Plot cell types per cluster

plotCellTypesPerCluster(object, ...)

# S4 method for SingleCellExperiment
plotCellTypesPerCluster(object, markers,
  min = 1L, max = Inf, reducedDim = "TSNE", expression = c("mean",
  "sum"), headerLevel = 2L, progress = FALSE, ...)

# S4 method for Seurat
plotCellTypesPerCluster(object, markers, min = 1L,
  max = Inf, reducedDim = "TSNE", expression = c("mean", "sum"),
  headerLevel = 2L, progress = FALSE, ...)

Arguments

object

Object.

markers

KnownMarkers.

min

numeric(1). Recommended minimum value cutoff.

max

numeric(1). Recommended maximum value cutoff.

reducedDim

character(1). Name of reduced dimension matrix slotted in reducedDims(). Includes TNSE, UMAP, PCA, for example.

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.

progress

logical(1). Show progress, using progress bars.

...

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.

Examples

data(seurat, seurat_known_markers) plotCellTypesPerCluster( object = seurat, markers = seurat_known_markers )
#> #> #> ## Cluster 1 {.tabset} #> #> #> #> ### Macrophage #>
#> #> #> ## Cluster 2 {.tabset} #> #> #> #> ### Dendritic Cell #>