VlnPlot {ILoReg} | R Documentation

## Gene expression visualization using violin plots

### Description

The VlnPlot function enables visualizing expression levels of a gene, or multiple genes, across clusters using Violin plots.

### Usage

    VlnPlot.SingleCellExperiment(
      object,
      clustering.type,
      genes,
      return.plot,
      rotate.x.axis.labels
    )

    ## S4 method for signature 'SingleCellExperiment'
    VlnPlot(
      object,
      clustering.type = "manual",
      genes = NULL,
      return.plot = FALSE,
      rotate.x.axis.labels = FALSE
    )

### Arguments

`object` | of `SingleCellExperiment` class
`clustering.type` | "manual" or "optimal". "manual" refers to the clustering formed using the "SelectKClusters" function and "optimal" to the clustering formed using the "CalcSilhInfo" function. Default is "manual".
`genes` | a character vector denoting the gene names that are visualized
`return.plot` | return.plot whether to return the ggplot2 object
`rotate.x.axis.labels` | a logical denoting whether the x-axis labels should be rotated 90 degrees. or just draw it. Default is `FALSE`.

### Value

ggplot2 object if return.plot=TRUE

### Examples

    library(SingleCellExperiment)
    sce <- SingleCellExperiment(assays = list(logcounts = pbmc3k_500))
    sce <- PrepareILoReg(sce)
    ## These settings are just to accelerate the example, use the defaults.
    sce <- RunParallelICP(sce,L=2,threads=1,C=0.1,k=5,r=1)
    sce <- RunPCA(sce,p=5)
    sce <- HierarchicalClustering(sce)
    sce <- SelectKClusters(sce,K=5)
    VlnPlot(sce,genes=c("CD3D","CD79A","CST3"))

[Package ILoReg version 1.2.0 Index]