Plot highly variable genes

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")
#> Warning: collapsing to unique 'x' values
plotTopHVG(mouseBrainSubsetSCE, method = "modelGeneVar",
           n = 1000, labelsCount = 0)
#> Warning: cannot xtfrm data frames