mogamun_postprocess: mogamun_postprocess

In elvanov/MOGAMUN: MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

Description

Postprocess the results: i) calculates the accumulated Pareto front, i.e. the individuals on the first Pareto front after re-ranking the results from multiple runs (NOTE. If there is a single run, the result is the set of individuals in the first Pareto front), ii) filters the networks to leave only the interactions between the genes that are included in the results, iii) generates some plots of interest, such as scatter plots and boxplots, and iv) (optional) creates a Cytoscape file to visualize the results, merging the subnetworks with a Jaccard similarity coefficient superior to JaccardSimilarityThreshold (NOTE. Make sure to open Cytoscape if VisualizeInCytoscape is TRUE)

Usage

mogamun_postprocess(
    ExperimentDir = ".",
    LoadedData = LoadedData,
    JaccardSimilarityThreshold = 70,
    VisualizeInCytoscape = TRUE
)

Arguments

ExperimentDir	folder containing the results to be processed. It is the same folder specified as ResultsDir in mogamun_run
LoadedData	list returned by mogamun_load_data()
JaccardSimilarityThreshold	subnetworks over this Jaccard similarity threshold are merged in a single subnetwork
VisualizeInCytoscape	TRUE if you wish to visualize the accumulated Pareto front in Cytoscape, FALSE otherwise

Value

None

Examples

DEGPath <- system.file("extdata/DE/Sample_DE.csv", package = "MOGAMUN")
NodesScoresPath <- 
    system.file("extdata/DE/Sample_NodesScore.csv", package = "MOGAMUN")
LayersPath <- 
    paste0(system.file("extdata/LayersMultiplex", package = "MOGAMUN"), "/")
EvolutionParameters <- mogamun_init(Generations = 1, PopSize = 10)
LoadedData <- 
    mogamun_load_data(
        EvolutionParameters = EvolutionParameters,
        DifferentialExpressionPath = DEGPath,
        NodesScoresPath = NodesScoresPath,
        NetworkLayersDir = LayersPath,
        Layers = "23"
    )
ResultsDir <- system.file("SampleResults", package="MOGAMUN")
mogamun_run(
    LoadedData = LoadedData,
    Cores = 1,
    NumberOfRunsToExecute = 1,
    ResultsDir = ResultsDir
)
mogamun_postprocess(
    ExperimentDir = ResultsDir,
    LoadedData = LoadedData,
    JaccardSimilarityThreshold = 70,
    VisualizeInCytoscape = FALSE
) 

elvanov/MOGAMUN documentation built on Oct. 26, 2021, 3:14 p.m.