plotSCEDensity {singleCellTK} | R Documentation

## Density plot of any data stored in the SingleCellExperiment object.

### Description

Visualizes values stored in any slot of a SingleCellExperiment object via a densityn plot.

### Usage

    plotSCEDensity(
      inSCE,
      slot,
      annotation,
      sample = NULL,
      useAssay = "counts",
      feature = NULL,
      groupBy = NULL,
      xlab = NULL,
      ylab = NULL,
      axisSize = 10,
      axisLabelSize = 10,
      defaultTheme = TRUE,
      title = NULL,
      titleSize = 18,
      cutoff = NULL,
      combinePlot = "none",
      plotLabels = NULL
    )

### Arguments

`inSCE` | Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required
`slot` | Desired slot of SingleCellExperiment used for plotting. Possible options: "assays", "colData", "metadata"
`annotation` | Desired vector within the slot used for plotting.
`sample` | Character vector. Indicates which sample each cell belongs to.
`useAssay` | Indicate which assay to use. Default "counts".
`feature` | name of feature stored in assay of SingleCellExperiment object. Will be used only if "assays" slot is chosen. 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.
`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 10.
`axisLabelSize` | Size of x/y-axis labels. Default 10.
`defaultTheme` | Removes grid in plot and sets axis title size to 10 when TRUE. Default TRUE.
`title` | Title of plot. Default NULL.
`titleSize` | Size of title of plot. Default 15.
`cutoff` | Numeric value. The plot will be annotated with a vertical line if set. 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 "none".
`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.

### Value

a ggplot object of the density plot.

### Examples

    plotSCEDensity(
      inSCE = mouseBrainSubsetSCE, slot = "assays",
      annotation = "counts", feature = "Apoe", groupBy = "sex"
    )

[Package singleCellTK version 2.2.0 Index]