@@ -44,102 +44,114 @@ plotBcdsResults(

 \arguments{

 \item{inSCE}{Input \linkS4class{SingleCellExperiment} object with saved

 dimension reduction components or a variable with saved results from

-\link{runBcds}. Required.}

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

-\item{sample}{Character vector. Indicates which sample each cell belongs to.

-Default NULL.}

+\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.}

+\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 the SingleCellExperiment

-object, or can be retrieved from the colData slot. Default NULL.}

+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 "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".}

+\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 TRUE, will plot the violin plot. Default TRUE.}

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

+\code{TRUE}.}

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

-Default TRUE.}

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

+plot. Default \code{TRUE}.}

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

-Default TRUE.}

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

+Default \code{TRUE}.}

-\item{reducedDimName}{Saved dimension reduction name in the

-\linkS4class{SingleCellExperiment} object. Required.}

+\item{reducedDimName}{Saved dimension reduction name in \code{inSCE}. 

+Default \code{"UMAP"}.}

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

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

-\item{ylab}{Character vector. Label for y-axis. Default 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 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. 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. Similar to \code{dim1}. 

+Default is \code{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{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 the `bin` parameter.

-Default 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 10

-when TRUE. Default TRUE.}

+\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 0.5.}

+\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 "mean" or "median". Default NULL.}

+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 3.}

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

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

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

+\code{1}.}

-\item{baseSize}{The base font size for all text. Default 15.

-Can be overwritten by titleSize, axisSize, and axisLabelSize,

-legendSize, legendTitleSize.}

+\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 NULL.}

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

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

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

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

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

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

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

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

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

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

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

+\code{1}.}

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

+\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.}

+\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.}

+\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 TRUE.}

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

+\code{TRUE}.}

-\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{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 "all",

-the relative heights for each plot.}

+\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 "all",

-the relative widths for each plot.}

+\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

- runBcds function stored in the colData slot of the

- SingleCellExperiment object via various plots.

+\code{\link{runBcds}} function stored in the colData slot of the

+\linkS4class{SingleCellExperiment} object via various plots.

 }

 \examples{

 data(scExample, package="singleCellTK")

@@ -148,3 +160,6 @@ sce <- runQuickUMAP(sce)

 sce <- runBcds(sce)

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

 }

+\seealso{

+\code{\link{runBcds}}

+}

@@ -144,8 +144,7 @@ A wrapper function which visualizes outputs from the

 \examples{

 data(scExample, package="singleCellTK")

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

-sce <- getUMAP(inSCE=sce, useAssay="counts", logNorm=TRUE, 

-               reducedDimName="UMAP")

+sce <- runQuickUMAP(sce)

 sce <- runBcds(sce)

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

 }

@@ -144,7 +144,8 @@ A wrapper function which visualizes outputs from the

 \examples{

 data(scExample, package="singleCellTK")

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

-sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP")

+sce <- getUMAP(inSCE=sce, useAssay="counts", logNorm=TRUE, 

+               reducedDimName="UMAP")

 sce <- runBcds(sce)

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

 }

@@ -13,7 +13,7 @@ plotBcdsResults(

   violin = TRUE,

   boxplot = FALSE,

   dots = TRUE,

-  reducedDimName = NULL,

+  reducedDimName = "UMAP",

   xlab = NULL,

   ylab = NULL,

   dim1 = NULL,

@@ -21,7 +21,7 @@ plotBcdsResults(

   bin = NULL,

   binLabel = NULL,

   defaultTheme = TRUE,

-  dotSize = 1,

+  dotSize = 0.5,

   summary = "median",

   summaryTextSize = 3,

   transparency = 1,

@@ -90,7 +90,7 @@ 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{dotSize}{Size of dots. Default 0.5.}

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

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

@@ -100,7 +100,7 @@ above the violin plot. Default 3.}

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

-\item{baseSize}{The base font size for all text. Default 12.

+\item{baseSize}{The base font size for all text. Default 15.

 Can be overwritten by titleSize, axisSize, and axisLabelSize,

 legendSize, legendTitleSize.}

@@ -25,7 +25,7 @@ plotBcdsResults(

   summary = "median",

   summaryTextSize = 3,

   transparency = 1,

-  baseSize = 14,

+  baseSize = 15,

   titleSize = NULL,

   axisLabelSize = NULL,

   axisSize = NULL,

@@ -92,17 +92,27 @@ when TRUE. Default TRUE.}

 \item{dotSize}{Size of dots. Default 1.}

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

+violin plot. Options are "mean" or "median". Default NULL.}

+

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

+above the violin plot. Default 3.}

+

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

-\item{titleSize}{Size of title of plot. Default 18.}

+\item{baseSize}{The base font size for all text. Default 12.

+Can be overwritten by titleSize, axisSize, and axisLabelSize,

+legendSize, legendTitleSize.}

+

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

-\item{axisLabelSize}{Size of x/y-axis labels. Default 18.}

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

-\item{axisSize}{Size of x/y-axis ticks. Default 15.}

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

-\item{legendSize}{size of legend. Default 15.}

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

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

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

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

@@ -22,20 +22,20 @@ plotBcdsResults(

   binLabel = NULL,

   defaultTheme = TRUE,

   dotSize = 1,

+  summary = "median",

+  summaryTextSize = 3,

   transparency = 1,

-  titleSize = 18,

-  axisLabelSize = 18,

-  axisSize = 15,

-  legendSize = 15,

-  legendTitleSize = 16,

-  relHeights = c(1.5, 1, 1),

+  baseSize = 14,

+  titleSize = NULL,

+  axisLabelSize = NULL,

+  axisSize = NULL,

+  legendSize = NULL,

+  legendTitleSize = NULL,

+  relHeights = 1,

   relWidths = c(1, 1, 1),

   plotNCols = NULL,

   plotNRows = NULL,

-  plotLabels = "default",

-  plotLabelSize = 20,

-  plotLabelPositionX = NULL,

-  plotLabelPositionY = NULL,

+  labelSamples = TRUE,

   samplePerColumn = TRUE,

   sampleRelHeights = 1,

   sampleRelWidths = 1

@@ -112,14 +112,7 @@ when TRUE. Default TRUE.}

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

 \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.}

@@ -130,6 +130,9 @@ the relative heights for each plot.}

 \item{sampleRelWidths}{If there are multiple samples and combining by "all",

 the relative widths for each plot.}

 }

+\value{

+list of .ggplot objects

+}

 \description{

 A wrapper function which visualizes outputs from the

  runBcds function stored in the colData slot of the

@@ -137,7 +137,7 @@ A wrapper function which visualizes outputs from the

 }

 \examples{

 data(scExample, package="singleCellTK")

-sce <- sce[, colData(sce)$type != "EmptyDroplet"]

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

 sce <- getUMAP(inSCE=sce, useAssay="counts", reducedDimName="UMAP")

 sce <- runBcds(sce)

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

@@ -55,7 +55,7 @@ Default NULL.}

 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,

+\item{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".}

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

@@ -30,6 +30,8 @@ plotBcdsResults(

   legendTitleSize = 16,

   relHeights = c(1.5, 1, 1),

   relWidths = c(1, 1, 1),

+  plotNCols = NULL,

+  plotNRows = NULL,

   plotLabels = "default",

   plotLabelSize = 20,

   plotLabelPositionX = NULL,

@@ -106,6 +108,10 @@ when TRUE. Default TRUE.}

 \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.}

@@ -8,8 +8,8 @@ plotBcdsResults(

   inSCE,

   sample = NULL,

   shape = NULL,

-  groupby = NULL,

-  combinePlot = NULL,

+  groupBy = NULL,

+  combinePlot = "all",

   violin = TRUE,

   boxplot = FALSE,

   dots = TRUE,

@@ -32,6 +32,8 @@ plotBcdsResults(

   relWidths = c(1, 1, 1),

   plotLabels = "default",

   plotLabelSize = 20,

+  plotLabelPositionX = NULL,

+  plotLabelPositionY = NULL,

   samplePerColumn = TRUE,

   sampleRelHeights = 1,

   sampleRelWidths = 1

@@ -47,7 +49,7 @@ 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

+\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.}

@@ -109,6 +111,10 @@ 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.}

@@ -9,7 +9,7 @@ plotBcdsResults(

   sample = NULL,

   shape = NULL,

   groupby = NULL,

-  combinePlot = FALSE,

+  combinePlot = NULL,

   violin = TRUE,

   boxplot = FALSE,

   dots = TRUE,

@@ -27,7 +27,14 @@ plotBcdsResults(

   axisLabelSize = 18,

   axisSize = 15,

   legendSize = 15,

-  legendTitleSize = 16

+  legendTitleSize = 16,

+  relHeights = c(1.5, 1, 1),

+  relWidths = c(1, 1, 1),

+  plotLabels = "default",

+  plotLabelSize = 20,

+  samplePerColumn = TRUE,

+  sampleRelHeights = 1,

+  sampleRelWidths = 1

 )

 }

 \arguments{

@@ -44,8 +51,8 @@ Default NULL.}

 equal length to the number of the samples in the SingleCellExperiment

 object, or can be retrieved from the colData slot. Default NULL.}

-\item{combinePlot}{Boolean. Will combine plots using `cowplot::plot_grid`.

-Default FALSE.}

+\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.}

@@ -92,6 +99,24 @@ when TRUE. Default TRUE.}

 \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{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{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

@@ -9,6 +9,7 @@ plotBcdsResults(

   sample = NULL,

   shape = NULL,

   groupby = NULL,

+  combinePlot = FALSE,

   violin = TRUE,

   boxplot = FALSE,

   dots = TRUE,

@@ -43,6 +44,9 @@ Default NULL.}

 equal length to the number of the samples in the SingleCellExperiment

 object, or can be retrieved from the colData slot. Default NULL.}

+\item{combinePlot}{Boolean. Will combine plots using `cowplot::plot_grid`.

+Default FALSE.}

+

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

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

@@ -19,10 +19,14 @@ plotBcdsResults(

   dim2 = NULL,

   bin = NULL,

   binLabel = NULL,

-  dotSize = 0.5,

-  transparency = 1,

   defaultTheme = TRUE,

-  titleSize = 18

+  dotSize = 1,

+  transparency = 1,

+  titleSize = 18,

+  axisLabelSize = 18,

+  axisSize = 15,

+  legendSize = 15,

+  legendTitleSize = 16

 )

 }

 \arguments{

@@ -68,14 +72,22 @@ 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{defaultTheme}{Removes grid in plot and sets axis title size to 10

-when TRUE. Default TRUE.}

+\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{titleSize}{Size of title of plot. Default 15.}

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

 }

 \description{

 A wrapper function which visualizes outputs from the

@@ -83,9 +95,9 @@ A wrapper function which visualizes outputs from 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")

+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")

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

 }

@@ -22,7 +22,7 @@ plotBcdsResults(

   dotSize = 0.5,

   transparency = 1,

   defaultTheme = TRUE,

-  titleSize = 15

+  titleSize = 18

 )

 }

 \arguments{

@@ -26,8 +26,9 @@ plotBcdsResults(

 )

 }

 \arguments{

-\item{inSCE}{Input SCtkExperiment object with saved dimension reduction

-components or a variable with saved results from runBcds. Required.}

+\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.}

@@ -46,8 +47,8 @@ Default TRUE.}

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

 Default TRUE.}

-\item{reducedDimName}{Saved dimension reduction name in the SCtkExperiment

-object. Required.}

+\item{reducedDimName}{Saved dimension reduction name in the

+\linkS4class{SingleCellExperiment} object. Required.}

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

new file mode 100644

@@ -0,0 +1,90 @@

+% 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,

+  violin = TRUE,

+  boxplot = FALSE,

+  dots = TRUE,

+  reducedDimName = NULL,

+  xlab = NULL,

+  ylab = NULL,

+  dim1 = NULL,

+  dim2 = NULL,

+  bin = NULL,

+  binLabel = NULL,

+  dotSize = 0.5,

+  transparency = 1,

+  defaultTheme = TRUE,

+  titleSize = 15

+)

+}

+\arguments{

+\item{inSCE}{Input SCtkExperiment object with saved dimension reduction

+components or a variable with saved results from 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{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 SCtkExperiment

+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{dotSize}{Size of dots. Default 1.}

+

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

+

+\item{defaultTheme}{Removes grid in plot and sets axis title size to 10

+when TRUE. Default TRUE.}

+

+\item{titleSize}{Size of title of plot. Default 15.}

+}

+\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")

+}