% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/ggPerQCWrapper.R
 \name{plotBcdsResults}
 \alias{plotBcdsResults}
 \title{Plots for runBcds outputs.}
 \usage{
 plotBcdsResults(
   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

 )
 }
 \arguments{

 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object with saved
 dimension reduction components or a variable with saved results from
 \link{runBcds}. Required.}

 
 \item{sample}{Character vector. Indicates which sample each cell belongs to.
 Default NULL.}
 
 \item{shape}{If provided, add shapes based on the value.}
 

 \item{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.}
 

 \item{combinePlot}{Must be either "all" or "sample". "all" will combine all plots into a single .ggplot object,
 while "sample" will output a list of plots separated by sample. Default "all".}

 \item{violin}{Boolean. If TRUE, will plot the violin plot. Default TRUE.}
 
 \item{boxplot}{Boolean. If TRUE, will plot boxplots for each violin plot.
 Default TRUE.}
 
 \item{dots}{Boolean. If TRUE, will plot dots for each violin plot.
 Default TRUE.}
 

 \item{reducedDimName}{Saved dimension reduction name in the
 \linkS4class{SingleCellExperiment} object. Required.}

 
 \item{xlab}{Character vector. Label for x-axis. Default NULL.}
 
 \item{ylab}{Character vector. Label for y-axis. Default NULL.}
 
 \item{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.}
 
 \item{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.}
 
 \item{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.}
 
 \item{binLabel}{Character vector. Labels for the bins created by the `bin` parameter.
 Default NULL.}
 

 \item{defaultTheme}{Removes grid in plot and sets axis title size to 10
 when TRUE. Default TRUE.}
 

 \item{dotSize}{Size of dots. Default 1.}
 
 \item{transparency}{Transparency of the dots, values will be 0-1. Default 1.}
 

 \item{titleSize}{Size of title of plot. Default 18.}
 
 \item{axisLabelSize}{Size of x/y-axis labels. Default 18.}
 
 \item{axisSize}{Size of x/y-axis ticks. Default 15.}
 
 \item{legendSize}{size of legend. Default 15.}

 \item{legendTitleSize}{size of legend title. Default 16.}

 
 \item{relHeights}{Relative heights of plots when combine is set.}
 
 \item{relWidths}{Relative widths of plots when combine is set.}
 

 \item{plotNCols}{Number of columns when plots are combined in a grid.}
 
 \item{plotNRows}{Number of rows when plots are combined in a grid.}
 

 \item{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.}
 
 \item{plotLabelSize}{size of labels}
 

 \item{plotLabelPositionX}{Numeric vector. The X position of the plot label.}
 
 \item{plotLabelPositionY}{Numeric vector. The Y position of the plot label.}
 

 \item{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.}
 
 \item{sampleRelHeights}{If there are multiple samples and combining by "all",
 the relative heights for each plot.}
 
 \item{sampleRelWidths}{If there are multiple samples and combining by "all",
 the relative widths for each plot.}

 }
 \description{
 A wrapper function which visualizes outputs from the
  runBcds function stored in the colData slot of the
  SingleCellExperiment object via various plots.
 }
 \examples{

 data(scExample, package="singleCellTK")
 sce <- sce[, colData(sce)$type != "EmptyDroplet"]
 sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP")

 sce <- runBcds(sce)

 plotBcdsResults(inSCE=sce, reducedDimName="UMAP")

 }