R/cAMARETTO_DataReadDownload.R

In broadinstitute/CommunityAMARETTO: CommunityAMARETTO: A Computational Tool for the Discovery of Shared and Distinct Regulatory Mechanisms Across Biological Systems

#' @title cAMARETTO_Read
#' 
#' Reads the AMARETTOinit and AMARETTOresults from (zipped)
#'  AMARETTO directories. The names of the list are assigned as run names.
#'
#' @param unzipParentDirectory the address where the files are unzipped in
#' @param AMARETTOdirectories a list of AMARETTO directories 
#'
#' @return a list with the AMARETTOinit and AMARETTOresults
#' 
#' @importFrom  rlist list.append
#' @importFrom  stringr str_count
#' @importFrom  utils zip unzip
#' @examples
#' try(
#'  AMARETTO_all <- cAMARETTO_Read(list(LIHC="LIHC.zip",BLCA="BLCA.zip"))
#'  )
#' @export
cAMARETTO_Read<-function(AMARETTOdirectories,unzipParentDirectory=getwd()){
    directories_to_unzip <- AMARETTOdirectories[
        grepl("zip$",AMARETTOdirectories)]
    # unzip directories if needed
    if(length(directories_to_unzip)>0){
        for(i in seq_len(length(directories_to_unzip))){
            if(file.exists(directories_to_unzip[[i]])){
                if (
                    stringr::str_count(directories_to_unzip[[i]],
                    "/")>=str_count(directories_to_unzip[[i]],
                    "\\\\")){
                            #linux or windows addresses
                            extdir=paste(sub("/$","",
                                unzipParentDirectory),
                                names(directories_to_unzip)[i],sep="/")
                            }
                else{
                    extdir=paste(sub("\\\\$","",unzipParentDirectory),
                        names(directories_to_unzip)[i],sep="\\")
                    }
            unzip(directories_to_unzip[[i]],exdir=extdir,junkpaths = TRUE)
            AMARETTOdirectories[[i]]<-extdir
            } else {
            stop(paste0("The ",directories_to_unzip[[i]]," is not existing"))
            }
        }
    }

    AMARETTOdirectories <- lapply(AMARETTOdirectories,
                                function(x) sub(".zip","",x))
    AMARETTOinit_all<-list()
    AMARETTOresults_all<-list()
    i = 1
    for (AMARETTOdirectory in AMARETTOdirectories){
        tmp = load(paste0(AMARETTOdirectory,"/amarettoInit.RData"))
        assign(paste0("AMARETTOinit_",names(AMARETTOdirectories)[i]),get(tmp))
        rm(tmp)
        AMARETTOinit_all<-rlist::list.append(AMARETTOinit_all,
                            eval(parse(text=paste0("AMARETTOinit_",
                                    names(AMARETTOdirectories)[i])),
                                        envir = environment()))
    tmp = load(paste0(AMARETTOdirectory,"/amarettoResults.RData"))
    assign(paste0("AMARETTOresults_",names(AMARETTOdirectories)[i]),get(tmp))
    rm(tmp)
    AMARETTOresults_all<-list.append(AMARETTOresults_all,eval(parse(
    text=paste0("AMARETTOresults_",
                        names(AMARETTOdirectories)[i])),
                        envir = environment()))
    i = i + 1
    }
    names(AMARETTOinit_all)<-names(AMARETTOdirectories)
    names(AMARETTOresults_all)<-names(AMARETTOdirectories)
    return(list(AMARETTOinit_all = AMARETTOinit_all,
                AMARETTOresults_all = AMARETTOresults_all))
}


#' Title cAMARETTO_HTML_Read
#'
#' @param unzipParentDirectory a directory address
#'  where the html report files are unzipped to
#' @param HTMLsAMARETTOZips a list of directories for each
#'  AMARETTO HTML.zip report, the output of AMARETTO.
#'
#' @return a named vector with directories of unzipped HTML reprorts.
#' @importFrom  utils zip unzip
#' @export
#' 
#' @examples 
#' try(
#' cAMARETTO_HTML_Read(list(TCGA_LIHC="TCGA_LIHC_report.zip",
#' TCGA_GBM="TCGA_GBM_report.zip"))
#' )

cAMARETTO_HTML_Read<-function(HTMLsAMARETTOZips,unzipParentDirectory=getwd()){
    HTMLsAMARETTOlist<-rep(NA,length(HTMLsAMARETTOZips))
    if (! is.null(HTMLsAMARETTOZips) ){
        for (i in seq_len(length(HTMLsAMARETTOZips))){
            if(file.exists(HTMLsAMARETTOZips[[i]])){
                extdir=sub("/$","",unzipParentDirectory)
                utils::unzip(HTMLsAMARETTOZips[[i]],exdir=extdir)
                print(paste(HTMLsAMARETTOZips[[i]],"is unzipped to",extdir))
                HTMLsAMARETTOlist[i]<-sub(".zip","",paste(extdir,
                    basename(HTMLsAMARETTOZips[[i]]),sep="/"))
            }
        else{
            stop(paste0("The ",HTMLsAMARETTOZips[[i]]," is not existing"))
        }
        }
        names(HTMLsAMARETTOlist)<-names(HTMLsAMARETTOZips)
    }
    print(HTMLsAMARETTOlist)
    return(HTMLsAMARETTOlist)
}
#' @title cAMARETTO_ExportResults
#'
#' @param cAMARETTOresults The output of the Results function.
#' @param cAMARETTOnetworkM The output of the Module Network function.
#' @param cAMARETTOnetworkC The output of the Identify Communities function.
#' @param output_address The address where the zipfile will be generated in. 
#' @importFrom  utils zip unzip
#' @return a zipfile containing cAmaretto results
#' @examples 
#' try(
#' cAMARETTO_ExportResults(  cAMARETTOresults,  cAMARETTOnetworkM,
#'   cAMARETTOnetworkC,   output_address="./")
#' )
#' @export
cAMARETTO_ExportResults<-function(cAMARETTOresults,cAMARETTOnetworkM,
                                    cAMARETTOnetworkC, output_address="./"){
    if (!dir.exists(output_address)){
        stop("Output directory is not existing.")
    }
    #add a date stamp to the output directory
    output_dir<-paste0("cAMARETTOresults_",gsub("-|:","",
                        gsub(" ","_",Sys.time())))
    dir.create(file.path(output_address,output_dir))

    #save rdata files for AMARETTO_Run and AMARETTO_Initialize output
    save(cAMARETTOresults, file=file.path(output_address,
            output_dir,"/cAMARETTOresults.RData"))
    save(cAMARETTOnetworkM, file=file.path(output_address,
            output_dir,"/cAMARETTOnetworkM.RData"))
    save(cAMARETTOnetworkC, file=file.path(output_address,
            output_dir,"/cAMARETTOnetworkC.RData"))

    utils::zip(zipfile = file.path(output_address,output_dir),
                files=file.path(output_address,output_dir))
    unlink(output_dir,recursive = TRUE)
}