#' @title integrationCircos
#' @description This function executes integrationCircos, which plots the integrated results of the analysis performed with gseaXLmHG, seuratIntegrationPermutation, integrationPsblk, integrationPblkae and BC
#' @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 gsea.file, a character string indicating the path of the final_score.csv generated with gseaXLmHG, file, with file name and extension included.
#' @param isc.file, a character string indicating the path of the final_score.csv generated with seuratIntegrationPermutation, file, with file name and extension included. included.
#' @param XYpb.file, a character string indicating the path of the final_score.csv generated with integrationPsblk, file, with file name and extension included.
#' @param pblkae.file, a character string indicating the path of the final_score.csv generated with integrationPblkae, file, with file name and extension included.
#' @param bcsc.file, a character string indicating the path of the FINAL_score.csv generated with BCscWrapper, file, with file name and extension included.
#' @param Xcls.groups, a vector of strings describing the groups of more similar clusters. The optimal order of the clusters can be deduced by the output of integrationPblkae function with the option type="intra". Format: c("1cl6", "1cl2-1cl3", "1cl1-1cl4-1cl5").
#' @param Ycls.groups, a vector of strings describing the order of the clusters. The optimal order of the clusters can be deduced by the output of integrationPblkae function with the option type="intra". Format: c("2cl1-2cl3", "2cl2-2cl4", "2cl5-2cl6")
#' @param outputFolder, where results are placed
#' @author Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
#'
#' @return A picture called integrated_score.png and a file called integrated_score.csv and all the final_scores.csv used to produce the integrated results. The colour ramp for Xgroups is yellow-magenta as instead for the Ygroups is green-blue. Clusters sharing the same colors are those characterized by belonging to the same subgroup detected using integrationPblkae with type="intra". Picture and data used for the integration are lccated in integrated_score folder. Inter cluster edges color code: 1 red; 1-0.7 green; 0.7-0.5 blue; 0.5-0.3 violet; 0.3-0.2 grey; 0.2-0 gold.
#' @examples
#' \dontrun{
#' library(rCASC)
#' integrationCircos(group="docker",
#' scratch.folder="/scratch",
#' gsea.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/GSEA/final_score.csv",
#' isc.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/ISC/final_score.csv",
#' XYpb.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/XYpb/XYpb_final_score.csv",
#' pblkae.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/pblkAE/final_score.csv",
#' bcsc.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/BCsc/FINAL_score.csv",
#' Xcls.order=NULL,
#' Ycls.order=NULL,
#' outputFolder="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2"
#' )
#'
#' integrationCircos(group="docker",
#' scratch.folder="/scratch",
#' gsea.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/GSEA/final_score.csv",
#' isc.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/ISC/final_score.csv",
#' XYpb.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/XYpb/XYpb_final_score.csv",
#' pblkae.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/pblkAE/final_score.csv",
#' bcsc.file="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2/BCsc/FINAL_score.csv",
#' Xcls.groups=c("1cl6", "1cl2-1cl3", "1cl1-1cl4-1cl5"),
#' Ycls.groups=c("2cl1-2cl3", "2cl2-2cl4", "2cl5-2cl6"),
#' outputFolder="/data/reanalysis_on_AIsc/comparing_CRC0327/NT1_NT2"
#' )
#'
#'}
#' @export
integrationCircos <- function(group=c("sudo","docker"), scratch.folder, gsea.file=NULL, isc.file=NULL, XYpb.file=NULL, pblkae.file=NULL, bcsc.file=NULL, Xcls.groups=NULL, Ycls.groups=NULL, outputFolder){
if(!is.null(Xcls.groups)){
Xcls.groups <- paste(Xcls.groups, collapse="_")
}
if(!is.null(Ycls.groups)){
Ycls.groups <- paste(Ycls.groups, collapse="_")
}
data.folder=outputFolder
#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(!is.null(gsea.file)){
if(file.exists(gsea.file)){
system(paste("cp ",gsea.file," ",scrat_tmp.folder,"/gsea_final_score.csv",sep=""))
}
}
if(!is.null(isc.file)){
if(file.exists(isc.file)){
system(paste("cp ",isc.file," ",scrat_tmp.folder,"/isc_final_score.csv",sep=""))
}
}
if(!is.null(XYpb.file)){
if(file.exists(XYpb.file)){
system(paste("cp ",XYpb.file," ",scrat_tmp.folder,"/XYpb_final_score.csv",sep=""))
}
}
if(!is.null(pblkae.file)){
if(file.exists(pblkae.file)){
system(paste("cp ",pblkae.file," ",scrat_tmp.folder,"/pblkae_final_score.csv",sep=""))
}
}
if(!is.null(bcsc.file)){
if(file.exists(bcsc.file)){
system(paste("cp ",bcsc.file," ",scrat_tmp.folder,"/bcsc_final_score.csv",sep=""))
}
}
if(is.null(Xcls.groups) && is.null(Ycls.groups)){
params <- paste("--cidfile ",data.folder,"/dockerID -v ",scrat_tmp.folder,":/scratch -d docker.io/repbioinfo/xlmhg.2021.01 Rscript /home/fs_circors.R", sep="")
}else{
params <- paste("--cidfile ",data.folder,"/dockerID -v ",scrat_tmp.folder,":/scratch -d docker.io/repbioinfo/xlmhg.2021.01 Rscript /home/fs_circors1.R ", Xcls.groups, " ", Ycls.groups, sep="")
}
resultRun <- runDocker(group=group, params=params)
#waiting for the end of the container work
if(resultRun==0){
#system(paste("cp ", scrat_tmp.folder, "/*top* ", 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,"/integrated_score ",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)
}
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