plotEmptyDropsResults {singleCellTK} | R Documentation

## Plots for runEmptyDrops outputs.

### Description

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

### Usage

    plotEmptyDropsResults(
      inSCE,
      sample = NULL,
      combinePlot = "all",
      fdrCutoff = 0.01,
      defaultTheme = TRUE,
      dotSize = 1,
      titleSize = 18,
      axisLabelSize = 18,
      axisSize = 15,
      legendSize = 15,
      legendTitleSize = 16,
      relHeights = 1,
      relWidths = 1,
      samplePerColumn = TRUE,
      sampleRelHeights = 1,
      sampleRelWidths = 1
    )

### Arguments

`inSCE` | Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results from runScrublet. Required.
`sample` | Character vector. Indicates which sample each cell belongs to. 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".
`fdrCutoff` | Numeric. Thresholds barcodes based on the FDR values from runEmptyDrops as "Empty Droplet" or "Putative Cell". Default 0.01.
`defaultTheme` | Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
`dotSize` | Size of dots. 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.
`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")
    sce <- runEmptyDrops(inSCE=sce)
    plotEmptyDropsResults(inSCE=sce)

[Package singleCellTK version 2.0.0 Index]