simulate_stripes: simulate_stripes

In TrigosTeam/spaSim: Spatial point data simulator for tissue images

simulate_stripes

Description

Based on an existing background image, simulate stripes of cells representing vessels. The cell types and widths of the stripes can be specified. The locations of the stripes are randomly simulated. Please refer to the examples to check what properties of the stripes can be specified. The default values for the arguments give an example of vessel simulation which enable an automatic simulation of vessels without the specification of any argument.

Usage

simulate_stripes(
  bg_sample = bg1,
  n_stripe_type = 2,
  stripe_properties = list(S1 = list(number_of_stripes = 1, name_of_stripe_cell =
    "Others", width_of_stripe = 80, infiltration_types = c("Immune"),
    infiltration_proportions = c(0.08)), S2 = list(number_of_stripes = 1,
    name_of_stripe_cell = "Others", width_of_stripe = 80, infiltration_types =
    c("Immune"), infiltration_proportions = c(0.08))),
  plot_image = TRUE,
  plot_categories = NULL,
  plot_colours = NULL
)

Arguments

bg_sample	(OPTIONAL) A data frame or SpatialExperiment class object with locations of points representing background cells. Further cell types will be simulated based on this background sample. The data.frame or the spatialCoords() of the SPE object should have colnames including "Cell.X.Positions" and "Cell.Y.Positions". By default use the internal bg1 background image.
n_stripe_type	Number of stripe types. Should be the same as ⁠length(stripe_properties⁠.
stripe_properties	List of the properties of the stripes. See examples for the format of the properties. Please refer to the examples for the structure of stripe_properties.
plot_image	Boolean. Whether the simulated image is plotted. Default is TRUE.
plot_categories	String Vector specifying the order of the cell categories to be plotted. Default is NULL - the cell categories under the "Cell.Type" column would be used for plotting.
plot_colours	String Vector specifying the order of the colours that correspond to the plot_categories arg. Default is NULL - the predefined colour vector would be used for plotting.

Value

A data.frame of the simulated image

See Also

simulate_background_cells for all cell simulation, simulate_mixing for mixed background simulation, simulate_clusters for cluster simulation, and simulate_immune_rings/simulate_double_rings for immune ring simulation

Other simulate pattern functions: simulate_background_cells(), simulate_clusters(), simulate_double_rings(), simulate_immune_rings(), simulate_mixing()

Examples

stripe_properties <- list(
S1 = list(
  number_of_stripes = 1,
  name_of_stripe_cell = "Others",
  width_of_stripe = 80,
  infiltration_types = c("Immune"),
  infiltration_proportions = c(0.08)
), S2 = list(
  number_of_stripes = 1,
  name_of_stripe_cell = "Others",
  width_of_stripe = 80,
  infiltration_types = c("Immune"),
  infiltration_proportions = c(0.08)))
set.seed(610)
stripe_image <- simulate_stripes(bg_sample = bg1, n_stripe_type=2,
stripe_properties = stripe_properties, plot_image = TRUE)

TrigosTeam/spaSim documentation built on May 25, 2023, 4:20 p.m.