02c-simulate_splatter_datasets.R

#' [Splatter](https://github.com/Oshlack/splatter), simulations of non-linear paths between different states

library(tidyverse)
library(dynbenchmark)
library(qsub)

experiment("01-datasets/02-synthetic")

# remove all datasets
# rm_remote(dataset_file(id = "synthetic/splatter", remote = TRUE), remote = TRUE, recursive = TRUE)

# generate design
set.seed(1)
design <- crossing(
  topology_model = c("linear", "bifurcating", "multifurcating", "binary_tree", "tree"),
  tibble(platform = select_platforms(10)) %>% mutate(platform_ix = row_number())
) %>%
  mutate(
    path.skew = runif(n(), 0, 1),
    path.nonlinearProb = runif(n(), 0, 1),
    path.sigmaFac = runif(n(), 0, 1),
    bcv.common.factor = runif(n(), 10, 200),
    dataset_id = paste0("synthetic/splatter/", topology_model, "_", platform_ix),
    seed = sample(1:100000, n())
  ) %>%
  select(-platform_ix)
write_rds(design, result_file("design_splatter.rds"))

# simulate datasets
qsub_config <- override_qsub_config(memory = "10G", max_wall_time = "24:00:00", num_cores = 1, name = "splatter", wait = F, stop_on_error = FALSE)

handle <- qsub_pmap(
  design,
  simulate_splatter,
  qsub_config = qsub_config
)

write_rds(handle, "handle_splatter.rds")

##
handle <- read_rds("handle_splatter.rds")
qsub::qsub_retrieve(handle)