simulate_immune_rings: simulate_immune_rings

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

simulate_immune_rings

Description

Based on an existing background image, simulate rings of immune cells that surround tumour clusters. The tumour clusters and immune rings are simulated at the same time. The default values for the arguments give an example of immune ring simulation which enable an automatic simulation of immune rings without the specification of any argument.

Usage

simulate_immune_rings(
  bg_sample = bg1,
  bg_type = "Others",
  n_ir = 2,
  ir_properties = list(I1 = list(name_of_cluster_cell = "Tumour", size = 600, shape =
    "Circle", centre_loc = data.frame(x = 930, y = 1000), infiltration_types =
    c("Immune1", "Immune2", "Others"), infiltration_proportions = c(0.15, 0.05, 0.05),
    name_of_ring_cell = "Immune1", immune_ring_width = 150,
    immune_ring_infiltration_types = c("Others"), immune_ring_infiltration_proportions =
    c(0.15)), I2 = list(name_of_cluster_cell = "Tumour", size = 500, shape = "Oval",
    centre_loc = data.frame(x = 1330, y = 1100), infiltration_types = c("Immune1", 
    
    "Immune2", "Others"), infiltration_proportions = c(0.15, 0.05, 0.05),
    name_of_ring_cell = "Immune1", immune_ring_width = 150,
    immune_ring_infiltration_types = c("Others"), immune_ring_infiltration_proportions =
    c(0.15))),
  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.
bg_type	(OPTIONAL) String The name of the background cell type. By default is "Others".
n_ir	Number of immune rings. This must match the arg length(ir_properties).
ir_properties	List of properties of the immune rings. Please refer to the examples for the structure of ir_properties.
plot_image	Boolean. Whether the simulated image is plotted.
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, simulate_double_rings for double immune ring simulation, and simulate_stripes for vessel simulation.

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

Examples

set.seed(610)
# manually define the properties of the immune ring
ir_properties <- list(I1=list(name_of_cluster_cell="Tumour", size=600,
shape="Circle",centre_loc=data.frame("x"=930, "y"=1000),
infiltration_types=c("Immune1", "Immune2", "Others"), infiltration_proportions
=c(0.15, 0.05, 0.05), name_of_ring_cell="Immune1", immune_ring_width=150,
immune_ring_infiltration_types=c("Others"), immune_ring_infiltration_proportions=c(0.15)),
I2=list(name_of_cluster_cell="Tumour", size=500, shape="Oval",
centre_loc=data.frame("x"=1330, "y"=1100), infiltration_types=c("Immune1", "Immune2", "Others"),
infiltration_proportions=c(0.15, 0.05, 0.05), name_of_ring_cell="Immune1",
immune_ring_width=150, immune_ring_infiltration_types=c("Others"),
immune_ring_infiltration_proportions=c(0.15)))
# simulate immune rings (`n_ir` should match the length of `ir_properties`)
immune_ring_image <- simulate_immune_rings(bg_sample=bg1,
n_ir=2, ir_properties=ir_properties)

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