plotTopMarkers: Plot top markers

In acidgenomics/r-pointillism: Single-cell RNA-seq toolkit

Plot top markers

Description

Plot top markers

Usage

plotTopMarkers(object, markers, ...)

## S4 method for signature '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: bpparam. SerialParam. MulticoreParam.

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.

Value

Show graphical output. Invisibly return a ggplot list.

Note

Updated 2022-06-09.

Examples

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

## Seurat, SeuratMarkersPerCluster ====
object <- Seurat
markers <- SeuratMarkersPerCluster
plotTopMarkers(
    object = object,
    markers = markers,
    reduction = "UMAP"
)

acidgenomics/r-pointillism documentation built on Oct. 13, 2023, 3:13 p.m.