plotRunPerCellQCResults {singleCellTK} | R Documentation

## 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.

### Usage

    plotRunPerCellQCResults(
      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
    )

### Arguments

`inSCE` | Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runPerCellQC. Required.
`sample` | Character vector. Indicates which sample each cell belongs to. Default NULL.
`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 FALSE.
`dots` | Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.
`dotSize` | Size of dots. Default 1.
`axisSize` | Size of x/y-axis ticks. Default 15.
`axisLabelSize` | Size of x/y-axis labels. Default 18.
`transparency` | Transparency of the dots, values will be 0-1. Default 1.
`defaultTheme` | Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
`titleSize` | Size of title of plot. Default 18.
`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.

### Value

list of .ggplot objects

### Examples

    data(scExample, package="singleCellTK")
    ## Not run:
    sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
    sce <- runPerCellQC(sce)
    plotRunPerCellQCResults(inSCE=sce)

    ## End(Not run)

[Package singleCellTK version 2.0.0 Index]