-Cell Data

Create simplex plots to visualize the similarity between single-cells and selected clusters in a 1-/2-/3-simplex space. Velocity information can be added as an additional layer. See Liu J, Wang Y et al (2023) for more details.

CytoSimplex

CytoSimplex is an R package that creates simplex plot showing similarity between single-cells and terminals represented by clusters of cells. RNA velocity can be added as another layer of information.

For Python users, we have a Python package CytoSimplex that provides the same functionalities.

Installation

The package is developed and tested under R>=4.2.0. Users can install R following the instruction provided on CRAN. RStudio is a recommended IDE for working with R projects.

To install CytoSimplex in R, run the following command in an R console:

install.packages("CytoSimplex")

For the latest developmental version, run the following command in an R console:

if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_github("welch-lab/CytoSimplex")

Tutorial

We have created a documentation website for posting example tutorials walking through the process from loading the provided example data and creating different types of visualization.

Citation

If you used CytoSimplex in your work, please cite the following work published on Bioinformatics:

Jialin Liu, Yichen Wang, Chen Li, Yichen Gu, Noriaki Ono and Joshua D. Welch, CytoSimplex: Visualizing Single-cell Fates and Transitions on a Simplex, 2025, Bioinformatics, (https://doi.org/10.1093/bioinformatics/btaf119)