R/schcl.R

In kendomaniac/rCASC: rCASC reproducible Classification Analysis of Single Cell Sequencing Data

#' @title Assigning cell types
#' @description This function execute scHCL to assign cell types from Han et al  Nature 2020, 581:303-309
#' @param group, a character string. Two options: sudo or docker, depending to which group the user belongs
#' @param file, a character string indicating the folder where input data are located. The input file is the output of scannobyGtf.
#' @param separator, separator used in count file, e.g. '\\t', ','
#' @author Raffaele Calogero, raffaele [dot] calogero [at] unito [dot] it, University of Torino
#' @return return a table summarizing the the cell type association for each cluster. The table is saved in the clusters folder in a file with the name including _celltypes_freq.
#' @examples
#'\dontrun{
#' example to be prepared
#' 
#' schcl(group="docker", file=paste(getwd(),"annotated_lorenz_testSCumi_mm10.csv", sep="/"), separator=",")
#' }
#' @export
schcl <- function(group=c("sudo","docker"), file, separator){
  
  data.folder=dirname(file)
  positions=length(strsplit(basename(file),"\\.")[[1]])
  matrixNameC=strsplit(basename(file),"\\.")[[1]]
  matrixName=paste(matrixNameC[seq(1,positions-1)],collapse="")
  format=strsplit(basename(basename(file)),"\\.")[[1]][positions]
  
  
  
  #running time 1
  ptm <- proc.time()
  #setting the data.folder as working folder
  if (!file.exists(data.folder)){
    cat(paste("\nIt seems that the ",data.folder, " folder does not exist\n"))
    return(2)
  }
  
  #storing the position of the home folder
  home <- getwd()
  setwd(data.folder)
  #initialize status
  system("echo 0 > ExitStatusFile 2>&1")
  
  #testing if docker is running
  test <- dockerTest()
  if(!test){
    cat("\nERROR: Docker seems not to be installed in your system\n")
    system("echo 10 > ExitStatusFile 2>&1")
    setwd(home)
    return(10)
  }
  
  #executing the docker job
  params <- paste("--cidfile ",data.folder,"/dockerID -v ", data.folder, ":/data -d docker.io/repbioinfo/schcl.2021.01 Rscript /home/schcl.R ", matrixName," ",format," ",separator, sep="")
  resultRun <- runDocker(group=group, params=params)
 
  ptm <- proc.time() - ptm
  dir <- dir(data.folder)
  dir <- dir[grep("run.info",dir)]
  if(length(dir)>0){
    con <- file("run.info", "r")
    tmp.run <- readLines(con)
    close(con)
    tmp.run[length(tmp.run)+1] <- paste("user run time mins ",ptm[1]/60, sep="")
    tmp.run[length(tmp.run)+1] <- paste("system run time mins ",ptm[2]/60, sep="")
    tmp.run[length(tmp.run)+1] <- paste("elapsed run time mins ",ptm[3]/60, sep="")
    writeLines(tmp.run,"run.info")
  }else{
    tmp.run <- NULL
    tmp.run[1] <- paste("run time mins ",ptm[1]/60, sep="")
    tmp.run[length(tmp.run)+1] <- paste("system run time mins ",ptm[2]/60, sep="")
    tmp.run[length(tmp.run)+1] <- paste("elapsed run time mins ",ptm[3]/60, sep="")
    
    writeLines(tmp.run,"run.info")
  }
  
  #saving log and removing docker container
  container.id <- readLines(paste(data.folder,"/dockerID", sep=""), warn = FALSE)
  system(paste("docker logs ", substr(container.id,1,12), " &> ",data.folder,"/", substr(container.id,1,12),".log", sep=""))
  system(paste("docker rm ", container.id, sep=""))
  
  system("rm -fR out.info")
  system("rm -fR dockerID")
  system("rm  -fR tempFolderID")
  system(paste("cp ",paste(path.package(package="rCASC"),"containers/containers.txt",sep="/")," ",data.folder, sep=""))
  setwd(home)
}