Plot cell types per cluster

Usage

plotCellTypesPerCluster(object, markers, ...)

# S4 method for class '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().

Value

Show graphical output. Invisibly return list.

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.

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"
)
#> 
#> 
#> ## Cluster 1 {.tabset}
#> 
#> 
#> 
#> ### Macrophage
#> 

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