plotCellTypesPerCluster: Plot cell types per cluster

In acidgenomics/r-acidplots: Acid Genomics Plot Functions and Themes

Plot cell types per cluster

Description

Plot cell types per cluster

Usage

plotCellTypesPerCluster(object, markers, ...)

## S4 method for signature 'SingleCellExperiment,KnownMarkers'
plotCellTypesPerCluster(
  object,
  markers,
  min = 1L,
  max = Inf,
  reduction = "UMAP",
  expression = c("mean", "sum"),
  headerLevel = 2L,
  ...
)

Arguments

object	Object.
markers	Object containing gene markers.
min	numeric(1). Recommended minimum value cutoff.
max	numeric(1). Recommended maximum value cutoff.
reduction	vector(1). Dimension reduction name or index position.
expression	character(1). Calculation to apply. Uses match.arg() internally and defaults to the first argument in the character vector.
headerLevel	integer(1) (1-7). Markdown header level.
...	Passthrough arguments to plotMarker().

Details

Plot the geometric mean of the significant marker genes for every known cell type (per unbiased cluster). Cell types with too few (min cutoff) or too many (max cutoff) marker genes will be skipped.

Value

Show graphical output. Invisibly return list.

Note

Updated 2023-08-17.

Examples

data(
    KnownMarkers,
    SingleCellExperiment_Seurat,
    package = "AcidTest"
)

## SingleCellExperiment ====
object <- SingleCellExperiment_Seurat
markers <- KnownMarkers
plotCellTypesPerCluster(
    object = object,
    markers = markers,
    reduction = "UMAP"
)

acidgenomics/r-acidplots documentation built on March 30, 2024, 10:16 p.m.