Dot Plot of Marker Expression — DotPlot • phenoscapR

Dot plot where dot size represents the percentage of cells expressing a marker (above a threshold) and colour represents the mean expression. Analogous to Seurat's DotPlot.

Usage

DotPlot(
  object,
  features,
  group_by = "phenotype",
  slot = "data",
  threshold = 0,
  palette = NULL
)

Arguments

object: An SpatialCellData object.
features: Character vector. Marker names to plot.
group_by: Character. Metadata column to group by. Default "phenotype".
slot: Character. "data" or "counts".
threshold: Numeric. Expression threshold to call a cell "expressing". Default 0.
palette: Character or character vector. Colour palette for mean expression. Default NULL (global palette).

Value

A ggplot object.

Examples

counts <- matrix(c(rnorm(60, 5), rnorm(60, 0)), ncol = 4,
                 dimnames = list(NULL, c("CD3", "CD8", "CD20", "PanCK")))
coords <- data.frame(x = runif(30), y = runif(30))
meta <- data.frame(cell_id = 1:30, sample_id = "s1",
                   phenotype = rep(c("T cell", "B cell", "Other"), each = 10))
obj <- CreateSpatialObject(counts, coords, meta)
DotPlot(obj, features = c("CD3", "CD8", "CD20", "PanCK"))