organismVisualization {DEsubs} | R Documentation

## Organism level visualization

### Description

Organism level measures

### Usage

    organismVisualization( DEsubs.out, references, topSubs, topTerms, colors,
                            export, width, height, outfiles, verbose )

### Arguments

`DEsubs.out` | Return value from `DEsubs`
`references` | Functional 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 corresponding options are 'KEGG', 'GO_bp', 'GO_cc', 'GO_mf', 'Disease_OMIM' , 'Disease_GAD', 'Drug_DrugBank', 'miRNA' and 'TF'. If no argument is supplied, no option is selected. 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.
`topSubs` | Default value is 10
`topTerms` | Default value is 20
`colors` | A custom color mode which overrides the default settings.
`export` | Export type of visualizations ('plot', 'pdf')
`width` | The width of the printable area (pdf)
`height` | The height of the printable area (pdf)
`outfiles` | Output filenames of the visualizations. If the argument is not specified, default filenames are used ('DEsubs/Output').
`verbose` | TRUE to display informative messages, FALSE to hide.

### Value

A list of matrices, containing Subpathway/Term/P-Value results for each reference.

### Examples

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

    outfile <- tempfile(fileext='.pdf')

    res <- organismVisualization(
                    DEsubs.out=DEsubs.out, references='KEGG',
                    topSubs=10, topTerms=20,
                    width=7, height=6,
                    export='pdf',
                    outfile=outfile,
                    verbose=FALSE)

[Package DEsubs version 1.13.1 Index]