You can use the bblego functions in order to create
custom backbones using various components. Please note that the bblego
functions currently only allow you to create tree-like backbones.
bblego(..., .list = NULL)
bblego_linear(
from,
to,
type = sample(c("simple", "doublerep1", "doublerep2"), 1),
num_modules = sample(4:6, 1),
burn = FALSE
)
bblego_branching(
from,
to,
type = "simple",
num_steps = 3,
num_modules = 2 + length(to) * (3 + num_steps),
burn = FALSE
)
bblego_start(
to,
type = sample(c("simple", "doublerep1", "doublerep2"), 1),
num_modules = sample(4:6, 1)
)
bblego_end(
from,
type = sample(c("simple", "doublerep1", "doublerep2"), 1),
num_modules = sample(4:6, 1)
)bblego components, either as separate args or as a list.
The begin state of this component.
The end state of this component.
Some components have alternative module regulatory networks.
bblego_start(), bblego_linear(), bblego_end():
"simple": a sequence of modules in which every module upregulates the next module.
"doublerep1": a sequence of modules in which every module downregulates the next
module, and each module has positive basal expression.
"doublerep2": a sequence of modules in which every module upregulates the next
module, but downregulates the one after that.
"flipflop": a sequence of modules in which every module upregulates the next module.
In addition, the last module upregulates itself and strongly downregulates the first module.
bblego_branching():
"simple": a set of n modules (with n = length(to)) which all downregulate
one another and upregulate themselves. This causes a branching to occur in the trajectory.
The number of modules this component is allowed to use. Various components might require a minimum number of components in order to work properly.
Whether or not these components are part of the warm-up simulation.
The number of branching steps to reduce the odds of double positive cells occurring.
A dyngen backbone.
A backbone always needs to start with a single bblego_start() state and
needs to end with one or more bblego_end() states.
The order of the mentioned states needs to be such that a state is never
specified in the first argument (except for bblego_start()) before
having been specified as the second argument.
backbone <- bblego(
bblego_start("A", type = "simple", num_modules = 2),
bblego_linear("A", "B", type = "simple", num_modules = 3),
bblego_branching("B", c("C", "D"), type = "simple", num_steps = 3),
bblego_end("C", type = "flipflop", num_modules = 4),
bblego_end("D", type = "doublerep1", num_modules = 7)
)