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,
      summary = "median",
      summaryTextSize = 3,
      baseSize = 15,
      axisSize = NULL,
      axisLabelSize = NULL,
      transparency = 1,
      defaultTheme = TRUE,
      titleSize = NULL,
      relHeights = 1,
      relWidths = 1,
      labelSamples = TRUE,
      plotNCols = NULL,
      plotNRows = 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.
`summary` | Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". Default "median".
`summaryTextSize` | The text size of the summary statistic displayed above the violin plot. Default 3.
`baseSize` | The base font size for all text. Default 15. Can be overwritten by titleSize, axisSize, and axisLabelSize.
`axisSize` | Size of x/y-axis ticks. Default NULL.
`axisLabelSize` | Size of x/y-axis labels. Default NULL.
`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 NULL.
`relHeights` | Relative heights of plots when combine is set.
`relWidths` | Relative widths of plots when combine is set.
`labelSamples` | Will label sample name in title of plot if TRUE. Default TRUE.
`plotNCols` | Number of columns when plots are combined in a grid.
`plotNRows` | Number of rows when plots are combined in a grid.
`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 2.2.0 Index]