examples/example_Deng_scena.R

In shaoqiangzhang/SCENA: Consensus clustering of single-cell RNA-seq data by enhancing network affinity

##install packages
requiredPackages = c('parallel','ggplot2','SNFtool',"apcluster","mclust")
for(p in requiredPackages){
  if(!require(p,character.only = TRUE)) install.packages(p)
  library(p,character.only = TRUE)
}
install.packages("devtools")
devtools::install_github("shaoqiangzhang/SCENA")

library(SCENA)

## Download Deng.zip from https://github.com/shaoqiangzhang/scRNAseq_Datasets
## unzip file to your working directory
##read file
Express=read.table("./Deng.txt", header = T,row.names = 1)

##preprocess input data
Express=datapreprocess(Express,log=T) #"log=T" is to do log-transformation

##do clustering using 5 CPUs
cc=scena_cpu(Express) 

#compute ARI
library(mclust)
presetlabel=c(substring(colnames(Express),1,6)[1:264],"zy","zy","zy","zy")## read the column names as preset cell types
adjustedRandIndex(presetlabel,as.vector(cc)) ## ARI=0.4587225

##plot scatter graph with PCA
plotPCA(Express,cc)