This method samples a set of tumour cells.
Arguments
- sample_name
The name of the sample.
- lower_corner
The lower corner of the sample bounding box (optional in pair with
upper_corner).- upper_corner
The upper corner of the sample bounding box (optional in pair with
lower_corner).- num_of_cells
The maximum number of tumour cells to collect (optional).
Details
It removes the cells from the simulated tissue and stores them in a sample that can be subsequently retrieved to build a samples forest.
Examples
# set the seed of the random number generator
set.seed(0)
# create a simulation
sim <- SpatialSimulation()
sim$add_mutant(name = "A",
growth_rate = 0.2,
death_rate = 0.01)
sim$place_cell("A", 500, 500)
sim$death_activation_level <- 100
sim$run_up_to_size(species = "A", num_of_cells = 50000)
#>
[████████████████████████████████████████] 100% [00m:00s] Saving snapshot
# randomly sample 50 tumour cells from the tissue
sim$sample_cells("S1", num_of_cells=50)
# sample the region [450,500]x[475,550]
sim$sample_cells("S2", lower_corner=c(450,475), upper_corner=c(500,550))
# randomly sample 50 tumour cells from the tissue region [500,550]x[500,550]
sim$sample_cells("S3", lower_corner=c(500,500), upper_corner=c(550,550),
num_of_cells=50)
sim$get_samples_info()
#> name xmin ymin xmax ymax tumour_cells tumour_cells_in_bbox time
#> 1 S1 0 0 999 999 50 50000 215.0761
#> 2 S2 450 475 500 550 3856 3856 215.0761
#> 3 S3 500 500 550 550 50 2543 215.0761