Plot a signatures exposures — plot_exposure

Plots the signatures exposure changes along a phylogenetic forest.

Usage

plot_exposure_timeline(
  phylogenetic_forest,
  linewidth = 0.8,
  emphatize_switches = FALSE
)

Arguments

phylogenetic_forest: A phylogenetic forest.
linewidth: The width of the lines in the plot.
emphatize_switches: A Boolean flag to emphatize the exposure switches.

Value

An editable ggplot plot.

Examples

sim <- SpatialSimulation()

sim$add_mutant(name = "A",
               growth_rates = 0.2,
               death_rates = 0.0)
sim$place_cell("A", 500, 500)

sim$run_up_to_time(150)
#> 
 [████████████████████████████████████████] 100% [00m:00s] Saving snapshot                                 


# sampling tissue

n_w <- n_h <- 50
ncells <- 0.8 * n_w * n_h
bbox <- sim$search_sample(c("A" = ncells), n_w, n_h)

sim$sample_cells("Sampling", bbox$lower_corner, bbox$upper_corner)

forest <- sim$get_samples_forest()

# placing mutations

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                               

 [██████████████████████████████----------] 73% [00m:02s] Processing chr. 22                               

 [████████████████████████████████████████] 100% [00m:03s] 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:01s] Processing chr. 22                                

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

 [█---------------------------------------] 0% [00m:05s] Processing chr. 22                                

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

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

 [█---------------------------------------] 0% [00m:10s] Processing chr. 22                                

 [█---------------------------------------] 0% [00m:14s] Processing chr. 22                                

 [████████████████████████████████████████] 100% [00m:14s] RS index built                                  

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

 [███████████████████████-----------------] 56% [00m:01s] Saving RS index                                  
done
#> 
 [████████████████████████████████████████] 100% [00m:01s] RS index saved                                  

#> 
 [█---------------------------------------] 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 = 8e-8))
#> 
 [█---------------------------------------] 0% [00m:00s] Retrieving "A" SNVs                               

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


m_engine$add_exposure(c(SBS1 = 0.2, SBS5 = 0.8, ID3 = 1))
m_engine$add_exposure(time = 50,
                      c(SBS5 = 0.3, SBS2 = 0.2, SBS3 = 0.5,
                        ID2 = 0.8, ID21 = 0.2))
phylo_forest <- m_engine$place_mutations(forest, 500, 10)
#> 
 [█---------------------------------------] 0% [00m:00s] Placing mutations                                 

 [████████████████████████████████--------] 79% [00m:01s] Placing mutations                                

 [████████████████████████████████████████] 100% [00m:01s] Mutations placed                                


# plotting the phylogenetic forest
plot_exposure_timeline(phylo_forest)


# plotting the phylogenetic forest emphatizing the exposure switches
plot_exposure_timeline(phylo_forest, emphatize_switches=TRUE)


# deleting the mutation engine directory
unlink("demo", recursive=TRUE)