plotEmptyDropsScatter {singleCellTK} | R Documentation

## Plots for runEmptyDrops outputs.

### Description

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

### Usage

    plotEmptyDropsScatter(
      inSCE,
      sample = NULL,
      fdrCutoff = 0.01,
      defaultTheme = TRUE,
      dotSize = 1,
      title = NULL,
      titleSize = 18,
      xlab = NULL,
      ylab = NULL,
      axisSize = 12,
      axisLabelSize = 15,
      legendTitle = NULL,
      legendTitleSize = 12,
      legendSize = 10,
      combinePlot = "none",
      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 runEmptyDrops. Required.
`sample` | Character vector. Indicates which sample each cell belongs to. Default NULL.
`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.
`title` | Title of plot. Default NULL.
`titleSize` | Size of title of plot. Default 18.
`xlab` | Character vector. Label for x-axis. Default NULL.
`ylab` | Character vector. Label for y-axis. Default NULL.
`axisSize` | Size of x/y-axis ticks. Default 12.
`axisLabelSize` | Size of x/y-axis labels. Default 15.
`legendTitle` | Title of legend. Default NULL.
`legendTitleSize` | size of legend title. Default 12.
`legendSize` | size of legend. Default 10.
`combinePlot` | Boolean. If multiple plots are generated (multiple samples, etc.), will combined plots using 'cowplot::plot_grid'. Default TRUE.
`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

a ggplot object of the scatter plot.

### Examples

    data(scExample, package="singleCellTK")
    sce <- runEmptyDrops(inSCE=sce)
    plotEmptyDropsScatter(inSCE=sce)

[Package singleCellTK version 2.0.0 Index]