Plot known markers

plotKnownMarkers(object, markers, ...)

# S4 method for SingleCellExperiment,KnownMarkers
plotKnownMarkers(object,
  markers, reducedDim = "TSNE", headerLevel = 2L, progress = FALSE,
  ...)

# S4 method for Seurat,KnownMarkers
plotKnownMarkers(object, markers,
  reducedDim = "TSNE", headerLevel = 2L, progress = FALSE, ...)

Arguments

object

Object.

markers

grouped_df. Marker genes, grouped by "cellType".

reducedDim

character(1). Name of reduced dimension matrix slotted in reducedDims(). Includes TNSE, UMAP, PCA, for example.

headerLevel

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

progress

logical(1). Show progress, using progress bars.

...

Passthrough arguments to plotMarker().

Value

Show graphical output. Invisibly return a ggplot list.

Examples

data(seurat, seurat_known_markers) plotKnownMarkers( object = seurat, markers = seurat_known_markers )
#> #> #> ## Dendritic Cell {.tabset} #>
#> #> #> ## Macrophage {.tabset} #>