networkPlot {HTSanalyzeR} | R Documentation

## Plot the enriched subnetwork

### Description

This function takes in a subnetwork module resulted from the function `networkAnalysis`, a vector of labels for nodes in the module and a phenotype vector (optional) to generate a figure.

### Usage

    networkPlot(nwAnalysisOutput, phenotypeVector=NULL)

### Arguments

`nwAnalysisOutput` | a list consisting of 'subnw' and 'labels', in which 'subnw' is the subnetwork module generated by the function `networkAnalysis`, while 'labels' is a character vector specifying the labels for all nodes in the module.
`phenotypeVector` | a numeric or integer vector characterizing the phenotypes of nodes in the subnetwork module.

### Details

The 'phenotypeVector' argument is optional. The subnetwork figure will be more readable if it is provided. See the function `plotModule` function in the 'BioNet' package for more details.

### Value

a subnetwork module of class `graphNEL`

### Author(s)

Xin Wang, Camille Terfve

### References

Beisser D, Klau GW, Dandekar T, Muller T, Dittrich MT. BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics. 2010 Apr 15;26(8):1129-30.

Dittrich MT, Klau GW, Rosenwald A., Dandekar T and Muller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 2008 24(13):i223-i231.

### See Also

`networkAnalysis`, `viewSubNet`, `plotSubNet`

### Examples

    ## Not run:
    library(BioNet)
    library(org.Dm.eg.db)
    ##load pvalues, interactome, and phenotype vector (see the vignette for
    ##preprocessing details about this dataset)
    data("KcViab_PVals", "Biogrid_DM_Interactome", "KcViab_Data4Enrich")
    ##Identify subnetworks
    enrichedSubNet <- networkAnalysis(pvalues=KcViab_PVals,
    graph=Biogrid_DM_Interactome, fdr=0.001, verbose=TRUE)
    dev.off()
    map <- as.list(get("org.Dm.egSYMBOL"))
    labels <- map[nodes(enrichedSubNet)]
    nwAnalysisResult <- list(subnw=enrichedSubNet, labels=labels)
    networkPlot(nwAnalysisOutput=nwAnalysisResult, phenotypeVector=
    KcViab_Data4Enrich)

    ## End(Not run)

[Package HTSanalyzeR version 2.36.0 Index]