write_ONOFFhistograms Function

Generate ON/OFF dwell time histograms for GRSM models.

Syntax

write_ONOFFhistograms(; kwargs...)

Arguments

Model Parameters

• G::Int = 2: Number of gene states
• R::Int = 0: Number of pre-RNA steps
• S::Int = 0: Number of splice sites
• insertstep::Int = 1: Reporter insertion step
• transitions::Tuple = (): State transitions
• rates::Vector{Float64}: Model rates
• nalleles::Int = 1: Number of alleles

Histogram Parameters

• ntraces::Int = 1000: Number of traces for histogram
• tspan::Tuple{Float64, Float64} = (0., 1000.): Time span for traces
• dt::Float64 = 1.0: Time step
• bins::Int = 100: Number of histogram bins
• maxtime::Float64 = 100.0: Maximum dwell time

Output Parameters

• outfolder::String = "histograms": Output folder
• label::String = "": Output file label
• write::Bool = true: Write histograms to file
• returnhist::Bool = false: Return histogram data

Returns

• hist: Tuple containing:
  • ON dwell time histogram
  • OFF dwell time histogram
  • Bin edges

Examples

# Generate histograms for a simple G model
write_ONOFFhistograms(
    G = 2,
    R = 0,
    rates = [0.1, 0.2],  # G1->G2, G2->G1
    ntraces = 1000,
    tspan = (0., 1000.),
    bins = 100,
    maxtime = 100.0
)

# Generate histograms for a GR model
write_ONOFFhistograms(
    G = 2,
    R = 3,
    S = 2,
    insertstep = 1,
    rates = [0.1, 0.2, 0.3, 0.4, 0.5, 0.6],
    ntraces = 5000,
    tspan = (0., 2000.),
    bins = 150,
    maxtime = 200.0
)

Notes

1. Histogram Generation

   • Traces are generated using Gillespie algorithm
   • ON/OFF states are determined by gene state
   • Histograms are normalized to total number of transitions

2. Rate Order

   • G transitions
   • R transitions
   • S transitions
   • Decay