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geneVisualization2.R
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geneVisualization2.R
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#' @title GeneVisualization2
#' @description This function executes a ubuntu docker that performs geneVisualization
#' @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 count matrix
#' @param clustering.output, a character string indicating the path of the clustering.output matrix
#' @param geneList, a character string indicating the path of the geneList matrix (no header, no row names)
#' @param separator, separator used in count file, e.g. '\\t', ','
#' @param finalName, name used for plot.
#' @param pvalueFile, name for pvalue file.
#' @param threshold, threshold value.
#' @author Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
#'
#' @return plot
#' @examples
#' \dontrun{
#' dir.create("scratch")
#' geneVisualization2(group="docker", scratch.folder="/scratch", file="/example/log2cpm.csv",clustering.output="/example/log2cpm_fake_clustering.output.csv",geneList="/example/geneList2.csv",separator=",",finalName="yo",pvalueFile="/example/log2cpmfisher.csv",threshold=0.05)
#' }
#' @export
geneVisualization2 <- function(group=c("sudo","docker"), scratch.folder, file,clustering.output,geneList,separator,finalName,pvalueFile,threshold){
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=""))
system(paste("cp ",clustering.output," ",scrat_tmp.folder,"/",sep=""))
system(paste("cp ",pvalueFile," ",scrat_tmp.folder,"/",sep=""))
system(paste("cp ",geneList," ",scrat_tmp.folder,"/",sep=""))
#executing the docker job
params <- paste("--cidfile ",data.folder1,"/dockerID -v ",scrat_tmp.folder,":/scratch -v ", data.folder1, ":/data -d repbioinfo/genevisualizationthreshold Rscript /home/main.R ",basename(file)," ",separator," ",basename(clustering.output)," ",basename(geneList)," ",finalName," ",basename(pvalueFile)," ",threshold,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,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)
}