Plot top markers

plotTopMarkers(object, markers, ...)

# S4 method for Seurat,SeuratMarkersPerCluster
plotTopMarkers(object, markers,
  n = 1L, direction = c("up", "down", "both"), reduction = "UMAP",
  headerLevel = 2L, progress = FALSE, ...)

Arguments

object

Object.

markers

Object containing cell marker expression data.

n

integer(1). Number of genes per cluster.

direction

character(1). Whether to include upregulated ("up"; positive LFC), downregulated ("down"; negative LFC) or "both" directions of association per cluster.

reduction

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

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.

Details

The number of markers to plot is determined by the output of the topMarkers() function. If you want to reduce the number of genes to plot, simply reassign first using that function. If necessary, we can add support for the number of genes to plot here in a future update.

Note

Updated 2019-07-31.

Examples

data(Seurat, package = "acidtest") data(seuratAllMarkers) ## Seurat, SeuratMarkersPerCluster ==== object <- Seurat markers <- seuratAllMarkers plotTopMarkers( object = object, markers = markers, reduction = "UMAP" )
#> Including upregulated markers.
#> #> #> ## Cluster 0 {.tabset} #>
#> #> #> ## Cluster 1 {.tabset} #>
#> #> #> ## Cluster 2 {.tabset} #>