Plot Spatial Network — SpatialNetworkPlot • phenoscapR

Plots cells as circles connected by edges from Delaunay triangulation or nearest-neighbour graph, coloured by phenotype. Matches the network visualisation style with coloured nodes on dark background.

Usage

SpatialNetworkPlot(
  object,
  edges = NULL,
  colour_by = "phenotype",
  colours = NULL,
  pt_size = 2,
  edge_alpha = 0.15,
  edge_colour = "grey60",
  dark_theme = TRUE
)

Arguments

object: An SpatialCellData object.
edges: Data frame with columns from and to (row indices), as returned by DelaunayNetwork or FindNeighbours. If NULL and the spatial slot contains delaunay_edges, those are used.
colour_by: Character. Metadata column for node colour. Default "phenotype".
colours: Named character vector or NULL.
pt_size: Numeric. Node size. Default 2.
edge_alpha: Numeric. Edge transparency. Default 0.15.
edge_colour: Character. Edge colour. Default "grey60".
dark_theme: Logical. Default TRUE.

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))
meta <- data.frame(cell_id = 1:50, sample_id = "s1",
                   phenotype = sample(c("A", "B"), 50, TRUE))
obj <- CreateSpatialObject(counts, coords, meta)
obj <- DelaunayNetwork(obj)
SpatialNetworkPlot(obj)