Annotate a plot of cell divisions. — annotate

It annotates a plot of cell divisions with information from sampling times and MRCAs for all available samples

Usage

annotate_forest(
  tree_plot,
  forest,
  samples = TRUE,
  MRCAs = TRUE,
  exposures = FALSE,
  facet_signatures = TRUE,
  drivers = TRUE,
  add_driver_label = TRUE
)

Arguments

tree_plot: The output of plot_forest.
forest: The original forest object from which the input to plot_forest has been derived.
samples: If TRUE it annotates samples.
MRCAs: If TRUE it annotates MRCAs.
exposures: If TRUE it annotates exposures to mutational signatures.
facet_signatures: If TRUE and if exposures is TRUE it creates a faceted forest plot where the exposure to each signature is annotated on a separated plot.
drivers: If TRUE it annotates drivers on the node they originated.
add_driver_label: If TRUE and if drivers is TRUE it annotates the driver name.

Value

A ggraph tree plot.

Examples

sim <- SpatialSimulation()
sim$add_mutant(name = "A", growth_rates = 0.08, death_rates = 0.01)
sim$place_cell("A", 500, 500)
sim$run_up_to_time(60)
#> 
 [████████████████████████████████████████] 100% [00m:00s] Saving snapshot                                    

sim$sample_cells("MySample", c(500, 500), c(510, 510))
m_engine = MutationEngine(setup_code = "demo")
#> Downloading reference genome...
#> Reference genome downloaded
#> Decompressing reference file...done
#> Downloading SBS file...
#> SBS file downloaded
#> Downloading indel file...
#> indel file downloaded
#> Downloading driver mutation file...
#> Driver mutation file downloaded
#> Downloading passenger CNAs file...
#> Passenger CNAs file downloaded
#> Downloading germline mutations...
#> Germline mutations downloaded
#> Building context index...
#> 
 [█---------------------------------------] 0% [00m:00s] Processing chr. 22                                   

 [█████████████████-----------------------] 40% [00m:01s] Processing chr. 22                                  

 [█████████████████████████████████-------] 81% [00m:02s] Processing chr. 22                                  

 [████████████████████████████████████████] 100% [00m:02s] Context index built                                

#> 
 [█---------------------------------------] 0% [00m:00s] Saving context index                                 

 [████████████████████████████████████████] 100% [00m:00s] Context index saved                                

#> done
#> Building repeated sequence index...
#> 
 [█---------------------------------------] 0% [00m:00s] Processing chr. 22                                   

 [█---------------------------------------] 0% [00m:00s] Processing chr. 22                                   

 [█---------------------------------------] 0% [00m:03s] Processing chr. 22                                   

 [█---------------------------------------] 0% [00m:04s] Processing chr. 22                                   

 [█---------------------------------------] 0% [00m:06s] Processing chr. 22                                   

 [█---------------------------------------] 0% [00m:07s] Processing chr. 22                                   

 [█---------------------------------------] 0% [00m:08s] Processing chr. 22                                   

 [█---------------------------------------] 0% [00m:12s] Processing chr. 22                                   

 [████████████████████████████████████████] 100% [00m:12s] RS index built                                     

#> 
 [█---------------------------------------] 0% [00m:00s] Saving RS index                                      

 [███████████████████████-----------------] 57% [00m:01s] Saving RS index                                     

 [████████████████████████████████████████] 100% [00m:01s] RS index saved                                     

#> done
#> 
 [█---------------------------------------] 0% [00m:00s] Loading germline                                     

 [████████████████████████████████████████] 100% [00m:00s] Germline loaded                                    

#> 
 [█---------------------------------------] 0% [00m:00s] Saving germline                                      

 [████████████████████████████████████████] 100% [00m:00s] Germline saved                                     


m_engine$add_mutant(mutant_name = "A",
                    passenger_rates = c(SNV = 1e-9),
                    drivers = list(SNV("22", 10510210, "C"),
                                   CNA(type = "A", "22", chr_pos = 10303470,
                                       len = 200000)))
#> 
 [█---------------------------------------] 0% [00m:00s] Retrieving "A" SNVs                                  

 [█---------------------------------------] 0% [00m:00s] Found 22                                             

 [█---------------------------------------] 0% [00m:00s] Reading 22                                           

 [█---------------------------------------] 0% [00m:01s] Reading 22                                           

 [████████████████████████████████████████] 100% [00m:01s] "A" SNVs retrieved                                 

m_engine$add_exposure(coefficients = c(SBS13 = 0.2, SBS1 = 0.8))
m_engine$add_exposure(time=50, coefficients = c(SBS17b = 0.2, SBS3 = 0.8))

forest = sim$get_samples_forest()
forest$get_samples_info()
#>       name xmin ymin xmax ymax tumour_cells tumour_cells_in_bbox     time
#> 1 MySample  500  500  510  510            5                    5 60.28207
forest_muts = m_engine$place_mutations(forest, 1000, 500)
#> 
 [█---------------------------------------] 0% [00m:00s] Placing mutations                                    

 [████████████████████████████████████████] 100% [00m:00s] Mutations placed                                   

tree_plot = plot_forest(forest)
annotate_forest(tree_plot, forest_muts, samples = T, MRCAs = T,
                exposures = T, drivers=T, add_driver_label = T)