#' @title Executing clustering with SHARP.
#' @description This function executes a ubuntu docker that produces a specific number of permutations using SHARP as clustering tool.
#' @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 nPerm, number of permutations to be executed
#' @param permAtTime, number of permutations computed in parallel
#' @param percent, percentage of randomly selected cells removed in each permutation
#' @param separator, separator used in count file, e.g. '\\t', ','
#' @param logTen, 1 if the count matrix is already in log10, 0 otherwise
#' @param seed, important value to reproduce the same results with same input
#' @author Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
#'
#' @return A folder Results containing a folder with the name of the experiment, which contains: VioPlot of silhouette cells value for each number of cluster used, a folder with the number of clusters used for SIMLR clustering, which contains: clusterP file with clustering results for each permutation, killedCell file with removed cells in each permutation, clustering.output a sommarize file with general information for each cells
#' @examples
#' \dontrun{
#' system("wget http://130.192.119.59/public/section4.1_examples.zip")
#' unzip("section4.1_examples.zip")
#' setwd("section4.1_examples")
#' sharpBootstrap(group="docker",scratch.folder="/data/scratch/",
#' file=paste(getwd(), "bmsnkn_5x100cells.txt", sep="/"),
#' nPerm=160, permAtTime=8, percent=10, separator="\t",logTen=0,
#' seed=111)
#'}
#' @export
sharpBootstrap <- function(group=c("sudo","docker"), scratch.folder, file, nPerm, permAtTime, percent, separator, logTen=0, seed=111){
permutationClusteringSHARP(group=group,scratch.folder=scratch.folder,file=file,nPerm=nPerm,permAtTime=permAtTime,percent=percent,separator=separator,logTen=logTen,seed=seed)
if(separator == ","){
matrixName=strsplit(file,"/")[[1]][length(strsplit(file,"/")[[1]])]
matrixName <- sub(".csv$", "", matrixName)
}else{
matrixName=strsplit(file,"/")[[1]][length(strsplit(file,"/")[[1]])]
matrixName <- sub(".txt$", "", matrixName)
}
cluster.path <- paste(data.folder=dirname(file), "Results", matrixName, sep="/")
cluster <- as.numeric(list.dirs(cluster.path, full.names = FALSE, recursive = FALSE))
if(length(cluster)==1){
permAnalysisGriph(group=group, scratch.folder=scratch.folder, file=file,cluster,separator,sp=0.8)
} else{
cat("\nIt seems that there is more than one cluster folders in the output of seuratPermutation\n")
cat("Check the results generated by clusterNgriph, and run permAnalysisGriph selecting the cluster of interest\n")
system("echo 5 > ExitStatusFile 2>&1")
return(5)
}
}
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