Updated to rRACES 0.7.0

CopyNumber/CopyNumber.Rmd

@@ -131,22 +131,22 @@ To observe the different nature of the two events will make the deletion span a
 m_engine$add_mutant(
   mutant_name = "A",
   passenger_rates = c(SNV = 1e-7, CNA = 0),
-  driver_SNVs = c(SNV("22", 10510210, "C"))
-  #driver_CNAs = c(CNA(type = "A", "22", pos_in_chr = 10303470,len = 1e7))
+  drivers = list(SNV("22", 10510210, "C"))
+  #driver_CNAs = c(CNA(type = "A", "22", chr_pos = 10303470,len = 1e7))
 )
 
 m_engine$add_mutant("B",
   passenger_rates = c(SNV=1e-7, CNA=1e-9),
-  driver_SNVs = c(SNV("22", 10510210, "C")),
-  driver_CNAs = c(CNA(type = "A", "22", pos_in_chr = 20303470,len = 2e7),
-                  CNA(type = "D", "22", pos_in_chr = 20303470,len = 1e7))
+  drivers = list(SNV("22", 10510210, "C"),
+                 CNA(type = "A", chr = "22", chr_pos = 20303470, len = 2e7),
+                 CNA(type = "D", chr = "22", chr_pos = 20303470, len = 1e7))
 )
 
 m_engine$add_mutant(
   mutant_name = "C",
   passenger_rates = c(SNV=1e-7, CNA = 1e-9),
-  driver_SNVs = c(SNV("22", 10510210, "C"))
-  #driver_CNAs = c(CNA(type = "A", "22", pos_in_chr = 10303470,len = 1e7))
+  drivers = list(SNV("22", 10510210, "C"))
+  #driver_CNAs = c(CNA(type = "A", chr = "22", chr_pos = 10303470, len = 1e7))
 )
 
 m_engine$add_exposure(coefficients = c(SBS13 = 0.4, SBS1 = 0.6))
@@ -169,15 +169,15 @@ seq_to_long <- function(seq_results) {
 
   sn <- sample_names[1]
   seq_df <- lapply(sample_names, function(sn) {
-    cc <- c("chromosome", "chr_pos", "ref", "alt", colnames(seq_results)[grepl(sn, colnames(seq_results), fixed = T)])
+    cc <- c("chr", "chr_pos", "ref", "alt", colnames(seq_results)[grepl(sn, colnames(seq_results), fixed = T)])
 
     seq_results[, cc] %>%
-      `colnames<-`(c("chromosome", "chr_pos", "ref", "alt", "occurences", "coverage", "VAF")) %>%
+      `colnames<-`(c("chr", "chr_pos", "ref", "alt", "occurences", "coverage", "VAF")) %>%
       dplyr::mutate(sample_name = sn)
   }) %>% do.call("bind_rows", .)
 
   seq_df %>%
-    dplyr::rename(chr = chromosome, from = chr_pos, DP = coverage, NV = occurences, ALT = alt) %>%
+    dplyr::rename(from = chr_pos, DP = coverage, NV = occurences, ALT = alt) %>%
     dplyr::mutate(to = from) %>%
     dplyr::select(chr, from, to, ALT, NV, DP, VAF, sample_name)
 }

SPN01/02_mutations.R

@@ -25,23 +25,20 @@ mu_CNA = 1e-11
 
 m_engine$add_mutant(mutant_name = "Clone 1",
                     passenger_rates = c(SNV = mu_SNV),
-                    driver_SNVs = c(SNV_Clone1),
-                    driver_CNAs = c())
+                    drivers = list(SNV_Clone1))
 
 m_engine$add_mutant(mutant_name = "Clone 2",
                     passenger_rates = c(CNA = mu_CNA),
-                    driver_SNVs = c(),
-                    driver_CNAs = c(CNA_Clone2))
+                    drivers = list(CNA_Clone2))
 
 m_engine$add_mutant(mutant_name = "Clone 3",
                     passenger_rates = c(SNV = mu_SNV),
-                    driver_SNVs = c(SNV_Clone3), 
-                    driver_CNAs = c())
+                    drivers = list(SNV_Clone3))
 
 m_engine$add_mutant(mutant_name = "Clone 4",
                     passenger_rates = c(SNV = mu_SNV),
-                    driver_SNVs = c(SNV_Clone4),
-                    driver_CNAs = c())
+                    drivers = list(SNV_Clone4))
+
 # Mutational signatures
 m_engine$add_exposure(
   time = 0,
@@ -56,7 +53,6 @@ phylo_forest$save("data/phylo_forest.sff")
 
 chromosomes <- c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y")
 
-
 seq_results <- parallel::mclapply(chromosomes, function(c) {
 	simulate_seq(phylo_forest, coverage = 80, chromosomes = c, write_SAM = FALSE)
 }, mc.cores = parallel::detectCores()) %>% do.call("bind_rows", .)

SPN02/SPN02.Rmd

@@ -131,5 +131,5 @@ plot_forest(sampled_phylogeny) %>%
 ```{r}
 # m_engine$add_mutant(mutant_name = "Clone 1",
 #                     passenger_rates = c(SNV = 3e-8, CNA = 1e-11),
-#                     driver_SNVs = SNV("7", 10510210, "A")) 
+#                     drivers = list(SNV("7", 10510210, "A")))
 ```

SPN02/mutations.R

@@ -13,15 +13,15 @@ m_engine <- build_mutation_engine(setup_code = "GRCh38")
 
 m_engine$add_mutant(mutant_name = "Clone 1",
                     passenger_rates = c(SNV = 3e-8, CNA = 1e-11),
-                    driver_SNVs = SNV("7", 10510210, "A")) 
+                    drivers = list(SNV("7", 10510210, "A")))
 
 m_engine$add_mutant(mutant_name = "Clone 2", 
                     passenger_rates = c(SNV = 3e-8, CNA = 1e-11),
-                    driver_SNVs = SNV("3",  179218303, "A"))
+                    drivers = list(SNV("3",  179218303, "A")))
 
 m_engine$add_mutant(mutant_name = "Clone 3", 
                     passenger_rates = c(SNV = 3e-5, CNA = 1e-11), # modelled as an hypermutant, so with higher passenger_rates
-                    driver_SNVs = SNV("2", 47799065, "A"))
+                    drivers = list(SNV("2", 47799065, "A")))
 
 m_engine$add_exposure(c(SBS1 = 0.5,SBS5 = 0.5))
 m_engine$add_exposure(clone3_born, c(SBS1 = 0.3,SBS5 = 0.3, SBS6 = 0.4))

SPN03/1_place_muts.R

@@ -14,7 +14,7 @@ plot_forest <- F
 m_engine$add_mutant(mutant_name = "Clone 1",
                     passenger_rates = c(SNV = 3e-8,
                                         CNA = 1e-10),
-                    driver_SNVs = c(SNV("9", 136496197, "C"))
+                    drivers = list(SNV("9", 136496197, "C"))
 )
 
 # Clone 2 
@@ -23,15 +23,15 @@ m_engine$add_mutant(mutant_name = "Clone 1",
 m_engine$add_mutant(mutant_name = "Clone 2",
                     passenger_rates = c(SNV = 3e-8, 
                                         CNA = 1e-10),
-                    driver_SNVs = c(SNV("12", 25398284, "T"))
+                    drivers = list(SNV("12", 25398284, "T"))
 )
 
 # Clone 3
 # Unknown
 m_engine$add_mutant(mutant_name = "Clone 3",
                     passenger_rates = c(SNV = 3e-8, 
                                         CNA = 1e-10),
-                    driver_SNVs = c(SNV("1", 59550210, "A"))
+                    drivers = list(SNV("1", 59550210, "A"))
 )
 
 # Signatures

SPN04/02_mutations.R

@@ -35,18 +35,17 @@ m_engine <- build_mutation_engine(setup_code = "GRCh37", context_sampling = 20)
 
 m_engine$add_mutant(mutant_name = "Clone 1",
                     passenger_rates = c(SNV = 2e-8, CNA = 1e-11),
-                    driver_SNVs = c(SNV("2", 209113113, "A")))
+                    drivers = list(SNV("2", 209113113, "A")))
 
 
 m_engine$add_mutant("Clone 2",
                     passenger_rates = c(SNV=2e-8, CNA=1e-11),
-                    driver_SNVs = c(),
-                    driver_CNAs = c(CNA(type = "A", "6", pos_in_chr = 25100000,len = 1e7)))
+                    drivers = list(CNA(type = "A", chr = "6",
+                                       chr_pos = 25100000, len = 1e7)))
 
 m_engine$add_mutant("Clone 3",
                     passenger_rates = c(SNV=2e-8, CNA=1e-11),
-                    driver_SNVs = c(SNV("1", 115256530, "T")),
-                    driver_CNAs = c())
+                    drivers = list(SNV("1", 115256530, "T")))
 
 # Mutational exposures ####
 treatment_info <- readRDS("data/treatment_info.rds")

SPN04/SPN04.Rmd

@@ -2,7 +2,9 @@
 title: 'rRACES: SPN04'
 author: "Giovanni Santacatterina"
 date: "`r Sys.Date()`"
-output: 
+output:
+  pdf_document:
+    toc: true
   html_document:
     theme: united
     highlight: tango
@@ -37,6 +39,9 @@ Set up the tissue sample and allow for internal duplication.
 
 ```{r tissue_preparation}
 sim <- new(Simulation, seed = seed, save_snapshot = F)
+
+sim$history_delta <- 0.1
+
 sim$update_tissue(1e3, 1e3)
 sim$duplicate_internal_cells <- TRUE
 sim$death_activation_level <- 50
@@ -64,7 +69,8 @@ We add the final mutant, i.e. the one that will sweep out the other two complete
 sim$add_mutant("Clone 3",growth_rates = 2, death_rates = 0.01)
 sim$mutate_progeny(sim$choose_cell_in("Clone 2"), "Clone 3")
 sim <- sweep_population(sim, "Clone 2", "Clone 3", .75, first_reduction = 10, delta_time = dt)
-sim <- run_up_to_size_by_steps(sim, "Clone 3", .75e5, dt)
+#sim <- run_up_to_size_by_steps(sim, "Clone 3", .75e5, dt)
+sim$run_until(sim$var("Clone 3")>=.75e5)
 plot_tissue(sim) | plot_muller(sim)
 ```
 
@@ -89,7 +95,12 @@ treatment_start <- sim$get_clock()
 sim$update_rates("Clone 1",rates = c(growth = 0, death=5))
 sim$update_rates("Clone 2",rates = c(growth = 0, death=5))
 sim$update_rates("Clone 3",rates = c(growth = 0, death=5))
-sim <- run_down_to_size_by_steps(sim, "Clone 3", 1e3, delta_time = .1)
+
+sim$history_delta <- 0.1
+
+#sim <- run_down_to_size_by_steps(sim, "Clone 3", 1e3, delta_time = .1)
+sim$run_until(sim$var("Clone 3")<=1e3)
+
 treatment_end <- sim$get_clock()
 plot_tissue(sim) | plot_muller(sim)
 ```
@@ -100,7 +111,9 @@ The effect of the treatment ends and the population can grow back.
 
 ```{r relapse, results='hide', message=FALSE, warning=FALSE}
 sim$update_rates("Clone 3",rates = c(growth = 2, death=0.01))
-sim <- run_up_to_size_by_steps(sim, "Clone 3", .75e5, delta_time = .1)
+#sim <- run_up_to_size_by_steps(sim, "Clone 3", .75e5, delta_time = .1)
+sim$run_until(sim$var("Clone 3")>=.75e5)
+
 plot_tissue(sim, num_of_bins = 300) | plot_muller(sim) + xlim(20, NA)
 ```
 

forest_annotation/forest_annotation.Rmd

@@ -49,9 +49,9 @@ m_engine = build_mutation_engine(setup_code = "demo")
 
 m_engine$add_mutant(mutant_name = "A",
                     passenger_rates = c(SNV = 1e-9),
-                    driver_SNVs = c(SNV("22", 10510210, "C")),
-                    driver_CNAs = c(CNA(type = "A", "22", pos_in_chr = 10303470,
-                                        len = 200000)))
+                    drivers = list(SNV("22", 10510210, "C"), 
+                                   CNA(type = "A", chr = "22",
+                                       chr_pos = 10303470, len = 200000)))
 
 m_engine
 ```