plotConsDynNet {pwOmics} | R Documentation

## Plot inferred net based on analysis analysis.

### Description

Dynamic analysis result is plotted to pdf file stored in current working directory.

### Usage

    plotConsDynNet(dynConsensusNet, sig.level, clarify = "TRUE",
      layout = layout.fruchterman.reingold, ...)

### Arguments

`dynConsensusNet` | result of dynamic analysis: inferred net generated by consDynamicNet function.
`sig.level` | significance level for plotting edges in network (between 0 and 1).
`clarify` | indicating if unconnected nodes should be removed; default = "TRUE".
`layout` | igraph layout parameter; default is layout.fruchterman.reingold.
`...` | further plotting/legend parameters.

### Value

pdf file in current working directory.

### Examples

    ## Not run:
    data(OmicsExampleData)
    data_omics = readOmics(tp_prots = c(0.25, 1, 4, 8, 13, 18, 24),
    tp_genes = c(1, 4, 8, 13, 18, 24), OmicsExampleData,
    PWdatabase = c("biocarta", "kegg", "nci", "reactome"),
    TFtargetdatabase = c("userspec"))
    data_omics = readPhosphodata(data_omics,
    phosphoreg = system.file("extdata", "phospho_reg_table.txt",
    package = "pwOmics.newupdown"))
    data_omics = readTFdata(data_omics,
    TF_target_path = system.file("extdata", "TF_targets.txt",
    package = "pwOmics.newupdown"))
    data_omics_plus = readPWdata(data_omics,
    loadgenelists = system.file("extdata/Genelists", package = "pwOmics.newupdown"))

    ## End(Not run)
    ## Not run:
    data_omics_plus = identifyPR(data_omics_plus)
    setwd(system.file("extdata/Genelists", package = "pwOmics.newupdown"))
    data_omics = identifyPWs(data_omics_plus)
    data_omics = identifyTFs(data_omics)
    data_omics = identifyRsofTFs(data_omics,
    noTFs_inPW = 1, order_neighbors = 10)
    data_omics = identifyPWTFTGs(data_omics)
    statConsNet = staticConsensusNet(data_omics)
    dynConsNet = consDynamicNet(data_omics, statConsNet)
    plotConsDynNet(dynConsNet, sig.level = 0.8)

    ## End(Not run)

[Package pwOmics version 1.26.0 Index]