R/spatialAnalysisPlus.R

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

#' @title spatial Analysis Plus
#' @description This function analyzes the data that came up from permutationClustering script with spatial transcriptomics data. The function integrates CSS with a score, which is related to the beloging cluster identity of a cell with respect to the other 6 cell neighborhood that surround it.
#' @param group, a character string. Two options: sudo or docker, depending to which group the user belongs
#' @param scratch.folder, a character string indicating the path of the scratch folder
#' @param file, a character string indicating the path of the file, with file name and extension included
#' @param nCluster, Last number of cluster that has to be analyzed
#' @param separator, separator used in count file, e.g. '\\t', ','
#' @param tissuePosition, file with tissue position name with extension
#' @param Sp, Threshold to assign the plus score. 1 mean that all 6 cells, sorrounding the central cell, belong to the same cluster of the central cell. 0.8 out mean 5 out of 6 are of the same cluster of the central cell, 0.6 mean 4 out of 6 are of the same cluster of the central cell. We do not suggest to go below these three value.  
#' @param percentageIncrease, percentage of the CSS score that has to be increased if the Threshold condition is satisfied. 

#' @author Luca Alessandri , alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
#'
#' @return stability plot for each nCluster,two files with score information for each cell for each permutation.
#' @examples
#'\dontrun{
#'spatialAnalysis2(group=c("sudo"), scratch.folder="/home/lucastormreig/temp/", file="/home/lucastormreig/test/spatialAnalysis/spatial/HLNrevised.csv",nCluster=5,separator=",",tissuePosition="/home/lucastormreig/test/spatialAnalysis/spatial/Results/tissue_positions_list.csv",Sp=0.8,percentageIncrease=10)

#'}
#' @export
spatialAnalysis2 <- function(group=c("sudo","docker"), scratch.folder, file,nCluster,separator,tissuePosition,Sp=0.8,percentageIncrease=10){

  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)
  }



  #check  if scratch folder exist
  if (!file.exists(scratch.folder)){
    cat(paste("\nIt seems that the ",scratch.folder, " folder does not exist\n"))
    system("echo 3 > ExitStatusFile 2>&1")
    setwd(data.folder)
    return(3)
  }
  tmp.folder <- gsub(":","-",gsub(" ","-",date()))
  scrat_tmp.folder=file.path(scratch.folder, tmp.folder)
  writeLines(scrat_tmp.folder,paste(data.folder,"/tempFolderID", sep=""))
  cat("\ncreating a folder in scratch folder\n")
  dir.create(file.path(scrat_tmp.folder))
  #preprocess matrix and copying files


if(separator=="\t"){
separator="tab"
}
   
system(paste("cp -r ",data.folder,"/Results/* ",scrat_tmp.folder,sep=""))
system(paste("cp ",data.folder,"/",matrixName,".",format," ",scrat_tmp.folder,sep=""))
system(paste("cp ",tissuePosition," ",scrat_tmp.folder,sep=""))





data.folderT=dirname(tissuePosition)
positionsT=length(strsplit(basename(tissuePosition),"\\.")[[1]])
matrixNameCT=strsplit(basename(tissuePosition),"\\.")[[1]]
matrixNameT=paste(matrixNameCT[seq(1,positionsT-1)],collapse="")
formatT=strsplit(basename(basename(tissuePosition)),"\\.")[[1]][positionsT]




  #executing the docker job
    params <- paste("--cidfile ",data.folder,"/dockerID -v ",scrat_tmp.folder,":/scratch -v ", data.folder, ":/data -d repbioinfo/spatialanalysis2 Rscript /home/extraScore.R ",matrixName," ",nCluster," ",format," ",separator," ",matrixNameT," ",Sp," ",percentageIncrease,sep="")

resultRun <- runDocker(group=group, params=params)

  #waiting for the end of the container work
  if(resultRun==0){
  #  system(paste("cp ", scrat_tmp.folder, "/* ", data.folder, sep=""))
  }
  #running time 2
  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=""))


  #Copy result folder
 cat("Copying Result Folder")
  system(paste("cp -r ",scrat_tmp.folder,"/* ",data.folder,"/Results",sep=""))
  #removing temporary folder
  cat("\n\nRemoving the temporary file ....\n")
  system(paste("rm -R ",scrat_tmp.folder))
  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)
}