R/HiddenUtils.R

In GreenleafLab/ArchR: Analyzing single-cell regulatory chromatin in R.

##########################################################################################
# Helper Intermediate Methods
##########################################################################################

.mergeParams <- function(paramInput = NULL, paramDefault = NULL){
  for(i in seq_along(paramDefault)){
    if(!(names(paramDefault)[i] %in% names(paramInput))){
      paramInput[[names(paramDefault)[i]]] <- paramDefault[[i]]
    }
  }
  return(paramInput)
}

.requirePackage <- function(x = NULL, load = TRUE, installInfo = NULL, source = NULL){
  if(x %in% rownames(installed.packages())){
    if(load){
      suppressPackageStartupMessages(require(x, character.only = TRUE))
    }else{
      return(0)
    }
  }else{
    if(!is.null(source) & is.null(installInfo)){
      if(tolower(source) == "cran"){
        installInfo <- paste0('install.packages("',x,'")')
      }else if(tolower(source) == "bioc"){
        installInfo <- paste0('BiocManager::install("',x,'")')
      }else{
        stop("Unrecognized package source, available are cran/bioc!")
      }
    }
    if(!is.null(installInfo)){
      stop(paste0("Required package : ", x, " is not installed/found!\n  Package Can Be Installed : ", installInfo))
    }else{
      stop(paste0("Required package : ", x, " is not installed/found!"))
    }
  }
}

##########################################################################################
# Safe saveRDS check
##########################################################################################

.safeSaveRDS <- function(
  object = NULL, 
  file = "", 
  ascii = FALSE, 
  version = NULL, 
  compress = TRUE, 
  refhook = NULL
  ){
  #Try to save a test data.frame in location
  testDF <- data.frame(a=1,b=2)
  canSave <- suppressWarnings(tryCatch({
    saveRDS(object = testDF, file = file, ascii = ascii, version = version, compress = compress, refhook = refhook)
    TRUE
  }, error = function(x){
    FALSE
  }))
  if(!canSave){
    dirExists <- dir.exists(dirname(file))
    if(dirExists){
      stop("Cannot saveRDS. File Path : ", file)
    }else{
      stop("Cannot saveRDS because directory does not exist (",dirname(file),"). File Path : ", file)
    }
  }else{
    saveRDS(object = object, file = file, ascii = ascii, version = version, compress = compress, refhook = refhook)
  }
}

##########################################################################################
# Stat/Summary Methods
##########################################################################################

.computeKNN <- function(
  data = NULL,
  query = NULL,
  k = 50,
  includeSelf = FALSE,
  ...
  ){
  .validInput(input = data, name = "data", valid = c("dataframe", "matrix"))
  .validInput(input = query, name = "query", valid = c("dataframe", "matrix"))
  .validInput(input = k, name = "k", valid = c("integer"))
  .validInput(input = includeSelf, name = "includeSelf", valid = c("boolean"))
  if(is.null(query)){
    query <- data
    searchSelf <- TRUE
  }else{
    searchSelf <- FALSE
  }
  .requirePackage("nabor", source = "cran")
  if(searchSelf & !includeSelf){
    knnIdx <- nabor::knn(data = data, query = query, k = k + 1, ...)$nn.idx
    knnIdx <- knnIdx[,-1,drop=FALSE]
  }else{
    knnIdx <- nabor::knn(data = data, query = query, k = k, ...)$nn.idx
  }
  knnIdx
}

.rowZscores <- function(m = NULL, min = -2, max = 2, limit = FALSE){
  z <- sweep(m - rowMeans(m), 1, matrixStats::rowSds(m),`/`)
  if(limit){
    z[z > max] <- max
    z[z < min] <- min
  }
  return(z)
}

.computeROC <- function(labels = NULL, scores = NULL, name="ROC"){
  .calcAUC <- function(TPR = NULL, FPR = NULL){
    # http://blog.revolutionanalytics.com/2016/11/calculating-auc.html
    dFPR <- c(diff(FPR), 0)
    dTPR <- c(diff(TPR), 0)
    out <- sum(TPR * dFPR) + sum(dTPR * dFPR)/2
    return(out)
  }
  labels <- labels[order(scores, decreasing=TRUE)]
  df <- data.frame(
    False_Positive_Rate = cumsum(!labels)/sum(!labels),
    True_Positive_Rate =  cumsum(labels)/sum(labels)
    )
  df$AUC <- round(.calcAUC(df$True_Positive_Rate,df$False_Positive_Rate),3)
  df$name <- name
  return(df)
}

.getQuantiles <- function(v = NULL, len = length(v)){
  if(length(v) < len){
    v2 <- rep(0, len)
    v2[seq_along(v)] <- v
  }else{
    v2 <- v
  }
  p <- trunc(rank(v2))/length(v2)
  if(length(v) < len){
    p <- p[seq_along(v)]
  }
  return(p)
}

.rowScale <- function(mat = NULL, min = NULL, max = NULL){
  if(!is.null(min)){
    rMin <- min
  }else{
    rMin <- matrixStats::rowMins(mat)
  }
  if(!is.null(max)){
    rMax <- max
  }else{
    rMax <- matrixStats::rowMaxs(mat)
  }
  rScale <- rMax - rMin
  matDiff <- mat - rMin
  matScale <- matDiff/rScale
  out <- list(mat=matScale, min=rMin, max=rMax)
  return(out)
}

.quantileCut <- function(x = NULL, lo = 0.025, hi = 0.975, maxIf0 = TRUE){
  q <- quantile(x, probs = c(lo,hi))
  if(q[2] == 0){
    if(maxIf0){
      q[2] <- max(x)
    }
  }
  x[x < q[1]] <- q[1]
  x[x > q[2]] <- q[2]
  return(x)
}

.normalizeCols <- function(mat = NULL, colSm = NULL, scaleTo = NULL){
    if(is.null(colSm)){
        colSm <- Matrix::colSums(mat)
    }
    if(!is.null(scaleTo)){
        mat@x <- scaleTo * mat@x / rep.int(colSm, Matrix::diff(mat@p))
    }else{
        mat@x <- mat@x / rep.int(colSm, Matrix::diff(mat@p))
    }
    return(mat)
}

.safeSubset <- function(mat = NULL, subsetRows = NULL, subsetCols = NULL){
  
  if(!is.null(subsetRows)){
    idxNotIn <- which(subsetRows %ni% rownames(mat))
    if(length(idxNotIn) > 0){
      subsetNamesNotIn <- subsetRows[idxNotIn]
      matNotIn <- Matrix::sparseMatrix(i=1,j=1,x=0,dims=c(length(idxNotIn), ncol = ncol(mat)))
      rownames(matNotIn) <- subsetNamesNotIn
      mat <- rbind(mat, matNotIn)
    }
    mat <- mat[subsetRows,]
  }

  if(!is.null(subsetCols)){
    idxNotIn <- which(subsetCols %ni% colnames(mat))
    if(length(idxNotIn) > 0){
      subsetNamesNotIn <- subsetCols[idxNotIn]
      matNotIn <- Matrix::sparseMatrix(i=1,j=1,x=0,dims=c(nrow(mat), ncol = length(idxNotIn)))
      colnames(matNotIn) <- subsetNamesNotIn
      mat <- cbind(mat, matNotIn)
    }
    mat <- mat[,subsetCols]
  }

  mat

}

.groupMeans <- function(mat = NULL, groups=NULL, na.rm = TRUE, sparse = FALSE){
  stopifnot(!is.null(groups))
  stopifnot(length(groups)==ncol(mat))
  gm <- lapply(unique(groups), function(x){
    if(sparse){
      Matrix::rowMeans(mat[,which(groups==x),drop=F], na.rm=na.rm)
    }else{
      rowMeans(mat[,which(groups==x),drop=F], na.rm=na.rm)
    }
  }) %>% Reduce("cbind",.)
  colnames(gm) <- unique(groups)
  return(gm)
}

.groupSums <- function(mat = NULL, groups=NULL, na.rm = TRUE, sparse = FALSE){
  stopifnot(!is.null(groups))
  stopifnot(length(groups)==ncol(mat))
  gm <- lapply(unique(groups), function(x){
    if(sparse){
      Matrix::rowSums(mat[,which(groups==x),drop=F], na.rm=na.rm)
    }else{
      rowSums(mat[,which(groups==x),drop=F], na.rm=na.rm)
    }
  }) %>% Reduce("cbind",.)
  colnames(gm) <- unique(groups)
  return(gm)
}

.groupSds <- function(mat = NULL, groups = NULL, na.rm = TRUE, sparse = FALSE){
  stopifnot(!is.null(groups))
  stopifnot(length(groups)==ncol(mat))
  gs <- lapply(unique(groups), function(x){
    if (sparse){
      matrixStats::rowSds(as.matrix(mat[, which(groups == x), drop = F]), na.rm = na.rm)
    }else{
      matrixStats::rowSds(mat[, which(groups == x), drop = F], na.rm = na.rm)
    }
  }) %>% Reduce("cbind",.)
  colnames(gs) <- unique(groups)
  return(gs)
}

.centerRollMean <- function(v = NULL, k = NULL){
  o1 <- data.table::frollmean(v, k, align = "right", na.rm = FALSE)
  if(k%%2==0){
    o2 <- c(rep(o1[k], floor(k/2)-1), o1[-seq_len(k-1)], rep(o1[length(o1)], floor(k/2)))
  }else if(k%%2==1){
    o2 <- c(rep(o1[k], floor(k/2)), o1[-seq_len(k-1)], rep(o1[length(o1)], floor(k/2)))
  }else{
    stop("Error!")
  }
  o2
}

##########################################################################################
# Miscellaneous Methods
##########################################################################################

.splitEvery <- function(x = NULL, n = NULL){
  #https://stackoverflow.com/questions/3318333/split-a-vector-into-chunks-in-r
  if(is.atomic(x)){
    split(x, ceiling(seq_along(x) / n))
  }else{
    split(x, ceiling(seq_len(nrow(x)) / n))
  }
}

.suppressAll <- function(expr = NULL){
  suppressPackageStartupMessages(suppressMessages(suppressWarnings(expr)))
}

.getAssay <- function(se = NULL, assayName = NULL){
  .assayNames <- function(se){
    names(SummarizedExperiment::assays(se))
  }
  if(is.null(assayName)){
    o <- SummarizedExperiment::assay(se)
  }else if(assayName %in% .assayNames(se)){
    o <- SummarizedExperiment::assays(se)[[assayName]]
  }else{
    stop(sprintf("assayName '%s' is not in assayNames of se : %s", assayName, paste(.assayNames(se),collapse=", ")))
  }
  return(o)
}

.fileExtension <- function (x = NULL){
  pos <- regexpr("\\.([[:alnum:]]+)$", x)
  ifelse(pos > -1L, substring(x, pos + 1L), "")
}

.checkPath <- function(u = NULL, path = NULL, throwError = TRUE){
  if(is.null(u)){
    out <- TRUE
  }
  out <- lapply(u, function(x, error = TRUE){
    if (Sys.which(x) == "") {
      if(!is.null(path) && file.exists(file.path(path, x))){
        o <- TRUE
      }else{
        if(throwError){
          stop(x, " not found in path, please add ", x, " to path!")
        }else{
          o <- FALSE
        }
      }
    }else{
      o <- TRUE
    }
    return(o)
  }) %>% unlist %>% all
  return(out)
}

.tempfile <- function(pattern = "tmp", tmpdir = "tmp", fileext = "", addDOC = TRUE){
  
  #if the directory doesnt already exist and file.exists evaluates to true, then a file exists with that name
  if(!dir.exists(tmpdir)){
    if(file.exists(tmpdir)){
      stop(paste0("Attempted to create temporary directory ", tmpdir," but a file already exists with this name. Please remove this file and try again!"))
    }
  }

  dir.create(tmpdir, showWarnings = FALSE)
  
  if(!dir.exists(tmpdir)){
    stop(paste0("Unable to create temporary directory ", tmpdir,". Check file permissions!")) 
  }

  if(addDOC){
    doc <- paste0("-Date-", Sys.Date(), "_Time-", gsub(":","-", stringr::str_split(Sys.time(), pattern=" ",simplify=TRUE)[1,2]))
  }else{
    doc <- ""
  }

  tempfile(pattern = paste0(pattern, "-"), tmpdir = tmpdir, fileext = paste0(doc, fileext))

}

.ArchRLogo <- function(ascii = "Logo", messageLogo = TRUE){
  Ascii <- list(
    Package = c("
           ___      .______        ______  __    __  .______      
          /   \\\     |   _  \\\      /      ||  |  |  | |   _  \\\     
         /  ^  \\\    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\\\  \\\   |      /     |  |     |   __   | |      /     
       /  _____  \\\  |  |\\\  \\\\___ |  `----.|  |  |  | |  |\\\  \\\\___.
      /__/     \\__\\ | _| `._____| \\______||__|  |__| | _| `._____|
    "),

    #modified from cyu@athena.mit.edu
    Logo = c("
                                                   / |
                                                 /    \\\
            .                                  /      |.
            \\\\\\                              /        |.
              \\\\\\                          /           `|.
                \\\\\\                      /              |.
                  \\\                    /                |\\\
                  \\\\#####\\\           /                  ||
                ==###########>      /                   ||
                 \\\\##==......\\\    /                     ||
            ______ =       =|__ /__                     ||      \\\\\\\
        ,--' ,----`-,__ ___/'  --,-`-===================##========>
       \\\               '        ##_______ _____ ,--,__,=##,__   ///
        ,    __==    ___,-,__,--'#'  ==='      `-'    | ##,-/
        -,____,---'       \\\\####\\\\________________,--\\\\_##,/
           ___      .______        ______  __    __  .______      
          /   \\\     |   _  \\\      /      ||  |  |  | |   _  \\\     
         /  ^  \\\    |  |_)  |    |  ,----'|  |__|  | |  |_)  |    
        /  /_\\\  \\\   |      /     |  |     |   __   | |      /     
       /  _____  \\\  |  |\\\  \\\\___ |  `----.|  |  |  | |  |\\\  \\\\___.
      /__/     \\__\\ | _| `._____| \\______||__|  |__| | _| `._____|
    ")
  )

  if(messageLogo){
    message(Ascii[[ascii]])
  }else{
    Ascii[[ascii]]
  }

}

##########################################################################################
# Batch Methods
##########################################################################################

.safelapply <- function(..., threads = 1, preschedule = FALSE){

  if(tolower(.Platform$OS.type) == "windows"){
    threads <- 1
  }

  if(threads > 1){
    .requirePackage("parallel", source = "cran")
    o <- mclapply(..., mc.cores = threads, mc.preschedule = preschedule)

    errorMsg <- list()

    for(i in seq_along(o)){ #Make Sure this doesnt explode!
      if(inherits(o[[i]], "try-error")){
        capOut <- utils::capture.output(o[[i]])
        capOut <- capOut[!grepl("attr\\(\\,|try-error", capOut)]
        capOut <- head(capOut, 10)
        capOut <- unlist(lapply(capOut, function(x) substr(x, 1, 250)))
        capOut <- paste0("\t", capOut)
        errorMsg[[length(errorMsg) + 1]] <- paste0(c(paste0("Error Found Iteration ", i, " : "), capOut), "\n")
      }
    }

    if(length(errorMsg) != 0){

      errorMsg <- unlist(errorMsg)
      errorMsg <- head(errorMsg, 50)
      errorMsg[1] <- paste0("\n", errorMsg[1])
      stop(errorMsg)

    }

  }else{

    o <- lapply(...)

  }

  o

}

.batchlapply <- function(args = NULL, sequential = FALSE){

  if(is.null(args$tstart)){
    args$tstart <- Sys.time()
  }

  #Determine Parallel Backend
  if(inherits(args$parallelParam, "BatchtoolsParam")){

    .logStop("Batchtools not yet fully supported please use local parallel threading!", logFile = args$logFile)

    .logDiffTime("Batch Execution w/ BatchTools through BiocParallel!", t1 = args$tstart, verbose = TRUE, logFile = args$logFile)

    require(BiocParallel)
    
    args$parallelParam <- btParam
    #Unlink registry Directory
    if(dir.exists(args$registryDir)){
      #Clean Up Registry
      unlink(args$registryDir, recursive = TRUE)# Delete registry directory
    }

    #Set Up Registry For Runnning
    args$parallelParam$registryargs <- batchtoolsRegistryargs(
      file.dir = args$registryDir,
      work.dir = getwd(),
      packages = character(0L),
      namespaces = character(0L),
      source = character(0L),
      load = character(0L)
    )

    #Register
    BPPARAM <- args$parallelParam
    register(BPPARAM)

    #Add To Args
    args$BPPARAM <- BPPARAM

    if("..." %in% names(args)){
      args["..."] <- NULL
    }

    #Run
    args <- args[names(args) %ni% c("threads", "parallelParam", "subThreading")]
    outlist <- do.call(bplapply, args)

  }else{

    .logDiffTime("Batch Execution w/ safelapply!", t1 = args$tstart, verbose = TRUE, logFile = args$logFile)
    if(sequential){
      args$subThreads <- args$threads
      args$threads <- 1
    }else{
      if(args$threads > length(args$X)){
        args$subThreads <- floor( args$threads / length(args$X) )
        args$threads <- length(args$X)
      }else{
        args$subThreads <- 1
      }
    }

    args <- args[names(args) %ni% c("registryDir", "parallelParam", "subThreading")]
    outlist <- do.call(.safelapply, args)

  }

  return(outlist)

}

.retryCatch <- function(expr, ..., maxAttempts = 3, warnAttempts = FALSE, nameFN = "FN", printInfo = NULL, logFile = NULL){
  currentAttempt <- 0
  completed <- FALSE
  while(!completed & currentAttempt <= maxAttempts){
    currentAttempt <- currentAttempt + 1
    if(currentAttempt > 1){
      .logMessage(nameFN, " : Error occured, attempting again (", currentAttempt - 1, " of ", maxAttempts, ")", logFile = logFile)
    }
    ###########################################################
    tryResult <- tryCatch({
      #########################################################
      #Try Catch Statement Here
      if(warnAttempts){
        out <- return(expr)
      }else{
        out <- suppressWarnings(return(expr))
      }
      #########################################################
      list(out = out, completed = TRUE)
    }, error = function(e){
      list(out = e, completed = FALSE)
    }, ...)
    ###########################################################
    completed <- tryResult$completed
  }
  if(!completed){
    .logMessage(nameFN, " : Error occured and could not be resolved after ", maxAttempts, " additional attempts!", logFile = logFile)
    if(!is.null(printInfo)){
      .logMessage("Error occured at ", printInfo, logFile = logFile)
    }
    print(tryResult[[1]])
    stop()
  }
  
  tryResult[[1]]

}


##########################################################################################
# Developer Utils
##########################################################################################

.devMode <- function(package = "ArchR"){
  # fn <- unclass(lsf.str(envir = asNamespace(package), all = TRUE))
  # for(i in seq_along(fn)){
  #   tryCatch({
  #     assign(fn[i], paste0(package,':::', fn[i]), envir=globalenv())
  #     #eval(parse(text=paste0(fn[i], paste0('<<-',package,':::'), fn[i])))
  #   }, error = function(x){
  #   })
  # }
  fn <- unclass(lsf.str(envir = asNamespace("ArchR"), all = TRUE))
  for(i in seq_along(fn)){
    tryCatch({
      eval(parse(text=paste0(fn[i], '<-ArchR:::', fn[i])))
    }, error = function(x){
    })
  }
}

.convertToPNG <- function(
  ArchRProj = NULL,
  paths = c("QualityControl"),
  recursive = TRUE,
  outDir = "Figures",
  command = "mv"
  ){

  #If error try
  #brew install fontconfig

  .requirePackage("pdftools", source = "cran")

  if(!is.null(ArchRProj)){
    paths <- c(paths, file.path(getOutputDirectory(ArchRProj), "Plots"))
  }
  
  pdfFiles <- lapply(seq_along(paths), function(i){
    if(recursive){
      dirs <- list.dirs(paths[i], recursive = FALSE, full.names = FALSE)
      if(length(dirs) > 0){
        pdfs <- lapply(seq_along(dirs), function(j){
          list.files(file.path(paths[i], dirs[j]), full.names = TRUE, pattern = "\\.pdf")
        }) %>% unlist
      }else{
        pdfs <- c()
      }
      pdfs <- c(list.files(paths[i], full.names = TRUE, pattern = "\\.pdf"), pdfs)
    }else{
      pdfs <- list.files(paths[i], full.names = TRUE, pattern = "\\.pdf")
    }
    pdfs
  }) %>% unlist

  dir.create(outDir, showWarnings = FALSE)

  for(i in seq_along(pdfFiles)){
    print(i)
    tryCatch({
      pdf_convert(
        pdfFiles[i], 
        format = "png", 
        pages = NULL, 
        filenames = file.path(outDir, gsub("\\.pdf", "_%d.png",basename(pdfFiles[i]))),
        dpi = 300, 
        opw = "", 
        upw = "", 
        verbose = TRUE
      )
    system(paste0(command, " ", pdfFiles[i], " ", file.path(outDir, basename(pdfFiles[i]))))
    },error=function(x){
      0
    })
  }

}