Tissue boundary and grid classification — plot_denmark

Left: all cells (gray), the cells of the analyzed type (colored) and the alpha-shape tissue boundary. Right (when grid is given): the grid cells colored by type (interior, boundary, exterior) with the boundary outline.

Usage

plot_denmark_boundary(
  cells,
  boundary,
  grid = NULL,
  highlight = NULL,
  xlab = "x",
  ylab = "y",
  point_size = 0.15
)

Arguments

cells: Data frame with the columns x and y (all cells).
boundary: Polygon from denmark_alpha_shape().
grid: Optional output of buildgridpp(..., boundary = boundary).
highlight: Optional logical vector, one element per row of cells: TRUE for the cells of the analyzed type.
xlab, ylab: Axis labels.
point_size: Size of the cell points.

Value

A ggplot object; with grid, the two panels combined with patchwork, or a list of two ggplot objects when patchwork is not installed.

Examples

toy <- denmark_toy_data()
tissue <- denmark_alpha_shape(toy$x, toy$y)
tumor <- subset(toy, celltype == "Tumor", select = -celltype)
g <- buildgridpp(grid_size = 10, dataset = tumor, gene = "geneA",
                 boundary = tissue)
plot_denmark_boundary(toy, tissue, grid = g,
                      highlight = toy$celltype == "Tumor")