plotSCEViolinAssayData {singleCellTK} | R Documentation

## Violin plot of assay data.

### Description

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

### Usage

    plotSCEViolinAssayData(
      inSCE,
      sample = NULL,
      useAssay = "counts",
      feature,
      groupBy = NULL,
      violin = TRUE,
      boxplot = TRUE,
      dots = TRUE,
      xlab = NULL,
      ylab = NULL,
      axisSize = 10,
      axisLabelSize = 10,
      dotSize = 1,
      transparency = 1,
      defaultTheme = TRUE,
      gridLine = FALSE,
      summary = NULL,
      title = NULL,
      titleSize = NULL,
      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.
`violin` | Boolean. If TRUE, will plot the violin plot. Default TRUE.
`boxplot` | Boolean. If TRUE, will plot boxplots for each violin plot. Default TRUE.
`dots` | Boolean. If TRUE, will plot dots for each violin plot. Default TRUE.
`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.
`dotSize` | Size of dots. Default 1.
`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.
`gridLine` | Adds a horizontal grid line if TRUE. Will still be drawn even if defaultTheme is TRUE. Default FALSE.
`summary` | Adds a summary statistic, as well as a crossbar to the violin plot. Options are "mean" or "median". 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 violin plot of assay data.

### Examples

    plotSCEViolinAssayData(
      inSCE = mouseBrainSubsetSCE,
      feature = "Apoe", groupBy = "sex"
    )

[Package singleCellTK version 2.0.0 Index]