% 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 = "UMAP",

   xlab = NULL,
   ylab = NULL,
   dim1 = NULL,
   dim2 = NULL,
   bin = NULL,
   binLabel = NULL,
   defaultTheme = TRUE,

   dotSize = 0.5,

   summary = "median",
   summaryTextSize = 3,

   transparency = 1,

   baseSize = 15,

   titleSize = NULL,
   axisLabelSize = NULL,
   axisSize = NULL,
   legendSize = NULL,
   legendTitleSize = NULL,
   relHeights = 1,

   relWidths = c(1, 1, 1),

   plotNCols = NULL,
   plotNRows = NULL,

   labelSamples = TRUE,

   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

 \code{\link{runBcds}}. Required.}

 \item{sample}{Character vector or colData variable name. Indicates which 
 sample each cell belongs to. Default \code{NULL}.}

 \item{shape}{If provided, add shapes based on the value. Default \code{NULL}.}

 \item{groupBy}{Groupings for each numeric value. A user may input a vector

 equal length to the number of the samples in \code{inSCE}, or can be 
 retrieved from the colData slot. Default \code{NULL}.}

 \item{combinePlot}{Must be either \code{"all"}, \code{"sample"}, or 
 \code{"none"}. \code{"all"} will combine all plots into a single .ggplot 
 object, while \code{"sample"} will output a list of plots separated by 
 sample. Default \code{"all"}.}

 \item{violin}{Boolean. If \code{TRUE}, will plot the violin plot. Default 
 \code{TRUE}.}

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

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

 \item{reducedDimName}{Saved dimension reduction name in \code{inSCE}. 
 Default \code{"UMAP"}.}

 \item{xlab}{Character vector. Label for x-axis. Default \code{NULL}.}

 \item{ylab}{Character vector. Label for y-axis. Default \code{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 \code{NULL}.}

 \item{dim2}{2nd dimension to be used for plotting. Similar to \code{dim1}. 
 Default is \code{NULL}.}

 \item{bin}{Numeric vector. If single value, will divide the numeric values 
 into \code{bin} groups. If more than one value, will bin numeric values using
 values as a cut point. Default \code{NULL}.}

 \item{binLabel}{Character vector. Labels for the bins created by \code{bin}.
 Default \code{NULL}.}

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

 \item{dotSize}{Size of dots. Default \code{0.5}.}

 \item{summary}{Adds a summary statistic, as well as a crossbar to the

 violin plot. Options are \code{"mean"} or \code{"median"}. Default 
 \code{NULL}.}

 
 \item{summaryTextSize}{The text size of the summary statistic displayed

 above the violin plot. Default \code{3}.}

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

 \item{baseSize}{The base font size for all text. Default \code{12}.
 Can be overwritten by \code{titleSize}, \code{axisSize}, and 
 \code{axisLabelSize}, \code{legendSize}, \code{legendTitleSize}.}

 \item{titleSize}{Size of title of plot. Default \code{NULL}.}

 \item{axisLabelSize}{Size of x/y-axis labels. Default \code{NULL}.}

 \item{axisSize}{Size of x/y-axis ticks. Default \code{NULL}.}

 \item{legendSize}{size of legend. Default \code{NULL}.}

 \item{legendTitleSize}{size of legend title. Default \code{NULL}.}

 \item{relHeights}{Relative heights of plots when combine is set. Default 
 \code{1}.}

 \item{relWidths}{Relative widths of plots when combine is set. Default 
 \code{c(1, 1, 1)}.}

 \item{plotNCols}{Number of columns when plots are combined in a grid. Default 
 \code{NULL}.}

 \item{plotNRows}{Number of rows when plots are combined in a grid. Default 
 \code{NULL}.}

 \item{labelSamples}{Will label sample name in title of plot if TRUE. Default 
 \code{TRUE}.}

 \item{samplePerColumn}{If \code{TRUE}, when there are multiple samples and 
 combining by \code{"all"}, the output .ggplot will have plots from each 
 sample on a single column. Default \code{TRUE}.}

 \item{sampleRelHeights}{If there are multiple samples and combining by 
 \code{"all"}, the relative heights for each plot. Default \code{1}.}

 \item{sampleRelWidths}{If there are multiple samples and combining by 
 \code{"all"}, the relative widths for each plot. Default \code{1}.}

 }

 \value{
 list of .ggplot objects
 }

 \description{
 A wrapper function which visualizes outputs from the

 \code{\link{runBcds}} function stored in the colData slot of the
 \linkS4class{SingleCellExperiment} object via various plots.

 }
 \examples{

 data(scExample, package="singleCellTK")

 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")

 sce <- runQuickUMAP(sce)

 sce <- runBcds(sce)

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

 }

 \seealso{
 \code{\link{runBcds}}
 }