Plot Marker Heatmap

Heatmap of mean marker intensity per phenotype. Analogous to Seurat's DoHeatmap.

Usage

MarkerHeatmap(
  object,
  markers = NULL,
  slot = "data",
  palette = NULL,
  title = NULL
)

Arguments

object

An SpatialCellData object with a phenotype column.

markers

Character vector or NULL. Markers to include. If NULL, all markers are shown.

slot

Character. Data slot to use: "data" (default) or "counts".

palette

Character or character vector. Default NULL (global palette).

title

Character or NULL.

Value

A ggplot object.

Examples

counts <- matrix(c(rnorm(30, 1), rnorm(30, 0), rnorm(30, 0),
                   rnorm(30, 1)), ncol = 2,
                 dimnames = list(NULL, c("CD3", "CD8")))
coords <- data.frame(x = runif(60), y = runif(60))
meta <- data.frame(cell_id = 1:60, sample_id = "s1",
                   phenotype = rep(c("A", "B"), each = 30))
obj <- CreateSpatialObject(counts, coords, meta)
MarkerHeatmap(obj)