R/htmlReports.R

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

#' @title Get runDropletQC .html report
#' @description A  function to generate .html Rmarkdown report containing the visualizations of the runDropletQC function output
#' @param inSCE A \link[SingleCellExperiment]{SingleCellExperiment} object containing
#' the full droplet count matrix with the output from runDropletQC function
#' @param subTitle subtitle of the QC HTML report. Default is NULL.
#' @param studyDesign description of the data set and experiment design. It would be shown at the top of QC HTML report. Default is NULL.
#' @param output_file name of the generated file. If NULL/default then the output file name will be based on the name of the Rmarkdown template
#' @param output_dir name of the output directory to save the rendered file. If NULL/default the file is stored to the current working directory
#' @return .html file
#' @examples
#' data(scExample, package = "singleCellTK")
#' \dontrun{
#' sce <- runDropletQC(sce)
#' reportDropletQC(inSCE = sce)
#' }
#' @export
reportDropletQC <- function(inSCE, output_file = NULL,
                                   output_dir = NULL,
                                   subTitle = NULL,
                                   studyDesign = NULL) {

  if (is.null(output_dir)){
    output_dir<- getwd()
    }

  #report_path <- tempfile(fileext = ".Rmd")
  #file.copy(system.file("rmarkdown/qc/DropletQC.Rmd", package = "singleCellTK"), report_path, overwrite = TRUE)

  ## create temp Rmd file to bypass permission issue on server
  rmarkdown::render(system.file("rmarkdown/qc/DropletQC.Rmd", package = "singleCellTK"),
    params = list(object = inSCE, subTitle = subTitle, studyDesign = studyDesign),
    output_file = output_file,
    output_dir = output_dir,
    intermediates_dir = output_dir,
    knit_root_dir = output_dir)
 }


#' @title Get runCellQC .html report
#' @description A  function to generate .html Rmarkdown report containing the visualizations of the runCellQC function output
#' @param inSCE A \link[SingleCellExperiment]{SingleCellExperiment} object containing
#' the filtered count matrix with the output from runCellQC function
#' @param subTitle subtitle of the QC HTML report. Default is NULL.
#' @param studyDesign description of the data set and experiment design. It would be shown at the top of QC HTML report. Default is NULL.
#' @param output_file name of the generated file. If NULL/default then the output file name will be based on the name of the Rmarkdown template.
#' @param output_dir name of the output directory to save the rendered file. If NULL/default the file is stored to the current working directory
#' @return .html file
#' @examples
#' data(scExample, package = "singleCellTK")
#' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
#' \dontrun{
#' sce <- runCellQC(sce)
#' reportCellQC(inSCE = sce)
#' }
#' @export
reportCellQC <- function(inSCE, output_file = NULL,
                                output_dir = NULL,
                                subTitle = NULL,
                                studyDesign = NULL) {
  if (is.null(output_dir)){
    output_dir<- getwd()
  }
  #report_path <- tempfile(fileext = ".Rmd")
  #file.copy(system.file("rmarkdown/qc/CellQC.Rmd", package = "singleCellTK"), report_path, overwrite = TRUE)

  rmarkdown::render(system.file("rmarkdown/qc/CellQC.Rmd", package = "singleCellTK"),
    params = list(object = inSCE, subTitle = subTitle, studyDesign = studyDesign),
    output_file = output_file,
    output_dir = output_dir,
    intermediates_dir = output_dir,
    knit_root_dir = output_dir)
}


#' @title Get .html report of the output of the selected QC algorithm
#' @description A  function to generate .html Rmarkdown report for the specified QC algorithm output
#' @param inSCE A \link[SingleCellExperiment]{SingleCellExperiment} object containing
#' the count matrix (full droplets or filtered matrix, depends on the selected QC algorithm) with the output from at least one of these functions:
#' runQCMetrics, runScrublet, runDoubletCells, runCxds, runBcds, runCxdsBcdsHybrid, runDecontX, runBarcodeRankDrops, runEmptyDrops
#' @param algorithm Character. Specifies which QC algorithm report to generate.
#'  Available options are "BarcodeRankDrops", "EmptyDrops", "QCMetrics", "Scrublet", "DoubletCells", "Cxds", "Bcds", "CxdsBcdsHybrid", "DoubletFinder"  and "DecontX".
#' @param output_file name of the generated file. If NULL/default then the output file name will be based on the name of the selected QC algorithm name .
#' @param output_dir name of the output directory to save the rendered file. If NULL/default the file is stored to the current working directory
#' @return .html file
#' @examples
#' data(scExample, package = "singleCellTK")
#' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
#' \dontrun{
#' sce <- runDecontX(sce)
#' sce <- getUMAP(sce)
#' reportQCTool(inSCE = sce, algorithm = "DecontX")
#' }
#' @export
reportQCTool <- function(inSCE, algorithm=c("BarcodeRankDrops",
                                            "EmptyDrops",
                                            "QCMetrics",
                                            "Scrublet",
                                            "DoubletCells",
                                            "Cxds",
                                            "Bcds",
                                            "CxdsBcdsHybrid",
                                            "DoubletFinder",
                                            "DecontX"),
                         output_file = NULL,
                            output_dir = NULL) {

  algorithm <- match.arg(algorithm)

  if (is.null(output_dir)){
    output_dir<- getwd()
  }

  if (algorithm =="BarcodeRankDrops"){
    rmarkdown::render(system.file("rmarkdown/qc/BarcodeRankDrops.Rmd", package="singleCellTK"), params = list(
      object=inSCE), output_file = output_file, output_dir = output_dir)
  }
  if (algorithm =="EmptyDrops"){
    rmarkdown::render(system.file("rmarkdown/qc/EmptyDrops.Rmd", package="singleCellTK"), params = list(
      object=inSCE), output_file = output_file, output_dir = output_dir)
  }
  if (algorithm =="Cxds"){
    rmarkdown::render(system.file("rmarkdown/qc/Cxds.Rmd", package="singleCellTK"), params = list(
      object=inSCE), output_file = output_file, output_dir = output_dir)
  }
  if (algorithm =="Bcds"){
    rmarkdown::render(system.file("rmarkdown/qc/Bcds.Rmd", package="singleCellTK"), params = list(
      object=inSCE), output_file = output_file, output_dir = output_dir)
  }
  if (algorithm =="CxdsBcdsHybrid"){
    rmarkdown::render(system.file("rmarkdown/qc/CxdsBcdsHybrid.Rmd", package="singleCellTK"), params = list(
      object=inSCE), output_file = output_file, output_dir = output_dir)
  }
  if (algorithm =="DecontX"){
    rmarkdown::render(system.file("rmarkdown/qc/DecontX.Rmd", package="singleCellTK"), params = list(
      object=inSCE), output_file = output_file, output_dir = output_dir)
  }
  if (algorithm =="DoubletCells"){
    rmarkdown::render(system.file("rmarkdown/qc/DoubletCells.Rmd", package="singleCellTK"), params = list(
      object=inSCE), output_file = output_file, output_dir = output_dir)
  }
  if (algorithm =="QCMetrics"){
    rmarkdown::render(system.file("rmarkdown/qc/QCMetrics.Rmd", package="singleCellTK"), params = list(
      object=inSCE), output_file = output_file, output_dir = output_dir)
  }
  if (algorithm =="Scrublet"){
    rmarkdown::render(system.file("rmarkdown/qc/Scrublet.Rmd", package="singleCellTK"), params = list(
      object=inSCE), output_file = output_file, output_dir = output_dir)
  }
  if (algorithm =="DoubletFinder"){
    rmarkdown::render(system.file("rmarkdown/qc/DoubletFinder.Rmd", package="singleCellTK"), params = list(
      object=inSCE), output_file = output_file, output_dir = output_dir)
  }
 }

#' @title Get runDEAnalysis .html report
#' @description A  function to generate .html Rmarkdown report containing the
#' visualizations of the \code{\link{runDEAnalysis}} function output
#' @param inSCE A \code{\link[SingleCellExperiment]{SingleCellExperiment}}
#' object containing the output from \code{\link{runDEAnalysis}} function
#' @param study The specific analysis to visualize, used as \code{analysisName}
#' argument when running differential expression.
#' @param output_file name of the generated file. If \code{NULL} then the output
#' file name will be based on the name of the Rmarkdown template. Default
#' \code{NULL}.
#' @param output_dir name of the output directory to save the rendered file. If
#' \code{NULL} the file is stored to the current working directory.
#' Default \code{NULL}.
#' @return .html file
#' @export
reportDiffExp <- function(inSCE, study,
                          output_file = NULL,
                          output_dir = NULL) {

  if (is.null(output_dir)){
    output_dir <- getwd()
  }
  if (!study %in% names(S4Vectors::metadata(inSCE)$diffExp)) {
    stop("Specified study not found in given SCE object")
  }
  rmarkdown::render(system.file("rmarkdown/de/DifferentialExpression.Rmd",
                                package="singleCellTK"),
                    params = list(object=inSCE, study=study),
                    output_file = output_file,
                    output_dir = output_dir )
}