plotSCEDensityAssayData {singleCellTK} | R Documentation

## Density plot of assay data.

### Description

Visualizes values stored in the assay slot of a SingleCellExperiment object via a density plot.

### Usage

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

### Arguments

`inSCE` | Input SingleCellExperiment object with saved dimension reduction components or a variable with saved results. Required.
`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.
`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.
`cutoff` | Numeric value. The plot will be annotated with a vertical line if set. Default NULL.
`title` | Title of plot. Default NULL.
`titleSize` | Size of title of plot. Default 15.
`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 of the density plot of assay data.

### Examples

    plotSCEDensityAssayData(
      inSCE = mouseBrainSubsetSCE,
      feature = "Apoe"
    )

[Package singleCellTK version 2.0.0 Index]