Nothing
context("1_initialisation")
backbone <- backbone(
module_info = tibble(
module_id = c("A", "B"),
basal = c(0.2, 0.8),
burn = c(TRUE, FALSE),
independence = c(0.4, 0.5)
),
module_network = tibble(
from = c("A", "A"),
to = c("A", "B"),
effect = c(-1L, 1L),
strength = c(10, 1),
hill = c(2, 3)
),
expression_patterns = tibble(
from = c("burn", "start"),
to = c("start", "end"),
module_progression = c("+A", "+B"),
start = c(TRUE, FALSE),
burn = c(TRUE, FALSE),
time = c(10, 10)
)
)
tf_network_params <- tf_network_default()
feature_network_params <- feature_network_default()
kinetics_params <- kinetics_default()
gold_standard_params <- gold_standard_default()
simulation_params <- simulation_default()
experiment_params <- experiment_snapshot()
test_that("Testing normal use case of initialisation", {
model <- initialise_model(
backbone = backbone,
num_cells = 100,
num_tfs = 10,
num_targets = 50,
num_hks = 40,
distance_metric = "euclidean",
tf_network_params = tf_network_params,
feature_network_params = feature_network_params,
kinetics_params = kinetics_params,
gold_standard_params = gold_standard_params,
simulation_params = simulation_params,
experiment_params = experiment_params,
verbose = FALSE,
download_cache_dir = "test_dir",
num_cores = 2
)
simulation_params$burn_time <- 12
simulation_params$total_time <- 24
expect_equal(model$backbone, backbone)
expect_equal(model$numbers, list(num_cells = 100, num_tfs = 10, num_targets = 50, num_hks = 40, num_features = 100, num_modules = 2))
expect_equal(model$distance_metric, "euclidean")
expect_equal(model$tf_network_params, tf_network_params)
expect_equal(model$feature_network_params, feature_network_params)
expect_equal(model$kinetics_params, kinetics_params)
expect_equal(model$gold_standard_params, gold_standard_params)
expect_equal(model$simulation_params, simulation_params)
expect_equal(model$experiment_params, experiment_params)
expect_false(model$verbose)
expect_equal(model$download_cache_dir, "test_dir")
expect_equal(model$num_cores, 2)
})
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