Plot known markers

plotKnownMarkers(object, markers, ...)

# S4 method for SingleCellExperiment,KnownMarkers
plotKnownMarkers(
  object,
  markers,
  reduction = "UMAP",
  headerLevel = 2L,
  ...,
  BPPARAM = BiocParallel::bpparam()
)

# S4 method for Seurat,KnownMarkers
plotKnownMarkers(
  object,
  markers,
  reduction = "UMAP",
  headerLevel = 2L,
  ...,
  BPPARAM = BiocParallel::bpparam()
)

Arguments

object

Object.

markers

Object.

reduction

vector(1). Dimension reduction name or index position.

headerLevel

integer(1) (1-7). Markdown header level.

...

Passthrough arguments to plotMarker().

BPPARAM

bpparamClass. BiocParallel parameter to specify the desired processor configuration.
We recommend using one of the following:

Value

Show graphical output. Invisibly return a ggplot list.

Note

Updated 2020-01-30.

Examples

data(Seurat, package = "acidtest") data(seurat_known_markers) ## Seurat ==== object <- Seurat markers <- seurat_known_markers plotKnownMarkers( object = object, markers = markers, reduction = "UMAP" )
#> #> #> ## Dendritic Cell {.tabset} #>
#> #> #> ## Macrophage {.tabset} #>