R/ggPerQCWrapper.R
In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Documented in plotBarcodeRankDropsResults plotBcdsResults plotCxdsResults plotDecontXResults plotDoubletCellsResults plotDoubletFinderResults plotEmptyDropsResults plotRunPerCellQCResults plotScdsHybridResults plotScrubletResults

#' @title Plots for runPerCellQC outputs.
#' @description A wrapper function which visualizes outputs from the
#'  runPerCellQC function stored in the colData slot of the SingleCellExperiment
#'  object via various plots.
#' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved
#' dimension reduction components or a variable with saved results from
#' runPerCellQC. Required.
#' @param sample Character vector. Indicates which sample each cell belongs to.
#'  Default NULL.
#' @param groupBy Groupings for each numeric value. A user may input a vector
#'  equal length to the number of the samples in the SingleCellExperiment
#'  object, or can be retrieved from the colData slot. Default NULL.
#' @param violin Boolean. If TRUE, will plot the violin plot. Default TRUE.
#' @param boxplot Boolean. If TRUE, will plot boxplots for each violin plot.
#'  Default FALSE.
#' @param dots Boolean. If TRUE, will plot dots for each violin plot.
#'  Default TRUE.
#' @param dotSize Size of dots. Default 1.
#' @param titleSize Size of title of plot. Default 18.
#' @param axisSize Size of x/y-axis ticks. Default 15.
#' @param axisLabelSize Size of x/y-axis labels. Default 18.
#' @param transparency Transparency of the dots, values will be 0-1. Default 1.
#' @param defaultTheme Removes grid in plot and sets axis title size to 10
#'  when TRUE. Default TRUE.
#' @param combinePlot Must be either "all", "sample", or "none". "all" will combine all plots into a single
#' .ggplot object, while "sample" will output a list of plots separated by sample. Default "all".
#' @param relHeights Relative heights of plots when combine is set.
#' @param relWidths Relative widths of plots when combine is set.
#' @param plotNCols Number of columns when plots are combined in a grid.
#' @param plotNRows Number of rows when plots are combined in a grid.
#' @param plotLabels labels to each plot. If set to "default", will use the name of the samples
#'  as the labels. If set to "none", no label will be plotted.
#' @param plotLabelSize size of labels
#' @param plotLabelPositionX Numeric vector. The X position of the plot label.
#' @param plotLabelPositionY Numeric vector. The Y position of the plot label.
#' @param samplePerColumn If TRUE, when there are multiple samples and combining by "all",
#'  the output .ggplot will have plots from each sample on a single column. Default TRUE.
#' @param sampleRelHeights If there are multiple samples and combining by "all",
#'  the relative heights for each plot.
#' @param sampleRelWidths If there are multiple samples and combining by "all",
#'  the relative widths for each plot.
#' @return list of .ggplot objects
#' @examples
#' data(scExample, package="singleCellTK")
#' \dontrun{
#' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
#' sce <- runPerCellQC(sce)
#' plotRunPerCellQCResults(inSCE=sce)
#' }
#' @export
plotRunPerCellQCResults <- function(inSCE,
                                    sample=NULL,
                                    groupBy=NULL,
                                    combinePlot="all",
                                    violin=TRUE,
                                    boxplot=FALSE,
                                    dots=TRUE,
                                    dotSize=1,
                                    axisSize=15,
                                    axisLabelSize=18,
                                    transparency=1,
                                    defaultTheme=TRUE,
                                    titleSize=18,
                                    relHeights=c(1.5, 1.5, 1, 1),
                                    relWidths=c(1, 1, 1, 1),
                                    plotNCols = NULL,
                                    plotNRows = NULL,
                                    plotLabels = "none",
                                    plotLabelSize = 20,
                                    plotLabelPositionX = NULL,
                                    plotLabelPositionY = NULL,
                                    samplePerColumn = TRUE,
                                    sampleRelHeights = 1,
                                    sampleRelWidths = 1) {
  if (!is.null(sample)) {
    if (length(sample) != ncol(inSCE)) {
      stop(
        "'sample' must be the same length as the number",
        " of columns in 'inSCE'"
      )
    }
  } else {
    sample <- rep(1, ncol(inSCE))
  }
  sampleVector <- sample

  samples <- unique(sample)

  if(combinePlot == "sample" && length(samples) == 1){
    warning("'combinePlot' was set to 'sample' but the sample was not set,
            or there is only one type of sample specified.")
    combinePlot = "all"
  }

  if (length(samples) > 1) {
    combined.sum <- plotSCEViolinColData(
      inSCE=inSCE,
      coldata="sum",
      groupBy=sampleVector,
      xlab="",
      ylab="Counts",
      violin=violin,
      boxplot=boxplot,
      dots=dots,
      transparency=transparency,
      title="Total counts per cell",
      dotSize=dotSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      gridLine=TRUE,
      summary="median",
      titleSize=titleSize,
      combinePlot = "all",
      plotLabels = "none"
    )

    combined.detected <- plotSCEViolinColData(
      inSCE=inSCE,
      coldata="detected",
      groupBy=sampleVector,
      xlab="",
      ylab="Features",
      violin=violin,
      boxplot=boxplot,
      dots=dots,
      transparency=transparency,
      title="Total features detected per cell",
      dotSize=dotSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      gridLine=TRUE,
      summary="median",
      titleSize=titleSize,
      combinePlot = "all",
      plotLabels = "none"
    )
    combined.toppercent <- plotSCEViolinColData(
      inSCE=inSCE,
      coldata="percent_top_50",
      groupBy=sampleVector,
      xlab="",
      ylab="Gene expression percentage (%)",
      violin=violin,
      boxplot=boxplot,
      dots=dots,
      transparency=transparency,
      title="Top 50 gene expression percentage",
      dotSize=dotSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      gridLine=TRUE,
      summary="median",
      titleSize=titleSize,
      combinePlot = "all",
      plotLabels = "none"
    )

    merged.plots <- list(combined.sum, combined.detected, combined.toppercent)
    names(merged.plots) <- c("Sum", "Detected", "TopPercent")

    if (any(grepl(
      pattern="subsets_",
      names(colData(inSCE))
    ))) {
      subsets <- grep(
        pattern="subsets_",
        names(colData(inSCE)), value=TRUE
      )

      combined.subset <- lapply(subsets, function(x) {
        plotSCEViolinColData(
          inSCE=inSCE,
          coldata=x,
          groupBy = sampleVector,
          xlab="",
          ylab=x,
          violin=violin,
          boxplot=boxplot,
          dots=dots,
          transparency=transparency,
          axisSize=axisSize,
          axisLabelSize=axisLabelSize,
          title=paste0(x, " per cell"),
          dotSize=dotSize,
          titleSize=titleSize,
          summary="median",
          combinePlot = "all",
          plotLabels = "none"
        )
      })
      names(combined.subset) <- c("Gene_Subset_Sum",
                                  "Gene_Subset_Features",
                                  "Gene_Subset_Top50_Percent")
      merged.plots <- c(merged.plots, combined.subset)
    } else {
      combined.subset <- NULL
    }

    merged.plots <- list(Violin = merged.plots)
  }

  res.list <- c()
  plotlist <- lapply(samples, function(x) {
    sampleInd <- which(sample == x)
    sampleSub <- sample[sampleInd]
    inSCESub <- inSCE[, sampleInd]

    if(combinePlot == "sample" | combinePlot == "none" | length(samples) == 1){
      violin.sum <- list(sum = plotSCEViolinColData(
        inSCE=inSCESub,
        coldata="sum",
        sample=sampleSub,
        xlab="",
        ylab="Counts",
        groupBy=groupBy,
        violin=violin,
        boxplot=boxplot,
        dots=dots,
        transparency=transparency,
        title="Total counts per cell",
        dotSize=dotSize,
        axisSize=axisSize,
        axisLabelSize=axisLabelSize,
        summary="median",
        titleSize=titleSize,
        combinePlot="all"
      ))
      res.list <- c(res.list, violin.sum)

      violin.detected <- list(detected = plotSCEViolinColData(
        inSCE=inSCESub,
        coldata="detected",
        sample=sampleSub,
        xlab="",
        ylab="Features",
        groupBy=groupBy,
        violin=violin,
        boxplot=boxplot,
        dots=dots,
        transparency=transparency,
        title="Total features detected per cell",
        dotSize=dotSize,
        axisSize=axisSize,
        axisLabelSize=axisLabelSize,
        summary="median",
        titleSize=titleSize,
        combinePlot="all"
      ))
      res.list <- c(res.list, violin.detected)

      violin.toppercent <- list(toppercent = plotSCEViolinColData(
        inSCE=inSCESub,
        coldata="percent_top_50",
        sample=sampleSub,
        xlab="",
        ylab="Gene expression percentage (%)",
        groupBy=groupBy,
        violin=violin,
        boxplot=boxplot,
        dots=dots,
        transparency=transparency,
        title="Top 50 gene expression percentage",
        dotSize=dotSize,
        axisSize=axisSize,
        axisLabelSize=axisLabelSize,
        summary="median",
        titleSize=titleSize,
        combinePlot="all"
      ))
      res.list <- c(res.list, violin.toppercent)
      names(res.list) <- c("Sum", "Detected", "TopPercent")

      if (any(grepl(
        pattern="subsets_",
        names(colData(inSCESub))
      ))) {
        subsets <- grep(
          pattern="subsets_",
          names(colData(inSCESub)), value=TRUE
        )

        violin.subset <- lapply(subsets, function(x) {
          plotSCEViolinColData(
            inSCE=inSCESub,
            coldata=x,
            sample=sampleSub,
            xlab="",
            ylab=x,
            groupBy=groupBy,
            violin=violin,
            boxplot=boxplot,
            dots=dots,
            transparency=transparency,
            axisSize=axisSize,
            axisLabelSize=axisLabelSize,
            title=paste0(x, " per cell"),
            dotSize=dotSize,
            titleSize=titleSize,
            summary="median",
            combinePlot="all"
          )
        })
        names(violin.subset) <- subsets
      } else {
        violin.subset <- NULL
      }

      if (!is.null(violin.subset)) {
        res.list <- c(res.list, violin.subset)
      }
    }

    return(res.list)
  })

  if (length(unique(samples)) > 1) {
    names(plotlist) <- samples
    if(combinePlot == "all"){
      plotlist <- c(merged.plots)
    }else if(combinePlot == "sample"){
      plotlist <- c(merged.plots, list(Sample = plotlist))
    }else if(combinePlot == "none"){
      plotlist <- c(merged.plots, list(Sample = plotlist))
    }
  } else {
    plotlist <- unlist(plotlist, recursive=FALSE)
    plotLabels <- "none"
    relHeights=1
  }

  if(!is.null(combinePlot)){
    if(combinePlot %in% c("all", "sample")){
      plotlist <- .ggSCTKCombinePlots(plotlist, combinePlot = combinePlot,
                                      relHeights = relHeights,
                                      relWidths = relWidths,
                                      labels = plotLabels,
                                      labelSize = plotLabelSize,
                                      labelPositionX = plotLabelPositionX,
                                      labelPositionY = plotLabelPositionY,
                                      nrows = plotNRows,
                                      ncols = plotNCols,
                                      samplePerColumn = samplePerColumn,
                                      sampleRelHeights = sampleRelHeights,
                                      sampleRelWidths = sampleRelWidths)
    }
  }
  return(plotlist)
}

#' @title Plots for runEmptyDrops outputs.
#' @description A wrapper function which visualizes outputs from the
#'  runEmptyDrops function stored in the colData slot of the SingleCellExperiment
#'  object via plots.
#' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved
#' dimension reduction components or a variable with saved results from
#' \link{runScrublet}. Required.
#' @param sample Character vector. Indicates which sample each cell belongs to.
#'  Default NULL.
#' @param fdrCutoff Numeric. Thresholds barcodes based on the FDR values from
#'  runEmptyDrops as "Empty Droplet" or "Putative Cell". Default 0.01.
#' @param defaultTheme Removes grid in plot and sets axis title size to 10
#'  when TRUE. Default TRUE.
#' @param dotSize Size of dots. Default 1.
#' @param titleSize Size of title of plot. Default 18.
#' @param axisSize Size of x/y-axis ticks. Default 15.
#' @param axisLabelSize Size of x/y-axis labels. Default 18.
#' @param legendSize size of legend. Default 15.
#' @param legendTitleSize size of legend title. Default 16.
#' @param combinePlot Must be either "all", "sample", or "none". "all" will combine all plots into a single
#' .ggplot object, while "sample" will output a list of plots separated by sample. Default "all".
#' @param relHeights Relative heights of plots when combine is set.
#' @param relWidths Relative widths of plots when combine is set.
#' @param samplePerColumn If TRUE, when there are multiple samples and combining by "all",
#'  the output .ggplot will have plots from each sample on a single column. Default TRUE.
#' @param sampleRelHeights If there are multiple samples and combining by "all",
#'  the relative heights for each plot.
#' @param sampleRelWidths If there are multiple samples and combining by "all",
#'  the relative widths for each plot.
#' @return list of .ggplot objects
#' @examples
#' data(scExample, package="singleCellTK")
#' sce <- runEmptyDrops(inSCE=sce)
#' plotEmptyDropsResults(inSCE=sce)
#' @export
plotEmptyDropsResults <- function(inSCE,
                                  sample=NULL,
                                  combinePlot="all",
                                  fdrCutoff=0.01,
                                  defaultTheme=TRUE,
                                  dotSize=1,
                                  titleSize=18,
                                  axisLabelSize=18,
                                  axisSize=15,
                                  legendSize=15,
                                  legendTitleSize=16,
                                  relHeights=1,
                                  relWidths=1,
                                  samplePerColumn = TRUE,
                                  sampleRelHeights = 1,
                                  sampleRelWidths = 1) {
  scatterEmptyDrops <- plotEmptyDropsScatter(inSCE,
    sample=sample,
    combinePlot=combinePlot,
    fdrCutoff=fdrCutoff,
    dotSize=dotSize,
    title="EmptyDrops, Total UMI counts vs Log-Probability",
    titleSize=titleSize,
    defaultTheme=TRUE,
    xlab="Total UMI count",
    ylab="-Log Probability",
    axisLabelSize=axisLabelSize,
    axisSize=axisSize,
    legendTitle=paste0("Cutoff:\nFDR < ", fdrCutoff),
    legendTitleSize=legendTitleSize,
    legendSize=legendSize,
    relHeights = relHeights,
    relWidths = relWidths,
    samplePerColumn = samplePerColumn,
    sampleRelHeights = sampleRelHeights,
    sampleRelWidths = sampleRelWidths
  )

  res.list <- list(scatterEmptyDrops)
  names(res.list) <- c("scatterEmptyDrops")
  return(res.list)
}

#' @title Plots for runEmptyDrops outputs.
#' @description A wrapper function which visualizes outputs from the
#'  runEmptyDrops function stored in the colData slot of the SingleCellExperiment
#'  object via plots.
#' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved
#' dimension reduction components or a variable with saved results from
#' \link{runBarcodeRankDrops}. Required.
#' @param sample Character vector. Indicates which sample each cell belongs to.
#'  Default NULL.
#' @param defaultTheme Removes grid in plot and sets axis title size to 10
#'  when TRUE. Default TRUE.
#' @param dotSize Size of dots. Default 1.
#' @param titleSize Size of title of plot. Default 18.
#' @param axisSize Size of x/y-axis ticks. Default 15.
#' @param axisLabelSize Size of x/y-axis labels. Default 18.
#' @param legendSize size of legend. Default 15.
#' @return list of .ggplot objects
#' @examples
#' data(scExample, package="singleCellTK")
#' sce <- runBarcodeRankDrops(inSCE=sce)
#' plotBarcodeRankDropsResults(inSCE=sce)
#' @export
plotBarcodeRankDropsResults <- function(inSCE,
                                  sample=NULL,
                                  defaultTheme=TRUE,
                                  dotSize=1,
                                  titleSize=18,
                                  axisLabelSize=18,
                                  axisSize=15,
                                  legendSize=15) {
    scatterBarcodeRank <- plotBarcodeRankScatter(inSCE,
                                               sample=sample,
                                               dotSize=dotSize,
                                               title="BarcodeRanks Rank Plot",
                                               titleSize=titleSize,
                                               defaultTheme=TRUE,
                                               axisLabelSize=axisLabelSize,
                                               axisSize=axisSize,
                                               legendSize=legendSize
    )

    res.list <- list(scatterBarcodeRank)
    names(res.list) <- c("scatterBarcodeRank")
    return(res.list)
}

#' @title Plots for runScrublet outputs.
#' @description A wrapper function which visualizes outputs from the
#'  runScrublet function stored in the colData slot of the SingleCellExperiment
#'  object via various plots.
#' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved
#' dimension reduction components or a variable with saved results from
#' \link{runScrublet}. Required.
#' @param sample Character vector. Indicates which sample each cell belongs to.
#'  Default NULL.
#' @param shape If provided, add shapes based on the value.
#' @param groupBy Groupings for each numeric value. A user may input a vector
#'  equal length to the number of the samples in the SingleCellExperiment
#'  object, or can be retrieved from the colData slot. Default NULL.
#' @param violin Boolean. If TRUE, will plot the violin plot. Default TRUE.
#' @param boxplot Boolean. If TRUE, will plot boxplots for each violin plot.
#'  Default TRUE.
#' @param dots Boolean. If TRUE, will plot dots for each violin plot.
#'  Default TRUE.
#' @param reducedDimName Saved dimension reduction name in the
#' \linkS4class{SingleCellExperiment} object. Required.
#' @param xlab Character vector. Label for x-axis. Default NULL.
#' @param ylab Character vector. Label for y-axis. Default NULL.
#' @param dim1 1st dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param dim2 2nd dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param bin Numeric vector. If single value, will divide the numeric values into the `bin` groups.
#'  If more than one value, will bin numeric values using values as a cut point.
#' @param binLabel Character vector. Labels for the bins created by the `bin` parameter.
#'  Default NULL.
#' @param defaultTheme Removes grid in plot and sets axis title size to 10
#'  when TRUE. Default TRUE.
#' @param dotSize Size of dots. Default 1.
#' @param transparency Transparency of the dots, values will be 0-1. Default 1.
#' @param titleSize Size of title of plot. Default 18.
#' @param axisSize Size of x/y-axis ticks. Default 15.
#' @param axisLabelSize Size of x/y-axis labels. Default 18.
#' @param legendSize size of legend. Default 15.
#' @param legendTitleSize size of legend title. Default 16.
#' @param combinePlot Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object,
#' while "sample" will output a list of plots separated by sample. Default "all".
#' @param relHeights Relative heights of plots when combine is set.
#' @param relWidths Relative widths of plots when combine is set.
#' @param plotNCols Number of columns when plots are combined in a grid.
#' @param plotNRows Number of rows when plots are combined in a grid.
#' @param plotLabels labels to each plot. If set to "default", will use the name of the samples
#'  as the labels. If set to "none", no label will be plotted.
#' @param plotLabelSize size of labels
#' @param plotLabelPositionX Numeric vector. The X position of the plot label.
#' @param plotLabelPositionY Numeric vector. The Y position of the plot label.
#' @param samplePerColumn If TRUE, when there are multiple samples and combining by "all",
#'  the output .ggplot will have plots from each sample on a single column. Default TRUE.
#' @param sampleRelHeights If there are multiple samples and combining by "all",
#'  the relative heights for each plot.
#' @param sampleRelWidths If there are multiple samples and combining by "all",
#'  the relative widths for each plot.
#' @return list of .ggplot objects
#' @examples
#' data(scExample, package="singleCellTK")
#' \dontrun{
#' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
#' sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP")
#' sce <- runScrublet(sce)
#' plotScrubletResults(inSCE=sce, reducedDimName="UMAP")
#' }
#' @export
plotScrubletResults <- function(inSCE,
                                sample=NULL,
                                shape=NULL,
                                groupBy=NULL,
                                combinePlot="all",
                                violin=TRUE,
                                boxplot=FALSE,
                                dots=TRUE,
                                reducedDimName,
                                xlab=NULL,
                                ylab=NULL,
                                dim1=NULL,
                                dim2=NULL,
                                bin=NULL,
                                binLabel=NULL,
                                defaultTheme=TRUE,
                                dotSize=1,
                                transparency=1,
                                titleSize=18,
                                axisLabelSize=18,
                                axisSize=15,
                                legendSize=15,
                                legendTitleSize=16,
                                relHeights=c(1.5, 1, 1),
                                relWidths=c(1, 1, 1),
                                plotNCols = NULL,
                                plotNRows = NULL,
                                plotLabels = "default",
                                plotLabelSize = 20,
                                plotLabelPositionX = NULL,
                                plotLabelPositionY = NULL,
                                samplePerColumn = TRUE,
                                sampleRelHeights = 1,
                                sampleRelWidths = 1) {
  if (!is.null(sample)) {
    if (length(sample) != ncol(inSCE)) {
      stop(
        "'sample' must be the same length as the number",
        " of columns in 'inSCE'"
      )
    }
  } else {
    sample <- rep(1, ncol(inSCE))
  }
  sampleVector <- sample
  samples <- unique(sample)

  if (length(samples) > 1) {
    merged.plots <- list(Score = plotSCEViolinColData(
      inSCE=inSCE,
      coldata="scrublet_score",
      groupBy=sampleVector,
      xlab="",
      ylab="Doublet Score",
      violin=violin,
      boxplot=boxplot,
      dots=dots,
      transparency=transparency,
      title="Scrublet Score",
      titleSize=titleSize,
      dotSize=dotSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      gridLine=TRUE,
      summary="median",
      combinePlot = "all",
      plotLabels = "none"
    ))
    merged.plots <- list(merged.plots)
    names(merged.plots) <- "Violin"
  }

  res.list <- list()
  plotlist <- lapply(samples, function(x) {
    sampleInd <- which(sample == x)
    sampleSub <- sample[sampleInd]
    inSCESub <- inSCE[, sampleInd]

    densityScore <- list(density_doubletScore = plotSCEDensityColData(
        inSCE=inSCESub,
        sample=sampleSub,
        coldata="scrublet_score",
        groupBy=groupBy,
        xlab="Score",
        ylab="Density",
        axisSize=15,
        axisLabelSize=18,
        defaultTheme=defaultTheme,
        cutoff=0.5,
        title="Density, Scrublet Score",
        titleSize=titleSize,
        combinePlot="all"
    ))
    res.list <- c(res.list, densityScore)

    scatterScore <- list(scatter_doubletScore = plotSCEDimReduceColData(
      inSCE=inSCESub,
      sample=sampleSub,
      colorBy="scrublet_score",
      conditionClass="numeric",
      shape=shape,
      reducedDimName=reducedDimName,
      xlab=xlab,
      ylab=ylab,
      dim1=dim1,
      dim2=dim2,
      bin=bin,
      binLabel=binLabel,
      dotSize=dotSize,
      transparency=transparency,
      defaultTheme=defaultTheme,
      title="Scrublet Doublet Score",
      titleSize=titleSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      labelClusters=FALSE,
      legendTitle="Doublet \nScore",
      legendSize=legendSize,
      legendTitleSize=legendTitleSize,
      combinePlot="all"
    ))
    res.list <- c(res.list, scatterScore)

    if(combinePlot != "all" | length(samples) == 1){
      violinScore <- list(violin_doubletScore = plotSCEViolinColData(
      inSCE=inSCESub, coldata="scrublet_score",
      sample=sampleSub,
      xlab="",
      ylab="Doublet Score",
      groupBy=groupBy,
      violin=violin,
      boxplot=boxplot,
      dots=dots,
      transparency=transparency,
      defaultTheme=defaultTheme,
      title="Scrublet Score",
      titleSize=titleSize,
      dotSize=dotSize,
      axisSize=axisSize, axisLabelSize=axisLabelSize,
      summary="median",
      combinePlot="all"
    ))
    res.list <- c(res.list, violinScore)
    }

    scatterCall <- list(scatter_doubletCall = plotSCEDimReduceColData(
      inSCE=inSCESub,
      sample=sampleSub,
      colorBy="scrublet_call",
      conditionClass="factor",
      shape=shape,
      reducedDimName=reducedDimName,
      xlab=xlab,
      ylab=ylab,
      dim1=dim1,
      dim2=dim2,
      bin=bin,
      binLabel=binLabel,
      dotSize=dotSize,
      transparency=transparency,
      colorScale = c("lightgray","red"),
      defaultTheme=defaultTheme,
      title="Scrublet Doublet Assignment",
      titleSize=titleSize,
      axisSize=axisSize, axisLabelSize=axisLabelSize,
      labelClusters=FALSE,
      legendTitle="Doublet \nAssignment",
      legendTitleSize=legendTitleSize,
      legendSize=legendSize,
      combinePlot="all"
    ))
    res.list <- c(res.list, scatterCall)

    return(res.list)
  })

  if (length(unique(samples)) > 1) {
      names(plotlist) <- samples
      plotlist <- c(merged.plots, list(Sample = plotlist))
  } else {
      plotlist <- unlist(plotlist, recursive=FALSE)
      plotLabels <- "none"
      relHeights=1
  }

  if(!is.null(combinePlot)){
    if(combinePlot %in% c("all", "sample")){
      plotlist <- .ggSCTKCombinePlots(plotlist, combinePlot = combinePlot,
                                      relHeights = relHeights,
                                      relWidths = relWidths,
                                      ncols = plotNCols,
                                      nrows = plotNRows,
                                      labels = plotLabels,
                                      labelSize = plotLabelSize,
                                      labelPositionX = plotLabelPositionX,
                                      labelPositionY = plotLabelPositionY,
                                      samplePerColumn = samplePerColumn,
                                      sampleRelHeights = sampleRelHeights,
                                      sampleRelWidths = sampleRelWidths)
    }
  }

  return(plotlist)
}

#' @title Plots for runDoubletFinder outputs.
#' @description A wrapper function which visualizes outputs from the
#'  runDoubletFinder function stored in the colData slot of the
#'  SingleCellExperiment object via various plots.
#' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved
#' dimension reduction components or a variable with saved results from
#' \link{runDoubletFinder}. Required.
#' @param sample Character vector. Indicates which sample each cell belongs to.
#'  Default NULL.
#' @param shape If provided, add shapes based on the value.
#' @param groupBy Groupings for each numeric value. A user may input a vector
#'  equal length to the number of the samples in the SingleCellExperiment
#'  object, or can be retrieved from the colData slot. Default NULL.
#' @param violin Boolean. If TRUE, will plot the violin plot. Default TRUE.
#' @param boxplot Boolean. If TRUE, will plot boxplots for each violin plot.
#'  Default TRUE.
#' @param dots Boolean. If TRUE, will plot dots for each violin plot.
#'  Default TRUE.
#' @param reducedDimName Saved dimension reduction name in the
#' \linkS4class{SingleCellExperiment} object. Required.
#' @param xlab Character vector. Label for x-axis. Default NULL.
#' @param ylab Character vector. Label for y-axis. Default NULL.
#' @param dim1 1st dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param dim2 2nd dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param bin Numeric vector. If single value, will divide the numeric values into the `bin` groups.
#'  If more than one value, will bin numeric values using values as a cut point.
#' @param binLabel Character vector. Labels for the bins created by the `bin` parameter.
#'  Default NULL.
#' @param defaultTheme Removes grid in plot and sets axis title size to 10
#'  when TRUE. Default TRUE.
#' @param dotSize Size of dots. Default 1.
#' @param transparency Transparency of the dots, values will be 0-1. Default 1.
#' @param titleSize Size of title of plot. Default 18.
#' @param axisSize Size of x/y-axis ticks. Default 15.
#' @param axisLabelSize Size of x/y-axis labels. Default 18.
#' @param legendSize size of legend. Default 15.
#' @param legendTitleSize size of legend title. Default 16.
#' @param combinePlot Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object,
#' while "sample" will output a list of plots separated by sample. Default "all".
#' @param relHeights Relative heights of plots when combine is set.
#' @param relWidths Relative widths of plots when combine is set.
#' @param plotNCols Number of columns when plots are combined in a grid.
#' @param plotNRows Number of rows when plots are combined in a grid.
#' @param plotLabels labels to each plot. If set to "default", will use the name of the samples
#'  as the labels. If set to "none", no label will be plotted.
#' @param plotLabelSize size of labels
#' @param plotLabelPositionX Numeric vector. The X position of the plot label.
#' @param plotLabelPositionY Numeric vector. The Y position of the plot label.
#' @param samplePerColumn If TRUE, when there are multiple samples and combining by "all",
#'  the output .ggplot will have plots from each sample on a single column. Default TRUE.
#' @param sampleRelHeights If there are multiple samples and combining by "all",
#'  the relative heights for each plot.
#' @param sampleRelWidths If there are multiple samples and combining by "all",
#'  the relative widths for each plot.
#' @return list of .ggplot objects
#' @examples
#' data(scExample, package="singleCellTK")
#' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
#' sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP")
#' sce <- runDoubletFinder(sce)
#' plotDoubletFinderResults(inSCE=sce, reducedDimName="UMAP")
#' @export
plotDoubletFinderResults <- function(inSCE,
                                     sample=NULL,
                                     shape=NULL,
                                     groupBy=NULL,
                                     combinePlot="all",
                                     violin=TRUE,
                                     boxplot=FALSE,
                                     dots=TRUE,
                                     reducedDimName=NULL,
                                     xlab=NULL,
                                     ylab=NULL,
                                     dim1=NULL,
                                     dim2=NULL,
                                     bin=NULL,
                                     binLabel=NULL,
                                     defaultTheme=TRUE,
                                     dotSize=1,
                                     transparency=1,
                                     titleSize=18,
                                     axisLabelSize=18,
                                     axisSize=15,
                                     legendSize=15,
                                     legendTitleSize=16,
                                     relHeights=c(1.5, 1, 1),
                                     relWidths=c(1, 1, 1),
                                     plotNCols = NULL,
                                     plotNRows = NULL,
                                     plotLabels = "default",
                                     plotLabelSize = 20,
                                     plotLabelPositionX = NULL,
                                     plotLabelPositionY = NULL,
                                     samplePerColumn = TRUE,
                                     sampleRelHeights = 1,
                                     sampleRelWidths = 1) {
  if (!is.null(sample)) {
    if (length(sample) != ncol(inSCE)) {
      stop(
        "'sample' must be the same length as the number",
        " of columns in 'inSCE'"
      )
    }
  } else {
    sample <- rep(1, ncol(inSCE))
  }
  sampleVector <- sample
  samples <- unique(sample)
  df.scores <- grep(
    pattern="doubletFinder_doublet_score_resolution_",
    names(colData(inSCE)), value=TRUE
  )

  df.labels <- grep(
    pattern="doubletFinder_doublet_label_resolution_",
    names(colData(inSCE)), value=TRUE
  )
  if (length(samples) > 1) {
    merged.plots <- lapply(df.scores, function(x) {
      plotSCEViolinColData(
        inSCE=inSCE,
        coldata=x,
        sample=NULL,
        xlab="",
        ylab="Doublet Score",
        groupBy=sampleVector,
        violin=violin,
        boxplot=boxplot,
        dots=TRUE,
        transparency=transparency,
        axisSize=axisSize,
        axisLabelSize=axisLabelSize,
        defaultTheme=defaultTheme,
        titleSize=titleSize,
        title=paste(
          "DoubletFinder Score Resolution",
          gsub(
            pattern="doubletFinder_doublet_score_Resolution_",
            "", x
          )
        ),
        dotSize=dotSize,
        summary="median",
        combinePlot = "all",
        plotLabels = "none"
      )
    })

    names(merged.plots) <- vapply(df.scores, function(x) {
      paste0("Violin_", gsub(
        pattern="doubletFinder_doublet_score_",
        "", x=x
      ))
    }, character(1))

    # merged.plots <- list(merged.plots)
    merged.plots <- list(Violin = merged.plots)
  }

  res.list <- list()
  plotlist <- lapply(samples, function(x) {
    sampleInd <- which(sample == x)
    sampleSub <- sample[sampleInd]
    inSCESub <- inSCE[, sampleInd]

    densityScore <- lapply(df.scores, function(x) {
        plotSCEDensityColData(
            inSCE=inSCESub,
            sample=sampleSub,
            coldata=x,
            groupBy=groupBy,
            xlab="Score",
            ylab="Density",
            axisSize=axisSize, axisLabelSize=axisLabelSize,
            defaultTheme=defaultTheme,
            cutoff=0.5,
            combinePlot="all",
            titleSize=titleSize,
            title=paste(
                "Density, Doublet Score Resolution",
                gsub(
                    pattern="doubletFinder_doublet_score_resolution_",
                    "", x
                )
            )
        )
    })
    names(densityScore) <- vapply(df.scores, function(x) {
        paste0("Density_", gsub(
            pattern="doubletFinder_doublet_score_",
            "", x=x
        ))
    }, character(1))
    res.list <- c(res.list, densityScore)

    scatterScore <- lapply(df.scores, function(x) {
      plotSCEDimReduceColData(
        inSCE=inSCESub,
        sample=sampleSub,
        conditionClass="numeric",
        shape=shape,
        colorBy=x,
        reducedDimName=reducedDimName,
        xlab=xlab,
        ylab=ylab,
        dim1=dim1,
        dim2=dim2,
        bin=bin,
        binLabel=binLabel,
        dotSize=dotSize,
        transparency=transparency,
        defaultTheme=defaultTheme,
        title=paste(
          "Doublet Score Resolution",
          gsub(
            pattern="doubletFinder_doublet_score_resolution_",
            "", x
          )
        ),
        titleSize=titleSize,
        axisSize=axisSize,
        axisLabelSize=axisLabelSize,
        labelClusters=FALSE,
        legendTitle="Doublet \nScore",
        legendSize=legendSize,
        legendTitleSize=legendTitleSize,
        combinePlot="all"
      )
    })

    names(scatterScore) <- vapply(df.scores, function(x) {
      paste0("Scatter_Score_", gsub(
        pattern="doubletFinder_doublet_score_",
        "", x=x
      ))
    }, character(1))
    res.list <- c(res.list, scatterScore)

    if(combinePlot != "all" | length(samples) == 1){
    violinScore <- lapply(df.scores, function(x) {
      plotSCEViolinColData(
        inSCE=inSCESub,
        coldata=x,
        sample=sampleSub,
        xlab="",
        ylab="Doublet Score",
        groupBy=groupBy,
        violin=violin,
        boxplot=boxplot,
        dots=dots,
        transparency=transparency,
        defaultTheme=defaultTheme,
        summary="median",
        title=paste(
          "Doublet Score Resolution",
          gsub(
            pattern="doubletFinder_doublet_score_resolution_",
            "", x
          )
        ),
        titleSize=titleSize,
        dotSize=dotSize,
        axisSize=axisSize,
        axisLabelSize=axisLabelSize,
        combinePlot="all"
      )
    })

    names(violinScore) <- vapply(df.scores, function(x) {
      paste0("violin_", gsub(
        pattern="doubletFinder_doublet_score_",
        "", x=x
      ))
    }, character(1))
    res.list <- c(res.list, violinScore)
    }


    scatterCall <- lapply(df.labels, function(x) {
      plotSCEDimReduceColData(
        inSCE=inSCESub,
        sample=sampleSub,
        conditionClass="factor",
        shape=shape,
        colorBy=x,
        reducedDimName=reducedDimName,
        xlab=xlab,
        ylab=ylab,
        dim1=dim1,
        dim2=dim2,
        bin=bin,
        binLabel=binLabel,
        dotSize=dotSize,
        transparency=transparency,
        colorScale = c("red","lightgray"),
        defaultTheme=defaultTheme,
        title=paste(
          "Doublet Call Resolution",
          gsub(
            pattern="doubletFinder_doublet_label_resolution_",
            "", x
          )
        ),
        titleSize=titleSize,
        axisSize=axisSize,
        axisLabelSize=axisLabelSize,
        labelClusters=FALSE,
        legendTitle="Doublet Score",
        legendSize=legendSize,
        legendTitleSize=legendTitleSize,
        combinePlot="all"
      )
    })

    names(scatterCall) <- vapply(df.labels, function(x) {
      paste0("Scatter_Call_", gsub(
        pattern="doubletFinder_doublet_label_",
        "", x=x
      ))
    }, character(1))
    res.list <- c(res.list, scatterCall)
    return(res.list)
  })
  if (length(unique(samples)) > 1) {
      names(plotlist) <- samples
      plotlist <- c(merged.plots, list(Sample = plotlist))
  } else {
      plotlist <- unlist(plotlist, recursive=FALSE)
      plotLabels <- "none"
      relHeights=1
  }
  if(!is.null(combinePlot)){
    if(combinePlot %in% c("all", "sample")){
      plotlist <- .ggSCTKCombinePlots(plotlist, combinePlot = combinePlot,
                                      relHeights = relHeights,
                                      relWidths = relWidths,
                                      ncols = plotNCols,
                                      nrows = plotNRows,
                                      labels = plotLabels,
                                      labelSize = plotLabelSize,
                                      labelPositionX = plotLabelPositionX,
                                      labelPositionY = plotLabelPositionY,
                                      samplePerColumn = samplePerColumn,
                                      sampleRelHeights = sampleRelHeights,
                                      sampleRelWidths = sampleRelWidths)
    }
  }
  return(plotlist)
}

#' @title Plots for runDoubletCells outputs.
#' @description A wrapper function which visualizes outputs from the
#'  runDoubletCells function stored in the colData slot of the
#'  SingleCellExperiment object via various plots.
#' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved
#' dimension reduction components or a variable with saved results from
#' \link{runDoubletCells}. Required.
#' @param sample Character vector. Indicates which sample each cell belongs to.
#'  Default NULL.
#' @param shape If provided, add shapes based on the value.
#' @param groupBy Groupings for each numeric value. A user may input a vector
#'  equal length to the number of the samples in the SingleCellExperiment
#'  object, or can be retrieved from the colData slot. Default NULL.
#' @param violin Boolean. If TRUE, will plot the violin plot. Default TRUE.
#' @param boxplot Boolean. If TRUE, will plot boxplots for each violin plot.
#'  Default TRUE.
#' @param dots Boolean. If TRUE, will plot dots for each violin plot.
#'  Default TRUE.
#' @param reducedDimName Saved dimension reduction name in the
#' \linkS4class{SingleCellExperiment} object. Required.
#' @param xlab Character vector. Label for x-axis. Default NULL.
#' @param ylab Character vector. Label for y-axis. Default NULL.
#' @param dim1 1st dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param dim2 2nd dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param bin Numeric vector. If single value, will divide the numeric values into the `bin` groups.
#'  If more than one value, will bin numeric values using values as a cut point.
#' @param binLabel Character vector. Labels for the bins created by the `bin` parameter.
#'  Default NULL.
#' @param defaultTheme Removes grid in plot and sets axis title size to 10
#'  when TRUE. Default TRUE.
#' @param dotSize Size of dots. Default 1.
#' @param transparency Transparency of the dots, values will be 0-1. Default 1.
#' @param titleSize Size of title of plot. Default 18.
#' @param axisSize Size of x/y-axis ticks. Default 15.
#' @param axisLabelSize Size of x/y-axis labels. Default 18.
#' @param legendSize size of legend. Default 15.
#' @param legendTitleSize size of legend title. Default 16.
#' @param combinePlot Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object,
#' while "sample" will output a list of plots separated by sample. Default "all".
#' @param relHeights Relative heights of plots when combine is set.
#' @param relWidths Relative widths of plots when combine is set.
#' @param plotNCols Number of columns when plots are combined in a grid.
#' @param plotNRows Number of rows when plots are combined in a grid.
#' @param plotLabels labels to each plot. If set to "default", will use the name of the samples
#'  as the labels. If set to "none", no label will be plotted.
#' @param plotLabelSize size of labels
#' @param plotLabelPositionX Numeric vector. The X position of the plot label.
#' @param plotLabelPositionY Numeric vector. The Y position of the plot label.
#' @param samplePerColumn If TRUE, when there are multiple samples and combining by "all",
#'  the output .ggplot will have plots from each sample on a single column. Default TRUE.
#' @param sampleRelHeights If there are multiple samples and combining by "all",
#'  the relative heights for each plot.
#' @param sampleRelWidths If there are multiple samples and combining by "all",
#'  the relative widths for each plot.
#' @return list of .ggplot objects
#' @examples
#' data(scExample, package="singleCellTK")
#' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
#' sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP")
#' sce <- runDoubletCells(sce)
#' plotDoubletCellsResults(inSCE=sce, reducedDimName="UMAP")
#' @export
plotDoubletCellsResults <- function(inSCE,
                                    sample=NULL,
                                    shape=NULL,
                                    groupBy=NULL,
                                    combinePlot="all",
                                    violin=TRUE,
                                    boxplot=FALSE,
                                    dots=TRUE,
                                    reducedDimName=NULL,
                                    xlab=NULL,
                                    ylab=NULL,
                                    dim1=NULL,
                                    dim2=NULL,
                                    bin=NULL,
                                    binLabel=NULL,
                                    defaultTheme=TRUE,
                                    dotSize=1,
                                    transparency=1,
                                    titleSize=18,
                                    axisLabelSize=18,
                                    axisSize=15,
                                    legendSize=15,
                                    legendTitleSize=16,
                                    relHeights=c(1.5, 1, 1),
                                    relWidths=c(1, 1, 1),
                                    plotNCols = NULL,
                                    plotNRows = NULL,
                                    plotLabels = "default",
                                    plotLabelSize = 20,
                                    plotLabelPositionX = NULL,
                                    plotLabelPositionY = NULL,
                                    samplePerColumn = TRUE,
                                    sampleRelHeights = 1,
                                    sampleRelWidths = 1) {
  if (!is.null(sample)) {
    if (length(sample) != ncol(inSCE)) {
      stop(
        "'sample' must be the same length as the number",
        " of columns in 'inSCE'"
      )
    }
  } else {
    sample <- rep(1, ncol(inSCE))
  }
  sampleVector <- sample


  coldata = "scran_doubletCells_score"
  titleDoubletCells <- "DoubletCells Doublet Score"

  samples <- unique(sample)
  if (length(samples) > 1) {
    merged.plots <- list(Score = plotSCEViolinColData(
      inSCE=inSCE,
      coldata=coldata,
      groupBy=sampleVector,
      xlab="",
      ylab="Doublet Score",
      violin=violin,
      boxplot=boxplot,
      dots=dots,
      transparency=transparency,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      title=titleDoubletCells,
      titleSize=titleSize,
      dotSize=dotSize,
      gridLine=TRUE,
      summary="median",
      combinePlot = "all",
      plotLabels = "none"
    ))
    merged.plots <- list(merged.plots)
    names(merged.plots) <- "Violin"
  }

  res.list <- list()
  plotlist <- lapply(samples, function(x) {
    sampleInd <- which(sample == x)
    sampleSub <- sample[sampleInd]
    inSCESub <- inSCE[, sampleInd]
    densityScore <- list(density_doubletScore = plotSCEDensityColData(
        inSCE=inSCESub,
        sample=sampleSub,
        coldata=coldata,
        groupBy=groupBy,
        xlab="Score",
        ylab="Density",
        axisSize=axisSize, axisLabelSize=axisLabelSize,
        defaultTheme=defaultTheme,
        title=paste0("Density, ", titleDoubletCells),
        titleSize=titleSize,
        combinePlot="all"
    ))
    res.list = c(res.list, densityScore)

    scatterScore <- list(scatter_doubletScore = plotSCEDimReduceColData(
      inSCE=inSCESub,
      sample=sampleSub,
      colorBy=coldata,
      conditionClass="numeric",
      shape=shape,
      reducedDimName=reducedDimName,
      xlab=xlab,
      ylab=ylab,
      dim1=dim1,
      dim2=dim2,
      bin=bin,
      binLabel=binLabel,
      dotSize=dotSize,
      colorLow="gray",
      colorHigh="blue",
      transparency=transparency,
      defaultTheme=defaultTheme,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      title=titleDoubletCells,
      titleSize=titleSize,
      labelClusters=FALSE,
      legendTitle="Doublet \nScore",
      legendSize=legendSize,
      legendTitleSize=legendTitleSize,
      combinePlot="all"
    ))
    res.list = c(res.list, scatterScore)

    if(combinePlot != "all" | length(samples) == 1){
    violinScore <- list(violin_doubletScore = plotSCEViolinColData(
      inSCE=inSCESub,
      coldata=coldata,
      sample=sampleSub,
      xlab="",
      ylab="Doublet Score",
      groupBy=groupBy,
      violin=violin,
      boxplot=boxplot,
      dots=dots,
      transparency=transparency,
      title=titleDoubletCells,
      titleSize=titleSize,
      defaultTheme=defaultTheme,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      dotSize=dotSize,
      summary="median",
      combinePlot="all"
    ))
    res.list = c(res.list, violinScore)
    }

    return(res.list)
  })
  if (length(unique(samples)) > 1) {
      names(plotlist) <- samples
      plotlist <- c(merged.plots, list(Sample = plotlist))
  } else {
      plotlist <- unlist(plotlist, recursive=FALSE)
      plotLabels <- "none"
      relHeights=1
  }
  if(!is.null(combinePlot)){
    if(combinePlot %in% c("all", "sample")){
      plotlist <- .ggSCTKCombinePlots(plotlist, combinePlot = combinePlot,
                                      relHeights = relHeights,
                                      relWidths = relWidths,
                                      ncols = plotNCols,
                                      nrows = plotNRows,
                                      labels = plotLabels,
                                      labelSize = plotLabelSize,
                                      labelPositionX = plotLabelPositionX,
                                      labelPositionY = plotLabelPositionY,
                                      samplePerColumn = samplePerColumn,
                                      sampleRelHeights = sampleRelHeights,
                                      sampleRelWidths = sampleRelWidths)
    }
  }
  return(plotlist)
}

#' @title Plots for runCxds outputs.
#' @description A wrapper function which visualizes outputs from the
#'  runCxds function stored in the colData slot of the
#'  SingleCellExperiment object via various plots.
#' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved
#' dimension reduction components or a variable with saved results from
#' \link{runCxds}.
#' @param sample Character vector. Indicates which sample each cell belongs to.
#'  Default NULL.
#' @param shape If provided, add shapes based on the value.
#' @param groupBy Groupings for each numeric value. A user may input a vector
#'  equal length to the number of the samples in the SingleCellExperiment
#'  object, or can be retrieved from the colData slot. Default NULL.
#' @param violin Boolean. If TRUE, will plot the violin plot. Default TRUE.
#' @param boxplot Boolean. If TRUE, will plot boxplots for each violin plot.
#'  Default TRUE.
#' @param dots Boolean. If TRUE, will plot dots for each violin plot.
#'  Default TRUE.
#' @param reducedDimName Saved dimension reduction name in the
#' \linkS4class{SingleCellExperiment} object. Required.
#' @param xlab Character vector. Label for x-axis. Default NULL.
#' @param ylab Character vector. Label for y-axis. Default NULL.
#' @param dim1 1st dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param dim2 2nd dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param bin Numeric vector. If single value, will divide the numeric values into the `bin` groups.
#'  If more than one value, will bin numeric values using values as a cut point.
#' @param binLabel Character vector. Labels for the bins created by the `bin` parameter.
#'  Default NULL.
#' @param defaultTheme Removes grid in plot and sets axis title size to 10
#'  when TRUE. Default TRUE.
#' @param dotSize Size of dots. Default 1.
#' @param transparency Transparency of the dots, values will be 0-1. Default 1.
#' @param titleSize Size of title of plot. Default 18.
#' @param axisSize Size of x/y-axis ticks. Default 15.
#' @param axisLabelSize Size of x/y-axis labels. Default 18.
#' @param legendSize size of legend. Default 15.
#' @param legendTitleSize size of legend title. Default 16.
#' @param combinePlot Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object,
#' while "sample" will output a list of plots separated by sample. Default "all".
#' @param relHeights Relative heights of plots when combine is set.
#' @param relWidths Relative widths of plots when combine is set.
#' @param plotNCols Number of columns when plots are combined in a grid.
#' @param plotNRows Number of rows when plots are combined in a grid.
#' @param plotLabels labels to each plot. If set to "default", will use the name of the samples
#'  as the labels. If set to "none", no label will be plotted.
#' @param plotLabelSize size of labels
#' @param plotLabelPositionX Numeric vector. The X position of the plot label.
#' @param plotLabelPositionY Numeric vector. The Y position of the plot label.
#' @param samplePerColumn If TRUE, when there are multiple samples and combining by "all",
#'  the output .ggplot will have plots from each sample on a single column. Default TRUE.
#' @param sampleRelHeights If there are multiple samples and combining by "all",
#'  the relative heights for each plot.
#' @param sampleRelWidths If there are multiple samples and combining by "all",
#'  the relative widths for each plot.
#' @return list of .ggplot objects
#' @examples
#' data(scExample, package="singleCellTK")
#' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
#' sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP")
#' sce <- runCxds(sce)
#' plotCxdsResults(inSCE=sce, reducedDimName="UMAP")
#' @export
plotCxdsResults <- function(inSCE,
                            sample=NULL,
                            shape=NULL,
                            groupBy=NULL,
                            combinePlot="all",
                            violin=TRUE,
                            boxplot=FALSE,
                            dots=TRUE,
                            reducedDimName=NULL,
                            xlab=NULL,
                            ylab=NULL,
                            dim1=NULL,
                            dim2=NULL,
                            bin=NULL,
                            binLabel=NULL,
                            defaultTheme=TRUE,
                            dotSize=1,
                            transparency=1,
                            titleSize=18,
                            axisLabelSize=18,
                            axisSize=15,
                            legendSize=15,
                            legendTitleSize=16,
                            relHeights=c(1.5, 1, 1),
                            relWidths=c(1, 1, 1),
                            plotNCols = NULL,
                            plotNRows = NULL,
                            plotLabels = "default",
                            plotLabelSize = 20,
                            plotLabelPositionX = NULL,
                            plotLabelPositionY = NULL,
                            samplePerColumn = TRUE,
                            sampleRelHeights = 1,
                            sampleRelWidths = 1) {
  if (!is.null(sample)) {
    if (length(sample) != ncol(inSCE)) {
      stop(
        "'sample' must be the same length as the number",
        " of columns in 'inSCE'"
      )
    }
  } else {
    sample <- rep(1, ncol(inSCE))
  }

  samples <- unique(sample)
  sampleVector <- sample
  if (length(samples) > 1) {
    merged.plots <- list(Score = plotSCEViolinColData(
      inSCE=inSCE,
      coldata="scds_cxds_score",
      groupBy=sampleVector,
      xlab="",
      ylab="Doublet Score",
      violin=violin,
      boxplot=boxplot,
      dots=dots,
      transparency=transparency,
      title="CXDS Doublet Score",
      titleSize=titleSize,
      dotSize=dotSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      gridLine=TRUE,
      summary="median",
      combinePlot = "all",
      plotLabels = "none"
    ))
    merged.plots <- list(merged.plots)
    names(merged.plots) <- "Violin"
  }

  res.list <- list()
  plotlist <- lapply(samples, function(x) {
    sampleInd <- which(sample == x)
    sampleSub <- sample[sampleInd]
    inSCESub <- inSCE[, sampleInd]

    densityScore <- list(density_doubletScore = plotSCEDensityColData(
        inSCE=inSCESub,
        sample=sampleSub,
        coldata="scds_cxds_score",
        groupBy=groupBy,
        xlab="Score",
        ylab="Density",
        axisSize=axisSize,
        axisLabelSize=axisLabelSize,
        defaultTheme=defaultTheme,
        title="Density, CXDS Score",
        titleSize=titleSize,
        plotLabels = NULL,
        combinePlot="all"
    ))
    res.list = c(res.list, densityScore)

    scatterScore <- list(scatter_doubletScore = plotSCEDimReduceColData(
      inSCE=inSCESub,
      sample=sampleSub,
      colorBy="scds_cxds_score",
      conditionClass="numeric",
      shape=shape,
      reducedDimName=reducedDimName,
      xlab=xlab,
      ylab=ylab,
      dim1=dim1,
      dim2=dim2,
      bin=bin,
      binLabel=binLabel,
      dotSize=dotSize,
      transparency=transparency,
      defaultTheme=defaultTheme,
      title="CXDS Doublet Score",
      titleSize=titleSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      labelClusters=FALSE,
      legendTitle="Doublet \nScore",
      legendSize=legendSize,
      legendTitleSize=legendTitleSize,
      plotLabels = NULL,
      combinePlot="all"
    ))
    res.list = c(res.list, scatterScore)

    if(combinePlot != "all" | length(samples) == 1){
    violinScore <- list(violin_doubletScore = plotSCEViolinColData(
      inSCE=inSCESub,
      coldata="scds_cxds_score",
      sample=sampleSub,
      xlab="",
      ylab="Doublet Score",
      groupBy=groupBy,
      violin=violin,
      boxplot=boxplot,
      dots=dots,
      transparency=transparency,
      title="CXDS Doublet Score",
      titleSize=titleSize,
      defaultTheme=defaultTheme,
      dotSize=dotSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      summary="median",
      combinePlot="all"
    ))
    res.list = c(res.list, violinScore)
  }

    if("scds_cxds_call" %in% names(SingleCellExperiment::colData(inSCE))){
      scatterCall <- list(scatter_doubletCall = plotSCEDimReduceColData(
          inSCE=inSCESub,
          sample=sampleSub,
          colorBy="scds_cxds_call",
          conditionClass="factor",
          shape=shape,
          reducedDimName=reducedDimName,
          xlab=xlab,
          ylab=ylab,
          dim1=dim1,
          dim2=dim2,
          bin=bin,
          binLabel=binLabel,
          dotSize=dotSize,
          transparency=transparency,
          colorScale = c("lightgray","red"),
          defaultTheme=defaultTheme,
          title="CXDS Doublet Assignment",
          titleSize=titleSize,
          axisSize=axisSize, axisLabelSize=axisLabelSize,
          labelClusters=FALSE,
          legendTitle="Doublet \nAssignment",
          legendTitleSize=legendTitleSize,
          legendSize=legendSize,
          combinePlot="all"
      ))
      res.list <- c(res.list, scatterCall)
    }
    return(res.list)
  })
  if (length(unique(samples)) > 1) {
      names(plotlist) <- samples
      plotlist <- c(merged.plots, list(Sample = plotlist))
  } else {
      plotlist <- unlist(plotlist, recursive=FALSE)
      plotLabels <- "none"
      relHeights=1
  }
  if(!is.null(combinePlot)){
    if(combinePlot %in% c("all", "sample")){
      plotlist <- .ggSCTKCombinePlots(plotlist, combinePlot = combinePlot,
                                      relHeights = relHeights,
                                      relWidths = relWidths,
                                      ncols = plotNCols,
                                      nrows = plotNRows,
                                      labels = plotLabels,
                                      labelSize = plotLabelSize,
                                      labelPositionX = plotLabelPositionX,
                                      labelPositionY = plotLabelPositionY,
                                      samplePerColumn = samplePerColumn,
                                      sampleRelHeights = sampleRelHeights,
                                      sampleRelWidths = sampleRelWidths)
    }
  }
  return(plotlist)
}

#' @title Plots for runBcds outputs.
#' @description A wrapper function which visualizes outputs from the
#'  runBcds function stored in the colData slot of the
#'  SingleCellExperiment object via various plots.
#' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved
#' dimension reduction components or a variable with saved results from
#' \link{runBcds}. Required.
#' @param sample Character vector. Indicates which sample each cell belongs to.
#'  Default NULL.
#' @param shape If provided, add shapes based on the value.
#' @param groupBy Groupings for each numeric value. A user may input a vector
#'  equal length to the number of the samples in the SingleCellExperiment
#'  object, or can be retrieved from the colData slot. Default NULL.
#' @param violin Boolean. If TRUE, will plot the violin plot. Default TRUE.
#' @param boxplot Boolean. If TRUE, will plot boxplots for each violin plot.
#'  Default TRUE.
#' @param dots Boolean. If TRUE, will plot dots for each violin plot.
#'  Default TRUE.
#' @param reducedDimName Saved dimension reduction name in the
#' \linkS4class{SingleCellExperiment} object. Required.
#' @param xlab Character vector. Label for x-axis. Default NULL.
#' @param ylab Character vector. Label for y-axis. Default NULL.
#' @param dim1 1st dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param dim2 2nd dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param bin Numeric vector. If single value, will divide the numeric values into the `bin` groups.
#'  If more than one value, will bin numeric values using values as a cut point.
#' @param binLabel Character vector. Labels for the bins created by the `bin` parameter.
#'  Default NULL.
#' @param defaultTheme Removes grid in plot and sets axis title size to 10
#'  when TRUE. Default TRUE.
#' @param dotSize Size of dots. Default 1.
#' @param transparency Transparency of the dots, values will be 0-1. Default 1.
#' @param titleSize Size of title of plot. Default 18.
#' @param axisSize Size of x/y-axis ticks. Default 15.
#' @param axisLabelSize Size of x/y-axis labels. Default 18.
#' @param legendSize size of legend. Default 15.
#' @param legendTitleSize size of legend title. Default 16.
#' @param combinePlot Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object,
#' while "sample" will output a list of plots separated by sample. Default "all".
#' @param relHeights Relative heights of plots when combine is set.
#' @param relWidths Relative widths of plots when combine is set.
#' @param plotNCols Number of columns when plots are combined in a grid.
#' @param plotNRows Number of rows when plots are combined in a grid.
#' @param plotLabels labels to each plot. If set to "default", will use the name of the samples
#'  as the labels. If set to "none", no label will be plotted.
#' @param plotLabelSize size of labels
#' @param plotLabelPositionX Numeric vector. The X position of the plot label.
#' @param plotLabelPositionY Numeric vector. The Y position of the plot label.
#' @param samplePerColumn If TRUE, when there are multiple samples and combining by "all",
#'  the output .ggplot will have plots from each sample on a single column. Default TRUE.
#' @param sampleRelHeights If there are multiple samples and combining by "all",
#'  the relative heights for each plot.
#' @param sampleRelWidths If there are multiple samples and combining by "all",
#'  the relative widths for each plot.
#' @return list of .ggplot objects
#' @examples
#' data(scExample, package="singleCellTK")
#' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
#' sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP")
#' sce <- runBcds(sce)
#' plotBcdsResults(inSCE=sce, reducedDimName="UMAP")
#' @export
plotBcdsResults <- function(inSCE,
                            sample=NULL,
                            shape=NULL,
                            groupBy=NULL,
                            combinePlot="all",
                            violin=TRUE,
                            boxplot=FALSE,
                            dots=TRUE,
                            reducedDimName=NULL,
                            xlab=NULL,
                            ylab=NULL,
                            dim1=NULL,
                            dim2=NULL,
                            bin=NULL,
                            binLabel=NULL,
                            defaultTheme=TRUE,
                            dotSize=1,
                            transparency=1,
                            titleSize=18,
                            axisLabelSize=18,
                            axisSize=15,
                            legendSize=15,
                            legendTitleSize=16,
                            relHeights=c(1.5, 1, 1),
                            relWidths=c(1, 1, 1),
                            plotNCols = NULL,
                            plotNRows = NULL,
                            plotLabels = "default",
                            plotLabelSize = 20,
                            plotLabelPositionX = NULL,
                            plotLabelPositionY = NULL,
                            samplePerColumn = TRUE,
                            sampleRelHeights = 1,
                            sampleRelWidths = 1) {
  if (!is.null(sample)) {
    if (length(sample) != ncol(inSCE)) {
      stop(
        "'sample' must be the same length as the number",
        " of columns in 'inSCE'"
      )
    }
  } else {
    sample <- rep(1, ncol(inSCE))
  }

  samples <- unique(sample)
  sampleVector <- sample
  if (length(samples) > 1) {
    merged.plots <- list(Score = plotSCEViolinColData(
      inSCE=inSCE,
      coldata="scds_bcds_score",
      groupBy=sampleVector,
      xlab="",
      ylab="Doublet Score",
      violin=violin,
      boxplot=boxplot,
      dots=dots,
      transparency=transparency,
      title="BCDS Doublet Score",
      titleSize=titleSize,
      dotSize=dotSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      gridLine=TRUE,
      summary="median",
      combinePlot = "all",
      plotLabels = "none"
    ))
    merged.plots <- list(merged.plots)
    names(merged.plots) <- "Violin"
  }

  res.list <- list()
  plotlist <- lapply(samples, function(x) {
    sampleInd <- which(sample == x)
    sampleSub <- sample[sampleInd]
    inSCESub <- inSCE[, sampleInd]

    densityScore <- list(density_doubletScore = plotSCEDensityColData(
      inSCE=inSCESub,
      sample=sampleSub,
      coldata="scds_bcds_score",
      groupBy=groupBy,
      xlab="Score",
      ylab="Density",
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      defaultTheme=defaultTheme,
      title="Density, BCDS Score",
      titleSize=titleSize,
      plotLabels = NULL,
      combinePlot="all"
    ))
    res.list = c(res.list, densityScore)

    scatterScore <- list(scatter_doubletScore = plotSCEDimReduceColData(
      inSCE=inSCESub,
      sample=sampleSub,
      colorBy="scds_bcds_score",
      conditionClass="numeric",
      shape=shape,
      reducedDimName=reducedDimName,
      xlab=xlab,
      ylab=ylab,
      dim1=dim1,
      dim2=dim2,
      bin=bin,
      binLabel=binLabel,
      dotSize=dotSize,
      transparency=transparency,
      defaultTheme=defaultTheme,
      title="BCDS Doublet Score",
      titleSize=titleSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      labelClusters=FALSE,
      legendTitle="Doublet \nScore",
      legendSize=legendSize,
      legendTitleSize=legendTitleSize,
      plotLabels = NULL,
      combinePlot="all"
    ))
    res.list = c(res.list, scatterScore)

    if(combinePlot != "all" | length(samples) == 1){
      violinScore <- list(violin_doubletScore = plotSCEViolinColData(
        inSCE=inSCESub,
        coldata="scds_bcds_score",
        sample=sampleSub,
        xlab="",
        ylab="Doublet Score",
        groupBy=groupBy,
        violin=violin,
        boxplot=boxplot,
        dots=dots,
        transparency=transparency,
        title="BCDS Doublet Score",
        titleSize=titleSize,
        defaultTheme=defaultTheme,
        dotSize=dotSize,
        axisSize=axisSize,
        axisLabelSize=axisLabelSize,
        summary="median",
        combinePlot="all"
      ))
      res.list = c(res.list, violinScore)
    }

    if("scds_bcds_call" %in% names(SingleCellExperiment::colData(inSCE))){
      scatterCall <- list(scatter_doubletCall = plotSCEDimReduceColData(
        inSCE=inSCESub,
        sample=sampleSub,
        colorBy="scds_bcds_call",
        conditionClass="factor",
        shape=shape,
        reducedDimName=reducedDimName,
        xlab=xlab,
        ylab=ylab,
        dim1=dim1,
        dim2=dim2,
        bin=bin,
        binLabel=binLabel,
        dotSize=dotSize,
        transparency=transparency,
        colorScale = c("lightgray","red"),
        defaultTheme=defaultTheme,
        title="BCDS Doublet Assignment",
        titleSize=titleSize,
        axisSize=axisSize, axisLabelSize=axisLabelSize,
        labelClusters=FALSE,
        legendTitle="Doublet \nAssignment",
        legendTitleSize=legendTitleSize,
        legendSize=legendSize,
        combinePlot="all"
      ))
      res.list <- c(res.list, scatterCall)
    }
    return(res.list)
  })
  if (length(unique(samples)) > 1) {
    names(plotlist) <- samples
    plotlist <- c(merged.plots, list(Sample = plotlist))
  } else {
    plotlist <- unlist(plotlist, recursive=FALSE)
    plotLabels <- "none"
    relHeights=1
  }
  if(!is.null(combinePlot)){
    if(combinePlot %in% c("all", "sample")){
      plotlist <- .ggSCTKCombinePlots(plotlist, combinePlot = combinePlot,
                                      relHeights = relHeights,
                                      relWidths = relWidths,
                                      ncols = plotNCols,
                                      nrows = plotNRows,
                                      labels = plotLabels,
                                      labelSize = plotLabelSize,
                                      labelPositionX = plotLabelPositionX,
                                      labelPositionY = plotLabelPositionY,
                                      samplePerColumn = samplePerColumn,
                                      sampleRelHeights = sampleRelHeights,
                                      sampleRelWidths = sampleRelWidths)
    }
  }
  return(plotlist)
}


#' @title Plots for runCxdsBcdsHybrid outputs.
#' @description A wrapper function which visualizes outputs from the
#'  runCxdsBcdsHybrid function stored in the colData slot of the
#'  SingleCellExperiment object via various plots.
#' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved
#' dimension reduction components or a variable with saved results from
#' \link{runCxdsBcdsHybrid}. Required.
#' @param sample Character vector. Indicates which sample each cell belongs to.
#'  Default NULL.
#' @param shape If provided, add shapes based on the value.
#' @param groupBy Groupings for each numeric value. A user may input a vector
#'  equal length to the number of the samples in the SingleCellExperiment
#'  object, or can be retrieved from the colData slot. Default NULL.
#' @param violin Boolean. If TRUE, will plot the violin plot. Default TRUE.
#' @param boxplot Boolean. If TRUE, will plot boxplots for each violin plot.
#'  Default TRUE.
#' @param dots Boolean. If TRUE, will plot dots for each violin plot.
#'  Default TRUE.
#' @param reducedDimName Saved dimension reduction name in the
#' \linkS4class{SingleCellExperiment} object. Required.
#' @param xlab Character vector. Label for x-axis. Default NULL.
#' @param ylab Character vector. Label for y-axis. Default NULL.
#' @param dim1 1st dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param dim2 2nd dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param bin Numeric vector. If single value, will divide the numeric values into the `bin` groups.
#'  If more than one value, will bin numeric values using values as a cut point.
#' @param binLabel Character vector. Labels for the bins created by the `bin` parameter.
#'  Default NULL.
#' @param defaultTheme Removes grid in plot and sets axis title size to 10
#'  when TRUE. Default TRUE.
#' @param dotSize Size of dots. Default 1.
#' @param transparency Transparency of the dots, values will be 0-1. Default 1.
#' @param titleSize Size of title of plot. Default 18.
#' @param axisSize Size of x/y-axis ticks. Default 15.
#' @param axisLabelSize Size of x/y-axis labels. Default 18.
#' @param legendSize size of legend. Default 15.
#' @param legendTitleSize size of legend title. Default 16.
#' @param combinePlot Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object,
#' while "sample" will output a list of plots separated by sample. Default "all".
#' @param relHeights Relative heights of plots when combine is set.
#' @param relWidths Relative widths of plots when combine is set.
#' @param plotNCols Number of columns when plots are combined in a grid.
#' @param plotNRows Number of rows when plots are combined in a grid.
#' @param plotLabels labels to each plot. If set to "default", will use the name of the samples
#'  as the labels. If set to "none", no label will be plotted.
#' @param plotLabelSize size of labels
#' @param plotLabelPositionX Numeric vector. The X position of the plot label.
#' @param plotLabelPositionY Numeric vector. The Y position of the plot label.
#' @param samplePerColumn If TRUE, when there are multiple samples and combining by "all",
#'  the output .ggplot will have plots from each sample on a single column. Default TRUE.
#' @param sampleRelHeights If there are multiple samples and combining by "all",
#'  the relative heights for each plot.
#' @param sampleRelWidths If there are multiple samples and combining by "all",
#'  the relative widths for each plot.
#' @return list of .ggplot objects
#' @examples
#' data(scExample, package="singleCellTK")
#' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
#' sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP")
#' sce <- runCxdsBcdsHybrid(sce)
#' plotScdsHybridResults(inSCE=sce, reducedDimName="UMAP")
#' @export
plotScdsHybridResults <- function(inSCE,
                                  sample=NULL,
                                  shape=NULL,
                                  groupBy=NULL,
                                  combinePlot="all",
                                  violin=TRUE,
                                  boxplot=FALSE,
                                  dots=TRUE,
                                  reducedDimName=NULL,
                                  xlab=NULL,
                                  ylab=NULL,
                                  dim1=NULL,
                                  dim2=NULL,
                                  bin=NULL,
                                  binLabel=NULL,
                                  defaultTheme=TRUE,
                                  dotSize=1,
                                  transparency=1,
                                  titleSize=18,
                                  axisLabelSize=18,
                                  axisSize=15,
                                  legendSize=15,
                                  legendTitleSize=16,
                                  relHeights=c(1.5, 1, 1),
                                  relWidths=c(1, 1, 1),
                                  plotNCols = NULL,
                                  plotNRows = NULL,
                                  plotLabels = "default",
                                  plotLabelSize = 20,
                                  plotLabelPositionX = NULL,
                                  plotLabelPositionY = NULL,
                                  samplePerColumn = TRUE,
                                  sampleRelHeights = 1,
                                  sampleRelWidths = 1) {
  if (!is.null(sample)) {
    if (length(sample) != ncol(inSCE)) {
      stop(
        "'sample' must be the same length as the number",
        " of columns in 'inSCE'"
      )
    }
  } else {
    sample <- rep(1, ncol(inSCE))
  }

  samples <- unique(sample)
  sampleVector <- sample
  if (length(samples) > 1) {
    merged.plots <- list(Score = plotSCEViolinColData(
      inSCE=inSCE,
      coldata="scds_hybrid_score",
      groupBy=sampleVector,
      xlab="",
      ylab="Doublet Score",
      violin=violin,
      boxplot=boxplot,
      dots=dots,
      transparency=transparency,
      title="CXDS BCDS Doublet Score",
      titleSize=titleSize,
      dotSize=dotSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      gridLine=TRUE,
      summary="median",
      combinePlot = "all",
      plotLabels = "none"
    ))
    merged.plots <- list(merged.plots)
    names(merged.plots) <- "Violin"
  }

  res.list <- c()
  plotlist <- lapply(samples, function(x) {
    sampleInd <- which(sample == x)
    sampleSub <- sample[sampleInd]
    inSCESub <- inSCE[, sampleInd]
    densityScore <- list(density_doubletScore = plotSCEDensityColData(
        inSCE=inSCESub,
        sample=sampleSub,
        coldata="scds_hybrid_score",
        groupBy=groupBy,
        xlab="Score",
        ylab="Density",
        axisSize=axisSize,
        axisLabelSize=axisLabelSize,
        defaultTheme=defaultTheme,
        title="Density, CXDS BCDS Hybrid Score",
        titleSize=titleSize,
        combinePlot="all"
    ))
    res.list = c(res.list, densityScore)

    scatterScore <- list(scatter_doubletScore = plotSCEDimReduceColData(
      inSCE=inSCESub,
      sample=sampleSub,
      colorBy="scds_hybrid_score",
      conditionClass="numeric",
      shape=shape,
      reducedDimName=reducedDimName,
      xlab=xlab,
      ylab=ylab,
      dim1=dim1,
      dim2=dim2,
      bin=bin,
      binLabel=binLabel,
      dotSize=dotSize,
      transparency=transparency,
      defaultTheme=defaultTheme,
      title="CXDS BCDS Doublet Score",
      titleSize=titleSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      labelClusters=FALSE,
      legendTitle="Doublet \nScore",
      legendTitleSize=legendTitleSize,
      legendSize=legendSize,
      combinePlot="all"
    ))
    res.list = c(res.list, scatterScore)

    if(combinePlot != "all" | length(samples) == 1){
    violinScore <- list(violin_doubletScore = plotSCEViolinColData(
      inSCE=inSCESub,
      coldata="scds_hybrid_score",
      sample=sampleSub,
      xlab="",
      ylab="Doublet Score",
      groupBy=groupBy,
      violin=violin,
      boxplot=boxplot,
      dots=dots,
      transparency=transparency,
      defaultTheme=defaultTheme,
      title="CXDS BCDS Doublet Score",
      titleSize=titleSize,
      dotSize=dotSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      summary="median",
      combinePlot="all"
    ))
    res.list = c(res.list, violinScore)
    }

    if("scds_hybrid_call" %in% names(SingleCellExperiment::colData(inSCE))){
      scatterCall <- list(scatter_doubletCall = plotSCEDimReduceColData(
        inSCE=inSCESub,
        sample=sampleSub,
        colorBy="scds_hybrid_call",
        conditionClass="factor",
        shape=shape,
        reducedDimName=reducedDimName,
        xlab=xlab,
        ylab=ylab,
        dim1=dim1,
        dim2=dim2,
        bin=bin,
        binLabel=binLabel,
        dotSize=dotSize,
        transparency=transparency,
        colorScale = c("lightgray","red"),
        defaultTheme=defaultTheme,
        title="CXDS BCDS Doublet Assignment",
        titleSize=titleSize,
        axisSize=axisSize, axisLabelSize=axisLabelSize,
        labelClusters=FALSE,
        legendTitle="Doublet \nAssignment",
        legendTitleSize=legendTitleSize,
        legendSize=legendSize,
        combinePlot="all"
      ))
      res.list <- c(res.list, scatterCall)
    }

    return(res.list)
  })

  if (length(unique(samples)) > 1) {
      names(plotlist) <- samples
      plotlist <- c(merged.plots, list(Sample = plotlist))
  } else {
      plotlist <- unlist(plotlist, recursive=FALSE)
      plotLabels <- "none"
      relHeights=1
  }
  if(!is.null(combinePlot)){
    if(combinePlot %in% c("all", "sample")){
      plotlist <- .ggSCTKCombinePlots(plotlist, combinePlot = combinePlot,
                                      relHeights = relHeights,
                                      relWidths = relWidths,
                                      ncols = plotNCols,
                                      nrows = plotNRows,
                                      labels = plotLabels,
                                      labelSize = plotLabelSize,
                                      labelPositionX = plotLabelPositionX,
                                      labelPositionY = plotLabelPositionY,
                                      samplePerColumn = samplePerColumn,
                                      sampleRelHeights = sampleRelHeights,
                                      sampleRelWidths = sampleRelWidths)
    }
  }
  return(plotlist)
}

#' @title Plots for runDecontX outputs.
#' @description A wrapper function which visualizes outputs from the
#'  runDecontX function stored in the colData slot of the
#'  SingleCellExperiment object via various plots.
#' @param inSCE Input \linkS4class{SingleCellExperiment} object with saved
#' dimension reduction components or a variable with saved results from
#' \link{runDecontX}. Required.
#' @param sample Character vector. Indicates which sample each cell belongs to.
#'  Default NULL.
#' @param shape If provided, add shapes based on the value.
#' @param groupBy Groupings for each numeric value. A user may input a vector
#'  equal length to the number of the samples in the SingleCellExperiment
#'  object, or can be retrieved from the colData slot. Default NULL.
#' @param violin Boolean. If TRUE, will plot the violin plot. Default TRUE.
#' @param boxplot Boolean. If TRUE, will plot boxplots for each violin plot.
#'  Default TRUE.
#' @param dots Boolean. If TRUE, will plot dots for each violin plot.
#'  Default TRUE.
#' @param reducedDimName Saved dimension reduction name in the
#' \linkS4class{SingleCellExperiment} object. Required.
#' @param xlab Character vector. Label for x-axis. Default NULL.
#' @param ylab Character vector. Label for y-axis. Default NULL.
#' @param dim1 1st dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param dim2 2nd dimension to be used for plotting. Can either be a string which specifies
#'  the name of the dimension to be plotted from reducedDims, or a numeric value which specifies
#'  the index of the dimension to be plotted. Default is NULL.
#' @param bin Numeric vector. If single value, will divide the numeric values into the `bin` groups.
#'  If more than one value, will bin numeric values using values as a cut point.
#' @param binLabel Character vector. Labels for the bins created by the `bin` parameter.
#'  Default NULL.
#' @param defaultTheme Removes grid in plot and sets axis title size to 10
#'  when TRUE. Default TRUE.
#' @param dotSize Size of dots. Default 1.
#' @param transparency Transparency of the dots, values will be 0-1. Default 1.
#' @param titleSize Size of title of plot. Default 18.
#' @param axisSize Size of x/y-axis ticks. Default 15.
#' @param axisLabelSize Size of x/y-axis labels. Default 18.
#' @param legendSize size of legend. Default 15.
#' @param legendTitleSize size of legend title. Default 16.
#' @param combinePlot Must be either "all", "sample", or "none". "all" will combine all plots into a single .ggplot object,
#' while "sample" will output a list of plots separated by sample. Default "all".
#' @param relHeights Relative heights of plots when combine is set.
#' @param relWidths Relative widths of plots when combine is set.
#' @param plotNCols Number of columns when plots are combined in a grid.
#' @param plotNRows Number of rows when plots are combined in a grid.
#' @param plotLabels labels to each plot. If set to "default", will use the name of the samples
#'  as the labels. If set to "none", no label will be plotted.
#' @param plotLabelSize size of labels
#' @param plotLabelPositionX Numeric vector. The X position of the plot label.
#' @param plotLabelPositionY Numeric vector. The Y position of the plot label.
#' @param samplePerColumn If TRUE, when there are multiple samples and combining by "all",
#'  the output .ggplot will have plots from each sample on a single column. Default TRUE.
#' @param sampleRelHeights If there are multiple samples and combining by "all",
#'  the relative heights for each plot.
#' @param sampleRelWidths If there are multiple samples and combining by "all",
#'  the relative widths for each plot.
#' @return list of .ggplot objects
#' @examples
#' data(scExample, package="singleCellTK")
#' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
#' sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP")
#' sce <- runDecontX(sce)
#' plotDecontXResults(inSCE=sce, reducedDimName="UMAP")
#' @export
plotDecontXResults <- function(inSCE,
                               sample=NULL,
                               shape=NULL,
                               groupBy=NULL,
                               combinePlot="all",
                               violin=TRUE,
                               boxplot=FALSE,
                               dots=TRUE,
                               reducedDimName=NULL,
                               xlab=NULL,
                               ylab=NULL,
                               dim1=NULL,
                               dim2=NULL,
                               bin=NULL,
                               binLabel=NULL,
                               defaultTheme=TRUE,
                               dotSize=1,
                               transparency=1,
                               titleSize=18,
                               axisLabelSize=18,
                               axisSize=15,
                               legendSize=15,
                               legendTitleSize=16,
                               relHeights=c(1.5, 1, 1),
                               relWidths=c(1, 1, 1),
                               plotNCols = NULL,
                               plotNRows = NULL,
                               plotLabels = "default",
                               plotLabelSize = 20,
                               plotLabelPositionX = NULL,
                               plotLabelPositionY = NULL,
                               samplePerColumn = TRUE,
                               sampleRelHeights = 1,
                               sampleRelWidths = 1) {
  if (!is.null(sample)) {
    if (length(sample) != ncol(inSCE)) {
      stop(
        "'sample' must be the same length as the number",
        " of columns in 'inSCE'"
      )
    }
  } else {
    sample <- rep(1, ncol(inSCE))
  }

  samples <- unique(sample)
  sampleVector <- sample
  if (length(samples) > 1) {
    merged.plots <- list(Score = plotSCEViolinColData(
      inSCE=inSCE,
      coldata="decontX_contamination",
      groupBy=sampleVector,
      xlab="",
      ylab="DecontX Contamination",
      violin=violin,
      boxplot=boxplot,
      dots=dots,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      transparency=transparency,
      title="DecontX Contamination Score",
      titleSize=titleSize,
      dotSize=dotSize,
      gridLine=TRUE,
      summary="median",
      combinePlot = "all",
      plotLabels = "none"
    ))
    merged.plots <- list(merged.plots)
    names(merged.plots) <- "Violin"
  }

  res.list = list()
  plotlist <- lapply(samples, function(x) {
    sampleInd <- which(sample == x)
    sampleSub <- sample[sampleInd]
    inSCESub <- inSCE[, sampleInd]
    densityContamination <- list(density_decontXContamination = plotSCEDensityColData(
        inSCE=inSCESub,
        sample=sampleSub,
        coldata="decontX_contamination",
        groupBy=groupBy,
        xlab="Score",
        ylab="Density",
        axisSize=axisSize,
        axisLabelSize=axisLabelSize,
        defaultTheme=defaultTheme,
        title="Density, DecontX Contamination Score",
        titleSize=titleSize,
        combinePlot="all"
    ))
    res.list = c(res.list, densityContamination)

    scatterContamination <- list(scatter_decontXContamination = plotSCEDimReduceColData(
      inSCE=inSCESub,
      sample=sampleSub,
      colorBy="decontX_contamination",
      conditionClass="numeric",
      shape=shape,
      reducedDimName=reducedDimName,
      xlab=xlab,
      ylab=ylab,
      dim1=dim1,
      dim2=dim2,
      bin=bin,
      binLabel=binLabel,
      dotSize=dotSize,
      axisSize=axisSize,
      axisLabelSize=axisLabelSize,
      transparency=transparency,
      defaultTheme=defaultTheme,
      title="DecontX Contamination",
      titleSize=titleSize,
      labelClusters=FALSE,
      legendTitle="Contamination",
      legendTitleSize=legendTitleSize,
      legendSize=legendSize,
      combinePlot="all"
    ))
    res.list = c(res.list, scatterContamination)

    if(combinePlot != "all" | length(samples) == 1){
    violinContamination <- list(violin_decontXContamination = plotSCEViolinColData(
        inSCE=inSCESub,
        coldata="decontX_contamination",
        sample=sampleSub,
        xlab="", ylab="DecontX Contamination",
        groupBy=groupBy,
        violin=violin,
        boxplot=boxplot,
        dots=dots,
        transparency=transparency,
        title="DecontX Contamination Score",
        titleSize=titleSize,
        defaultTheme=defaultTheme,
        axisSize=axisSize,
        axisLabelSize=axisLabelSize,
        dotSize=dotSize,
        summary="median",
        combinePlot="all"
    ))
    res.list = c(res.list, violinContamination)
    }


    scatterCluster <- list(scatter_decontXClusters = plotSCEDimReduceColData(
        inSCE=inSCESub,
        sample=sampleSub,
        colorBy="decontX_clusters",
        conditionClass="factor",
        shape=shape,
        reducedDimName=reducedDimName,
        xlab=xlab,
        ylab=ylab,
        dim1=dim1,
        dim2=dim2,
        bin=bin,
        binLabel=binLabel,
        axisSize=axisSize,
        axisLabelSize=axisLabelSize,
        dotSize=dotSize,
        transparency=transparency,
        defaultTheme=defaultTheme,
        title="DecontX Clusters",
        titleSize=titleSize,
        labelClusters=TRUE,
        legendTitle="Clusters",
        legendSize=legendSize,
        legendTitleSize=legendTitleSize,
        combinePlot="all"
    ))
    res.list = c(res.list, scatterCluster)

    return(res.list)
  })

  if (length(unique(samples)) > 1) {
      names(plotlist) <- samples
      plotlist <- c(merged.plots, list(Sample = plotlist))
  } else {
      plotlist <- unlist(plotlist, recursive=FALSE)
      plotLabels <- "none"
      relHeights=1
  }
  if(!is.null(combinePlot)){
    if(combinePlot %in% c("all", "sample")){
      plotlist <- .ggSCTKCombinePlots(plotlist, combinePlot = combinePlot,
                                      relHeights = relHeights,
                                      relWidths = relWidths,
                                      ncols = plotNCols,
                                      nrows = plotNRows,
                                      labels = plotLabels,
                                      labelSize = plotLabelSize,
                                      labelPositionX = plotLabelPositionX,
                                      labelPositionY = plotLabelPositionY,
                                      samplePerColumn = samplePerColumn,
                                      sampleRelHeights = sampleRelHeights,
                                      sampleRelWidths = sampleRelWidths)
    }
  }
  return(plotlist)
}
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singleCellTK
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

R/ggPerQCWrapper.R
In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Defines functions plotDecontXResults plotScdsHybridResults plotBcdsResults plotCxdsResults plotDoubletCellsResults plotDoubletFinderResults plotScrubletResults plotBarcodeRankDropsResults plotEmptyDropsResults plotRunPerCellQCResults

Documented in plotBarcodeRankDropsResults plotBcdsResults plotCxdsResults plotDecontXResults plotDoubletCellsResults plotDoubletFinderResults plotEmptyDropsResults plotRunPerCellQCResults plotScdsHybridResults plotScrubletResults

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

R/ggPerQCWrapper.R In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Defines functions plotDecontXResults plotScdsHybridResults plotBcdsResults plotCxdsResults plotDoubletCellsResults plotDoubletFinderResults plotScrubletResults plotBarcodeRankDropsResults plotEmptyDropsResults plotRunPerCellQCResults

Documented in plotBarcodeRankDropsResults plotBcdsResults plotCxdsResults plotDecontXResults plotDoubletCellsResults plotDoubletFinderResults plotEmptyDropsResults plotRunPerCellQCResults plotScdsHybridResults plotScrubletResults

Try the singleCellTK package in your browser

R Package Documentation

Browse R Packages

We want your feedback!

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

R/ggPerQCWrapper.R
In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
