R/getClusterInputData.R

In mmkhan19/singleCellTK: Interactive Analysis of Single Cell RNA-Seq Data

#' Get data to use as input clustering algorithms
#'
#' @param inSCE Input SCtkExperiment object. Required
#' @param inputData A string ("Raw Data", "PCA Components", "tSNE Components", "UMAP Components")
#' @param useAssay Indicate which assay to use for PCA. Default is "logcounts"
#' @param reducedDimName If clustering on PCA, t-SNE or UMAP data, dimension name.
#' The toolkit will store data with the pattern <ASSAY>_<ALGORITHM>.
#'
#' @return Cluster input data
#' @export
#' @examples
#' data("mouseBrainSubsetSCE")
#' getClusterInputData(mouseBrainSubsetSCE, "PCA Components",
#'                     useAssay = "logcounts", reducedDimName = "PCA_logcounts")
#'
getClusterInputData <- function(inSCE, inputData, useAssay="logcounts",
                                reducedDimName=NULL){
  if (inputData == "Raw Data"){
    e <- SummarizedExperiment::assay(inSCE, useAssay)
  } else if (inputData == "PCA Components") {
    if (is.null(reducedDimName)){
      stop("You must supply a PCA dim name")
    }
    if(!(reducedDimName %in% names(SingleCellExperiment::reducedDims(inSCE)))){
      inSCE <- getPCA(inSCE, useAssay = useAssay,
                      reducedDimName = reducedDimName)
    }
    e <- SingleCellExperiment::reducedDim(inSCE, reducedDimName)
  } else if (inputData == "tSNE Components") {
    if (is.null(reducedDimName)){
      stop("You must supply a tSNE dim name")
    }
    if(!(reducedDimName %in% names(SingleCellExperiment::reducedDims(inSCE)))){
      inSCE <- getTSNE(inSCE, useAssay = useAssay,
                           reducedDimName = reducedDimName)
    }
    e <- SingleCellExperiment::reducedDim(inSCE, reducedDimName)
  } else if (inputData == "UMAP Components") {
    if (is.null(reducedDimName)){
      stop("You must supply a UMAP dim name")
    }
    if(!(reducedDimName %in% names(SingleCellExperiment::reducedDims(inSCE)))){
      inSCE <- getUMAP(inSCE, useAssay = useAssay,
                       reducedDimName = reducedDimName)
    }
    e <- SingleCellExperiment::reducedDim(inSCE, reducedDimName)
  }
  return(e)
}