geneVisualization {DEsubs} | R Documentation

## Gene level visualization

### Description

Visualizes topologically and functionally significant genes using graph theory measures as well as their correlation to pathway, disease, drug, ontology, microRNA and Transcription Factor terms based on external references.

### Usage

    geneVisualization(DEsubs.out, measures.topological, measures.functional,
        measures.barplot, topGenes, colors.topological, colors.functional,
        colors.barplot, size.topological, size.functional, size.barplot,
        outfile.topological, outfile.functional, outfile.barplot,
        export, verbose)

### Arguments

`DEsubs.out` | Return value from `DEsubs`
`measures.topological` | Functional visualization type(s).
`measures.functional` | Topological visualization type(s).
`measures.barplot` | Gene level Visualization type
`topGenes` | Number of genes with greater Q-values. Default value is 10.
`colors.topological` | A custom color mode which overrrides the default settings.
`colors.functional` | A custom color mode which overrrides the default settings.
`colors.barplot` | A custom color mode which overrrides the default settings.
`size.topological` | A vector storing width and height of the topological measures visualization
`size.functional` | A vector storing width and height of the functional measures visualization
`size.barplot` | A vector storing width and height of the barplot visualization
`outfile.topological` | Output file name of the topological measures visualization.
`outfile.functional` | Output file name of the functional measures visualization.
`outfile.barplot` | Output file name of the barplot visualization.
`export` | Export type of visualizations ('plot', 'pdf')
`verbose` | TRUE to display informative messages, FALSE to hide.

### Details

- Topological visualization type contains six topological graph theory measures, namely degree, betweeness centrality, closeness centrality, hub_score, eccentricity and page_rank. The availiable options are 'degree', 'betweenness', 'closeness', 'hub_score', 'eccentricity' and 'page_rank'. If no argument is supplied, all availiable options are selected by default. If the argument is NULL, no visualization is exported.

- Functional visualization type contains associations with (i) KEGG's pathway terms, (ii) Gene Ontologies of Molecular function, biological processes and cellular components) (iii) Disease terms from OMIM and GAD databases), (iv) Drug substances from DrugBank) and the influence of (v) microRNA targets from miRecords and (vi) Transcription Factor targets from Transfac and Jaspar. The availiable options are 'KEGG', 'GO_bp', 'GO_cc', 'GO_mf', 'Disease_OMIM' , 'Disease_GAD', 'Drug_DrugBank', 'miRNA' and 'TF'. If no argument is supplied, all availiable options are selected by default. If the argument is NULL, no visualization is exported. Using option 'all' results in the selection of all afforementioned options, along with any other custom gene sets within the 'DEsubs/Data' user specified-directory.

### Value

Individual measure results in matrix form.

### Examples

    load(system.file('extdata', 'data.RData', package='DEsubs'))

    outfile.topological <- tempfile(fileext='.pdf')
    outfile.functional <- tempfile(fileext='.pdf')
    outfile.barplot <- tempfile(fileext='.pdf')

    res <- geneVisualization(
                DEsubs.out=DEsubs.out, top=10,
                measures.topological=c( 'degree', 'betweenness', 'closeness',
                                        'eccentricity', 'page_rank'),
                measures.functional=c(  'KEGG',
                                        'Disease_OMIM', 'Disease_GAD',
                                        'Drug_DrugBank','miRNA', 'TF'),
                size.topological=c(5,4),
                size.functional=c(7,4),
                size.barplot=c(5,6),
                export='pdf',
                outfile.topological=outfile.topological,
                outfile.functional=outfile.functional,
                outfile.barplot=outfile.barplot,
                verbose=FALSE)

[Package DEsubs version 1.10.0 Index]