#' @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)
}
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