Retrieving the most recent common ancestors

This method retrieves the most recent common ancestors of a set of cells.

Arguments

cell_ids

The list of the identifiers of the cells whose most recent common ancestors are aimed (optional).

Value

A dataframe representing, for each of the identified cells, the identified (column "cell_id"), whenever the node is not a root, the ancestor identifier (column "ancestor"), whenever the node was sampled, i.e., it is one of the forest leaves, the name of the sample containing the node, (column "sample"), the mutant (column "mutant"), the epistate (column "epistate"), and the birth time (column "birth_time").

Details

If the optional parameter cell_ids is used, this method find the most recent common ancestors of the cells having an identifier among those in cell_ids. If, otherwise, the optional parameter is not used, this method find the most recent common ancestors of the forest leaves.

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                                        


# sample the region [450,500]x[475,550]
sim$sample_cells("S1", lower_corner=c(450,475), upper_corner=c(500,550))

# build the samples forest
forest <- sim$get_samples_forest()

forest$get_coalescent_cells()
#>   cell_id ancestor mutant epistate sample birth_time
#> 1       0       NA      A            <NA>          0