a R version PAGA (partition-based graph abstraction)
origin code:
pagaR package can be easily installed from Github using devtools:
devtools::install_github("CaoWei-UM/pagaR")
How to use:
library(Seurat)
library(pagaR)
load(pbmc) #pbmc is a seurat object
CalculatePAGA(pbmc,group.by='celltype')
PlotPAGA(pbmc,group.by='celltype')