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Plot Cell Map

Source: R/plot.R
CellMap.Rd

Scatter plot of cell positions coloured by phenotype, cluster, or any metadata column. Analogous to Seurat's DimPlot but in tissue space.

Usage

CellMap(
  object,
  colour_by = "phenotype",
  colours = NULL,
  pt_size = 0.5,
  title = NULL,
  dark_theme = FALSE
)

Arguments

object

An SpatialCellData object.

colour_by

Character. Column name in meta_data to colour by. Default "phenotype".

colours

Named character vector or NULL for automatic colours via the global palette.

pt_size

Numeric. Point size. Default 0.5.

title

Character or NULL. Plot title.

dark_theme

Logical. Use a dark background (useful for tissue images). Default FALSE.

Value

A ggplot object.

Examples

counts <- matrix(rnorm(100), nrow = 50,
                 dimnames = list(NULL, c("CD3", "CD8")))
coords <- data.frame(x = runif(50, 0, 500), y = runif(50, 0, 500))
obj <- CreateSpatialObject(counts, coords)
obj <- PhenotypeCells(obj, thresholds = list(CD3 = 0, CD8 = 0))
CellMap(obj)