spatstat_layout: Generate spatial layout using 'spatstat'

In MetaNet: Network Analysis for Omics Data

Generate spatial layout using spatstat

Description

Generate spatial layout using spatstat

Usage

spatstat_layout(
  go,
  win,
  type = c("random", "regular"),
  mode = c("surface", "boundary"),
  jitter = 0,
  curved = NULL,
  order_by = NULL,
  order_ls = NULL,
  order_circle = FALSE,
  seed = 1234,
  rescale = TRUE
)

Arguments

go	igraph or metanet object
win	A spatstat window object (owin), e.g. disc(), owin(poly=...); Or sf object.
type	Type of distribution: "random", "regular"
mode	"surface", "boundary"
jitter	for surface-regular, defalut 0
curved	Optional curved attribute for coors
order_by	order nodes according to a node attribute
order_ls	manual the discrete variable with a vector, or continuous variable with "desc" to decreasing
order_circle	order nodes from the center of a circle
seed	random seed
rescale	rescale the coordinates to (0,1)

Value

A coors object (data.frame with class "coors" and attribute "curved")

Examples

if (requireNamespace("spatstat.geom") && requireNamespace("spatstat.random")) {
  poly_x <- c(0, 2, 2, 0)
  poly_y <- c(0, 0, 1, 1)
  win_poly <- spatstat.geom::owin(poly = list(x = poly_x, y = poly_y))
  plot(win_poly)
  coors1 <- spatstat_layout(co_net, win_poly, type = "regular", mode = "surface")
  plot(co_net, coors = coors1)
  coors2 <- spatstat_layout(co_net2, win_poly, type = "random", mode = "boundary")
  plot(co_net2, coors = coors2)

  if (requireNamespace("sf")) {
    nc <- sf::st_read(system.file("shape/nc.shp", package = "sf"), quiet = TRUE)
    poly <- nc[1, ]
    coors <- spatstat_layout(go = multi1, win = poly, type = "regular", mode = "surface")
    plot(multi1, coors = coors)
  }
}

MetaNet documentation built on June 26, 2025, 5:07 p.m.