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)

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