#' @title hfc, heatmap for clustering
#' @description This function generate heatmap and other plot based on clustering and on a specific gene list
#' @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 counts.table name and extension included
#' @param status, 0 if is raw count, 1 otherwise
#' @param lower.range, the lower range of signal in the heatmap.
#' @param upper.range, the upper range of signal in the heatmap.
#' @author Luca Alessandri , alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
#'
#' @return A heatmap.
#' @examples
#'\dontrun{
#' system("wget http://130.192.119.59/public/heatmap_test.zip")
#' system("unzip heatmap_test.zip")
#' setwd("heatmap_test")
#' heatmapBase(group="docker",scratch.folder="/data/scratch",file=paste(getwd(),"DEfiltered__log2TPM.txt", sep="/"), status=1, lower.range=-1, upper.range=1)
#'}
#' @export
heatmapBase <- function(group=c("sudo","docker"), scratch.folder, file, status=0, lower.range=-1, upper.range=1){
b1=lower.range
b2=upper.range
if(b1<0){b1=paste("/",b1,sep="")}
if(b2<0){b2=paste("/",b2,sep="")}
if(is.null(lower.range)){b1=0}
if(is.null(upper.range)){b2=0}
geneNameControl=1
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]
separator2="tab"
#updating rownames structure
tmp <- read.table(file, sep="\t", header=T, row.names=1)
tmp.n <- rownames(tmp)
if(length(grep("-miR-", tmp.n)) > 0){
tmp.n1 <- strsplit(tmp.n, "-")
tmp.ensembl <- sapply(tmp.n1, function(x){
paste(x[2:length(x)], collapse="-")
})
tmp.symbol <- sapply(tmp.n1, function(x){
paste(x[2:length(x)],collapse='.')
})
}else{
tmp.n <- strsplit(tmp.n, ":")
tmp.ensembl <- sapply(tmp.n, function(x)x[2])
tmp.symbol <- sapply(tmp.n, function(x)x[1])
}
rownames(tmp) <- paste(tmp.ensembl, tmp.symbol, sep=":")
#updating samples names
tmp.c <- names(tmp)
tmp.c <- strsplit(tmp.c, "_")
tmp.samples <- sapply(tmp.c, function(x)x[1])
names(tmp) <- tmp.samples
write.table(tmp, paste(data.folder, "heatmap.txt", sep="/"), sep="\t", col.names=NA)
#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
system(paste("cp ",data.folder,"/heatmap.txt ",scrat_tmp.folder,sep=""))
#executing the docker job
params <- paste("--cidfile ",data.folder,"/dockerID -v ",scrat_tmp.folder,":/scratch -v ", data.folder, ":/data -d docker.io/rcaloger/heatmapbase4seq Rscript /home/main.R heatmap txt tab ",status, " ", b1," ", b2, 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,"/",matrixName,"_heatmap.pdf ",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="docker4seq"),"containers/containers.txt",sep="/")," ",data.folder, sep=""))
setwd(home)
}
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.