R/03_exploreThresholds.R

In AUCell: AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

# Help files will be automatically generated from the coments starting with #'
# (https://cran.r-project.org/web/packages/roxygen2/vignettes/rd.html)
#
#' @title AUCell_exploreThresholds
#' @description Plots all the AUC histograms (per gene-set)
#' and calculates several likely thresholds for each gene-set
#' @param cellsAUC AUC object returned by \code{\link{AUCell_calcAUC}}.
#' @param thrP Probability to determine outliers in some of the distributions
#'  (see 'details' section).
#'
#' By default it is set to 1\% (thrP):
#' if there are 3000 cells in the dataset,
#' it is expected that approximately 30 cells are over this threshold
#' if the AUC is normally distributed.
#' @param nCores Number of cores to use for computation.
#' @param smallestPopPercent Size (percentage) of the smallest population
#' of cells expected. Used to calculate some of the thresholds.
#' @param plotHist Whether to plot the AUC histograms. (TRUE / FALSE)
#' @param densAdjust Parameter for the density curve. (See \code{density} for details).
#' @param assignCells Return the list of cells that pass the
#' automatically selected threshold? (TRUE/FALSE)
#' @param nBreaks Number of bars to plot in the histograms.
#' @param verbose Should the function show progress messages? (TRUE / FALSE)
#' @param aucellThresholds For aux functions: Output from AUCell_exploreThresholds
#' @return List with the following elements for each gene-set:
#' \itemize{
#' \item 'aucThr' Thresholds calculated with each method (see 'details' section),
#' and the number of cells that would be assigned using that threshold.
#'
#' If assignCells=TRUE, the threshold selected automatically is the highest
#' value (in most cases, excluding the global distribution).
#' \item 'assignment' List of cells that pass the selected AUC threshold (if \code{assignCells=TRUE})
#' }
#' If \code{plotHist=TRUE} the AUC histogram is also plot,
#' including the distributions calculated and the corresponding thresholds
#' in the same color (dashed vertical lines).
#' The threshold that is automatically selected is shown as a thicker
#'  non-dashed vertical line.
#'
#' @details To ease the selection of an assignment theshold,
#' this function adjusts the AUCs of each gene-set to several distributions
#'  and calculates possible thresholds:
#' \itemize{
#' \item \code{minimumDens} (plot in Blue):
#' Inflection point of the density curve.
#' This is usually a good option for the ideal situation
#' with bimodal distributions.
#'
#' To avoid false positives, by default this threshold will not be chosen
#' if the second distribution is higher
#' (i.e. the majority of cells have the gene-set "active").
#' \item \code{L_k2} (plot in Red): Left distribution,
#' after adjusting the AUC to a mixture of two distributions.
#' The threshold is set to the right (prob: \code{1-(thrP/nCells)}).
#' Only available if 'mixtools' package is installed.
#' \item \code{R_k3} (plot in Pink): Right distribution,
#' after adjusting the AUC to a mixture of three distributions.
#' The threshold is set to the left (prob: \code{thrP}).
#' Only available if 'mixtools' package is installed.
#' \item \code{Global_k1} (plot in Grey): "global" distribution
#'(i.e. mean and standard deviations of all cells).
#'The threshold is set to the right (prob: \code{1-(thrP/nCells)}).
#'
#' The threshold based on the global distribution is ignored from the automatic
#' selection unless the mixed models are overlapping.
#' }
#' Note: If \code{assignCells=TRUE}, the highest threshold is used to select cells.
#' However, keep in mind that this function is only meant to ease the selection
#' of the threshold, and we highly recommend to look at the AUC histograms and
#' adjust the threshold manually if needed.
#' We recommend to be specially aware on gene-sets with few genes (10-15) and
#' thresholds that are set extremely low.
#'
#' @seealso Previous step in the workflow: \code{\link{AUCell_calcAUC}}.
#'
#' See the package vignette for examples and more details:
#' \code{vignette("AUCell")}
#' @example inst/examples/example_AUCell_exploreThresholds.R
#' @export


# Runs .auc_assignmnetThreshold on each gene set (AUC)
AUCell_exploreThresholds <- function(cellsAUC, thrP=0.01, nCores=1,
     smallestPopPercent=.25, plotHist=TRUE, densAdjust=2, assignCells=FALSE,
     nBreaks=100, verbose=TRUE) # nDist=NULL,
{
  aucMatrix <- NULL
  if(methods::is(cellsAUC,"aucellResults")){
    aucMatrix <- getAUC(cellsAUC)
  }
  
  if(methods::is(cellsAUC,"matrixWrapper"))
  {
    stop('The AUC was calculated with a previous AUCell version. \n",
         "Please update them with updateAucellResults(..., objectType="AUC")')
  }

  if(is.matrix(cellsAUC)) {
    aucMatrix <- cellsAUC
  }
  if(!is.matrix(aucMatrix)) stop("cellsAUC should contain the AUC values.")
  
  rowSumAUC <- rowSums(aucMatrix)
  if(any(rowSumAUC==0)) warning("Skipping genesets with all AUC 0: ", 
                                paste(names(rowSumAUC)[which(rowSumAUC==0)], collapse=", "), 
                                immediate. = TRUE)
  aucMatrix <- aucMatrix[rowSumAUC>0,,drop=FALSE]

  if(nCores > 1 && plotHist) {
    nCores <- 1
    warning("Cannot plot in paralell")
  }

  if(nCores==1)
  {
    gSetName <- NULL
    assigment <- lapply(rownames(aucMatrix), function(gSetName)
    {
      aucThr <- .auc_assignmnetThreshold_v6(
                      aucRow=aucMatrix[gSetName,, drop=FALSE],
                      thrP=thrP,
                      smallestPopPercent=smallestPopPercent,
                      plotHist=plotHist,
                      densAdjust=densAdjust,
                      nBreaks=nBreaks)
      assignedCells <- NULL
      if(!is.null(aucThr)){
        auc <- aucMatrix[gSetName,]
        assignedCells <- names(auc)[which(auc>aucThr$selected)]
      }

      list(aucThr=aucThr, assignment=assignedCells)

    })
    names(assigment) <- rownames(aucMatrix)

  }else
  {
    # Run each geneSet in parallel
    doRNG::registerDoRNG(nCores)
    if(verbose)
      message("Using ", foreach::getDoParWorkers(), " cores.")

    "%dopar%"<- foreach::"%dopar%"
    suppressPackageStartupMessages(assigment <-
              doRNG::"%dorng%"(foreach::foreach(gSetName=rownames(aucMatrix)),
    {
      aucThr <- .auc_assignmnetThreshold_v6(
                          aucRow=aucMatrix[gSetName,, drop=FALSE],
                          thrP=thrP,
                          smallestPopPercent=smallestPopPercent,
                          plotHist=plotHist,
                          densAdjust=densAdjust,
                          nBreaks=nBreaks)
      assignedCells <- NULL
      if(!is.null(aucThr)){
        auc <- aucMatrix[gSetName,]
        assignedCells <- names(auc)[which(auc>aucThr$selected)]
      }
      tmp <- list(aucThr=aucThr, assignment=assignedCells)
      return(setNames(list(tmp), gSetName))
    }))
    attr(assigment, "rng") <- NULL
    assigment <- unlist(assigment, recursive = FALSE)[rownames(aucMatrix)]
  }
  # If cell assignment is not requested, remove from the output
  # (it was initially calculated to know the number of cells)
  if(!assignCells)
    assigment <- lapply(assigment, function(x)
      x[which(!names(x) %in% "assignment")])

  return(assigment)
}