plotDecontXResults: Plots for runDecontX outputs.
In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description Usage Arguments Value Examples

A wrapper function which visualizes outputs from the runDecontX function stored in the colData slot of the SingleCellExperiment object via various plots.

plotDecontXResults(
  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
)

`inSCE`	Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runDecontX. Required.
`sample`	Character vector. Indicates which sample each cell belongs to. Default NULL.
`shape`	If provided, add shapes based on the value.
`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.
`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".
`violin`	Boolean. If TRUE, will plot the violin plot. Default TRUE.
`boxplot`	Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.
`dots`	Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.
`reducedDimName`	Saved dimension reduction name in the SingleCellExperiment object. Required.
`xlab`	Character vector. Label for x-axis. Default NULL.
`ylab`	Character vector. Label for y-axis. Default NULL.
`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.
`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.
`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.
`binLabel`	Character vector. Labels for the bins created by the 'bin' parameter. Default NULL.
`defaultTheme`	Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
`dotSize`	Size of dots. Default 1.
`transparency`	Transparency of the dots, values will be 0-1. Default 1.
`titleSize`	Size of title of plot. Default 18.
`axisLabelSize`	Size of x/y-axis labels. Default 18.
`axisSize`	Size of x/y-axis ticks. Default 15.
`legendSize`	size of legend. Default 15.
`legendTitleSize`	size of legend title. Default 16.
`relHeights`	Relative heights of plots when combine is set.
`relWidths`	Relative widths of plots when combine is set.
`plotNCols`	Number of columns when plots are combined in a grid.
`plotNRows`	Number of rows when plots are combined in a grid.
`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.
`plotLabelSize`	size of labels
`plotLabelPositionX`	Numeric vector. The X position of the plot label.
`plotLabelPositionY`	Numeric vector. The Y position of the plot label.
`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.
`sampleRelHeights`	If there are multiple samples and combining by "all", the relative heights for each plot.
`sampleRelWidths`	If there are multiple samples and combining by "all", the relative widths for each plot.

list of .ggplot objects

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")