plotSubNet {HTSanalyzeR} | R Documentation

## Plot and save a figure of the enriched subnetwork

### Description

This is an generic function.

When implemented as the S4 method for class `NWA`, this function invokes the function `networkPlot` to plot and save the subnetwork identified by the 'BioNet' package.

To use this function for objects of class `NWA`:

plotSubNet(object, filepath, filename, output, ...)

### Usage

    plotSubNet(object, ...)

### Arguments

`object` | an object. When implemented as S4 methods of class `NWA`, this argument is an object of class `NWA`.
`...` | other arguments. (see below for the arguments supported by the method of class `NWA`)

filepath:

  a single character value specifying the directory where the figure will be stored

filename:

  a single character value specifying the name of the figure to save

output:

  a single character value specifying the format of output image: "pdf" or "png"

...:

  all other arguments for the function `pdf` or `png` such as the argument 'width' and 'height'

### Details

After the analyses step for an object of class 'NWA', users can generate the enriched subnetwork identified by the 'BioNet' package. If the slot 'phenotype' was inputted when initializing the object, this function will send it to the function `networkPlot` as the argument `phenotypeVector` to highlight nodes in different colors. If the argument `species` of the function `analyze` has been assigned, labels of nodes of this subnetwork will be mapped to gene symbols corresponding to the species; otherwise, Entrez identifiers will be used as the labels.

### Author(s)

Xin Wang xw264@cam.ac.uk

### See Also

`networkPlot`, `viewSubNet`, `analyze`

### Examples

    ## Not run:
    library(BioNet)
    ##load p-values and phenotypes
    data("KcViab_Data4Enrich","KcViab_PVals")
    ##load Biogrid interactome for Drosophila Melanogaster
    data("Biogrid_DM_Interactome")
    ##create a NWA (NetWork Analysis) object
    nwa <- new("NWA", pvalues=KcViab_PVals, phenotypes=KcViab_Data4Enrich,
    interactome=Biogrid_DM_Interactome)
    ##preprocessing
    nwa <- preprocess(nwa, species="Dm", initialIDs="Entrez.gene",
    keepMultipleMappings=TRUE, duplicateRemoverMethod="max")
    ##To create an interactome:
    ##nwa<-interactome(nwa, species="Dm", reportDir="HTSanalyzerReport",
    ##genetic=FALSE)
    ##do network analysis
    nwa <- analyze(nwa, fdr=0.001, species="Dm")
    graphics.off()
    ##plot and save the identified subnetwork
    plotSubNet(nwa, filepath=".", filename="subnetwork.pdf",
    output="pdf", width=8, height=8)

    ## End(Not run)

[Package HTSanalyzeR version 2.38.0 Index]