plotTopHVG {singleCellTK} | R Documentation

## Plot highly variable genes

### Description

Plot highly variable genes

### Usage

    plotTopHVG(
      inSCE,
      method = c("vst", "mean.var.plot", "dispersion", "modelGeneVar"),
      hvgList = NULL,
      n = NULL,
      labelsCount = NULL
    )

### Arguments

`inSCE` | Input `SingleCellExperiment` object containing the computations.
`method` | Select either "vst", "mean.var.plot", "dispersion" or "modelGeneVar".
`hvgList` | Character vector indicating the labels of highly variable genes.
`n` | Specify the number of top genes to highlight in red. If `hvgList` parameter is not provided, this parameter can be used simply to specify the number of top genes to highlight in red.
`labelsCount` | Specify the number of data points/genes to label. By default, all top genes will be labeled.

### Value

plot object

### Examples

    data("mouseBrainSubsetSCE", package = "singleCellTK")
    mouseBrainSubsetSCE <- scranModelGeneVar(mouseBrainSubsetSCE, "logcounts")
    plotTopHVG(mouseBrainSubsetSCE, method = "modelGeneVar",
               n = 1000, labelsCount = 0)

[Package singleCellTK version 2.2.0 Index]