Plot top markers — plotTopMarkers • pointillism

Plot top markers

Usage

plotTopMarkers(object, markers, ...)

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

Arguments

object

Object.

markers

Object containing cell marker expression data.

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.

n

integer(1). Number of genes per cluster.

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.

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 2022-06-09.

Examples

data(Seurat, SeuratMarkersPerCluster, package = "AcidTest")

## Seurat, SeuratMarkersPerCluster ====
object <- Seurat
markers <- SeuratMarkersPerCluster
plotTopMarkers(
    object = object,
    markers = markers,
    reduction = "UMAP"
)
#> ℹ Including both up- and down-regulated markers.
#> 
#> 
#> ## Cluster 0 {.tabset}
#> 

#> 
#> 
#> ## Cluster 1 {.tabset}
#> 

#> 
#> 
#> ## Cluster 2 {.tabset}
#>