Clone the repository. Change directory into TopoFiles.
Run julia as project julia --project. Optionally, specify number of threads.
Include the necessary files using include("scriptEvolutionGeneral.jl").
To run the algorithm, call simulateRacipe with the required arguments (see docstring in the code file). Remeber to capture the return values.
To do multiple runs from the same initial network, call multiRacipe with the required arguments. Automatically stores the results in a file with .jld extension (see extras).
Include the necessary files using include"plotFunctions.jl".
Call plotNetwork to plot the GRN as a graph. See docstring in code file for arguments.
Call plotNetworkHeatmap to plot the GRN as a heatmap of the interaction matrix.
Multiple networks can be plotted in the same plot using the functions plotNetworkHeatmapMulti and plotNetworkMulti. See docstrings in the code file.
To plot the convergence pattern of the result of multiRacipe, call plotConvergence with the required arguments.
Open the jldResultsutils.jld file and edit the first line to the required file.
Include the necessary files using include("jldResultsutils.jld").
The results of the multiRacipe run is now stored in variables X (the matrix of scores), and XM (the matrix of networks).