inst/app/applySimpleR.R

In C3BI-pasteur-fr/UTechSCB-SCHNAPPs: Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

if ("SingleR" %in% installed.packages()) {
  require(SingleR)


  #' attach data on cell types using SingleR
  #'
  #' @details using the SingleR functionaly to attach that information to a scEx (SingleCellExperiment object)
  #'
  #'
  #' @param scEx singleCellExperiment object
  #' @param hpca.se e.g. HumanPrimaryCellAtlasData()
  #' @param colName name for the new col
  #'
  #' @importFrom SingleR SingleR pruneScores
  #'
  #' @export applySimpleR
  #'
  applySimpleR <- function(scEx, hpca.se, colName) {
    if (!"logcounts" %in% names(SummarizedExperiment::assays(scEx))) {
      scEx <- scater::normalize(scEx)
    }

    common <- dplyr::intersect(rownames(scEx), rownames(hpca.se))
    hpca.se <- hpca.se[common, ]
    scExC <- scEx[common, ]
    pred.hpca <- SingleR::SingleR(test = scExC, ref = hpca.se, labels = hpca.se$label.main)
    to.remove <- SingleR::pruneScores(pred.hpca)
    new.pruned <- pred.hpca$labels
    new.pruned[pruneScores(pred.hpca, nmads = 5)] <- NA
    cdata <- SingleCellExperiment::colData(scEx)
    cdata[, colName] <- NA
    cdata[colnames(scExC), colName] <- new.pruned
    SingleCellExperiment::colData(scEx) <- cdata
    return(scEx)
  }
}