R/logTransform.R

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

#' @title Shifted logarithm transformation
#' @description This function executes a ubuntu docker that performs shifted logarithm transformation (Ahlmann-Eltze Nature Methods, vol. 20, pg. 665, 2023; transformGamPoi Bioconductor package)
#' @param group, a character string. Two options: sudo or docker, depending to which group the user belongs
#' @param file, a character string indicating the path of the count matrix
#' @param separator, separator used in count file, e.g. '\\t', ','
#' @param overdispersion, the simplest count model is the Poisson model. However, the Poisson model assumes that variance = mean. For many applications this is too rigid and the Gamma-Poisson allows a more flexible mean-variance relation (variance = mean + mean^2 * overdispersion).
#' @param pseudo_count, it is set to 4, which is use internally in pseudo-count = 1/( pseudo_count * overdispersion)).
#' @param size_factors,TRUE or False in large scale experiments, each sample is typically of different size (for example different sequencing depths). A size factor is an internal mechanism of GLMs to correct for this effect. normed_sum and poscounts are fairly simple methods and can lead to suboptimal results. For the best performance, I recommend to use deconvolution.
#' @param minimum_overdispersion, the 'acosh_transform' converges against 2 * sqrt(x) for 'overdispersion == 0'. However, the 'shifted_log_transform' would just become '0', thus here we apply the 'minimum_overdispersion' to avoid this behavior.
#' @param scratch.folder, a character string indicating the path of the scratch folder
#' @param outputFolder, a character string indicating the path of the output folder
#' @author Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
#'
#' @return plot
#' @examples
#'\dontrun{
#'dir.create("scratch")
#'logTransform(group="docker",file="/home/gianluca/newFunction/setA.csv",separator=",",scratch.folder="/home/gianluca/newFunction/scratch/","/home/gianluca/newFunction/res/")
#' }
#' @export
logTransform <- function(group=c("sudo","docker"),file,separator, overdispersion=0.05,pseudo_count=4,size_factors=TRUE,minimum_overdispersion=0.001, scratch.folder,outputFolder){

  data.folder1=dirname(file)
  positions1=length(strsplit(basename(file),"\\.")[[1]])
  matrixNameC1=strsplit(basename(file),"\\.")[[1]]
  matrixName1=paste(matrixNameC1[seq(1,positions1-1)],collapse="")
  format1=strsplit(basename(basename(file)),"\\.")[[1]][positions1]

  data.folder=data.folder1
  #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 ",file," ",scrat_tmp.folder,"/",sep=""))
  dir.create(outputFolder)
  #executing the docker job
  params <- paste("--cidfile ",data.folder1,"/dockerID -v ",scrat_tmp.folder,":/scratch -v ", data.folder1, ":/data -d repbioinfo/transformgampoi Rscript /home/main.R ",separator," ",format1," ",matrixName1," ",overdispersion," ",pseudo_count," ",minimum_overdispersion," ",size_factors,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,"/* ",outputFolder,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")
  setwd(home)
}