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.