Plot the signature exposure timeline of a phylogenetic forest
Source:R/plot_exposure_timeline.R
plot_exposure_timeline.RdPlots the signatures exposure changes along a phylogenetic forest.
Usage
plot_exposure_timeline(
phylogenetic_forest,
linewidth = 0.8,
emphasize_switches = FALSE,
pal_name = "Dark2"
)Examples
sim <- TissueSimulation()
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_sample_forest()
# placing mutations
m_engine <- MutationEngine(setup_code = "demo")
#> Downloading reference genome...
#> Reference genome downloaded
#> Decompressing reference genome...done
#> Downloading signature files...
#> Signature file downloaded
#> Downloading driver mutation file...
#> Driver mutation file downloaded
#> Decompressing driver mutation file...done
#> Downloading passenger CNAs file...
#> Passenger CNAs file downloaded
#> Decompressing passenger CNAs file...done
#> Downloading germline...
#> Germline downloaded
#> Decompressing mutations...
#> done
#> 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] Reading 22
[█---------------------------------------] 0% [00m:01s] Reading 22
[████████████████████████████████████████] 100% [00m:02s] Reading 22
#>
[████████████████████████████████████████] 100% [00m:02s] Reading 22
#>
[████████████████████████████████████████] 100% [00m:02s] Reading 22
#>
[████████████████████████████████████████] 100% [00m:02s] Reading 22
#>
[████████████████████████████████████████] 100% [00m:02s] Reading 22
#>
[████████████████████████████████████████] 100% [00m:02s] Reading 22
#>
[████████████████████████████████████████] 100% [00m:02s] Reading 22
#>
[████████████████████████████████████████] 100% [00m:02s] RS index built
#>
[█---------------------------------------] 0% [00m:00s] Saving RS index
[█---------------------------------------] 0% [00m:00s] Saving RS index
[██████████████████████------------------] 54% [00m:02s] Saving RS index
done
#>
[████████████████████████████████████████] 100% [00m:02s] 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$add_mutant(mutant_name = "A",
passenger_rates = c(SNV = 8e-8))
#>
[█---------------------------------------] 0% [00m:00s] Retrieving "A" SIDs
[█---------------------------------------] 0% [00m:00s] Found 22
[█---------------------------------------] 0% [00m:00s] Reading 22
[███████---------------------------------] 17% [00m:01s] Reading 22
[███████████████-------------------------] 35% [00m:02s] Reading 22
[██████████████████████------------------] 52% [00m:03s] Reading 22
[████████████████████████████------------] 69% [00m:04s] Reading 22
[███████████████████████████████████-----] 86% [00m:05s] Reading 22
[████████████████████████████████████████] 100% [00m:05s] "A"'s SIDs validated
m_engine$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
[████████████████████████████████████████] 100% [00m:00s] Mutations placed
# plotting the phylogenetic forest
plot_exposure_timeline(phylo_forest)
# plotting the phylogenetic forest emphatizing the exposure switches
plot_exposure_timeline(phylo_forest, emphasize_switches=TRUE)
# deleting the mutation engine directory
unlink("demo", recursive=TRUE)