plotCeldaViolin {celda} | R Documentation

## Feature Expression Violin Plot

### Description

Outputs a violin plot for feature expression data.

### Usage

    plotCeldaViolin(
      x,
      celdaMod,
      features,
      displayName = NULL,
      useAssay = "counts",
      altExpName = "featureSubset",
      exactMatch = TRUE,
      plotDots = TRUE,
      dotSize = 0.1
    )

    ## S4 method for signature 'SingleCellExperiment'
    plotCeldaViolin(
      x,
      features,
      displayName = NULL,
      useAssay = "counts",
      altExpName = "featureSubset",
      exactMatch = TRUE,
      plotDots = TRUE,
      dotSize = 0.1
    )

    ## S4 method for signature 'ANY'
    plotCeldaViolin(
      x,
      celdaMod,
      features,
      exactMatch = TRUE,
      plotDots = TRUE,
      dotSize = 0.1
    )

### Arguments

`x` | Numeric matrix or a SingleCellExperiment object with the matrix located in the assay slot under `useAssay`. Rows represent features and columns represent cells.
`celdaMod` | Celda object of class "celda_G" or "celda_CG". Used only if `x` is a matrix object.
`features` | Character vector. Uses these genes for plotting.
`displayName` | Character. The column name of `rowData(x)` that specifies the display names for the features. Default `NULL`, which displays the row names. Only works if `x` is a SingleCellExperiment object.
`useAssay` | A string specifying which assay slot to use if `x` is a SingleCellExperiment object. Default "counts".
`altExpName` | The name for the altExp slot to use. Default "featureSubset".
`exactMatch` | Logical. Whether an exact match or a partial match using `grep()` is used to look up the feature in the rownames of the counts matrix. Default `TRUE`.
`plotDots` | Boolean. If `TRUE`, the expression of features will be plotted as points in addition to the violin curve. Default `TRUE`.
`dotSize` | Numeric. Size of points if `plotDots = TRUE`. Default `0.1`.

### Value

Violin plot for each feature, grouped by celda cluster

### Examples

    data(sceCeldaCG)
    plotCeldaViolin(x = sceCeldaCG, features = "Gene_1")
    data(celdaCGSim, celdaCGMod)
    plotCeldaViolin(x = celdaCGSim$counts,
       celdaMod = celdaCGMod,
       features = "Gene_1")

[Package celda version 1.8.1 Index]