plotNetwork {geNetClassifier} | R Documentation

## Plot GenesNetwork

### Description

Plots the coexpression and/or mutual information network for the given genes.

### Usage

    plotNetwork(genesNetwork, classificationGenes=NULL, genesRanking=NULL,
    genesInfo=NULL, geneLabels=NULL, returniGraphs=FALSE,
    plotType="dynamic", fileName=NULL,
    plotAllNodesNetwork=TRUE, plotOnlyConnectedNodesNetwork=FALSE,
    plotClassifcationGenesNetwork=FALSE,
    labelSize=0.5, vertexSize=NULL, width=NULL, height=NULL, verbose=TRUE)

### Arguments

`genesNetwork` | List of GenesNetwork returned by `geNetClassifier`. (`@genesNetwork`)
`classificationGenes` | Matrix or classificationGenes returned by `geNetClassifier`. (`@classificationGenes`)
`genesRanking` | Matrix or genesRanking returned by `geNetClassifier`. (`@genesRanking`)
`genesInfo` | List or data.frame with the properties of the genes to plot: `genesDetails(_@genesRanking)`
`geneLabels` | Vector or Matrix. Gene name, ID or label which should be shown in the returned results and plots.
`returniGraphs` | deprecated. A list with the plotted networks as igraph objects is always returned (see `invisible`), assign it to a variable if needed.
`plotType` | Character. "dynamic": Interactive plot. "static": One canvas split for the different networks. "pdf": All the networks are saved into a pdf file.
`fileName` | Character. File name to save the plot with. If not provided, the plots will be shown through the standard output device.
`plotAllNodesNetwork` | Logical. If TRUE, plots a network only with all the available genes
`plotOnlyConnectedNodesNetwork` | Logical. If TRUE, plots a network only with the connected nodes/genes
`plotClassifcationGenesNetwork` | Logical. If TRUE, plots a network only with the classification genes
`labelSize` | Integer. Gene/node label size for static and pdf plots.
`vertexSize` | Integer. Vertex minimum size.
`width` | Numeric. Dinamic or pdf plot width.
`height` | Numeric. Dinamic or pdf plot height.
`verbose` | Logical. If TRUE, messages indicating the execution progress will be shown.

### Value

`Graph list` | List with the plotted `igraph` objects.
`Network plots` | Shown throught the standard output devide or saved in the working directory as 'fileName.pdf' if `fileName` was provided.

### Author(s)

Bioinformatics and Functional Genomics Group. Centro de Investigacion del Cancer (CIC-IBMCC, USAL-CSIC). Salamanca. Spain

### References

Main package function and classifier training: `geNetClassifier`

Package `igraph`

### See Also

`plot.GenesNetwork()` is an alias to this function. It can allso be called as i.e. `plotNetwork(clGenesSubNet$ALL)` Note: The slot @genesNetwork returned by geNetClassifier is a List of GenesNetworks!

### Examples

    data(leukemiasClassifier)

    # Step 1: Select a network or sub network
    # Sub-network containing only the classification genes:
    clGenesSubNet <- getSubNetwork(leukemiasClassifier@genesNetwork,
        leukemiasClassifier@classificationGenes)
    # Step 2: Select the details/info about the genes to plot
    # Classification genes' info:
    clGenesInfo <- genesDetails(leukemiasClassifier@classificationGenes)

    # Step 3: Plot the network
    # Network plots can be interactive or plotted as PDF file.
    #  - - Use plotType="pdf" to save the network as a static pdf file.
    #       This option is recommended for getting an overview of several networks.
    #  - - To get an interactive network, just skip this argument.

    # Plot ALL network:
    plotNetwork(clGenesSubNet$ALL, genesInfo=clGenesInfo)

    # Plot AML network containing only the conected nodes:
    plotNetwork(clGenesSubNet$ALL, genesInfo=clGenesInfo,
     plotAllNodesNetwork=FALSE, plotOnlyConnectedNodesNetwork=TRUE)

    # The equivalent code to the plot geNetClassifier creates by default is:
    topRanking <- getTopRanking(leukemiasClassifier@genesRanking, numGenesClass=100)
    netTopGenes <- getSubNetwork(leukemiasClassifier@genesNetwork,
     getRanking(topRanking, showGeneID=TRUE)$geneID)
    plotNetwork(netTopGenes,  classificationGenes=leukemiasClassifier@classificationGenes,
     genesRanking=topRanking, plotAllNodesNetwork=TRUE,
     plotOnlyConnectedNodesNetwork=TRUE, plotType="pdf",
     labelSize=0.3, fileName="leukemiasClassifier")

    # In order to save the network as text file, you can use:
    network2txt(leukemiasClassifier@genesNetwork, filePrefix="leukemiasNetwork")

[Package geNetClassifier version 1.20.0 Index]