organismVisualization: Organism level visualization

Description Usage Arguments Value Examples

Description

Organism level measures

Usage

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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

No value is returned.

Examples

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

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

balomenos/DEsubs documentation built on May 11, 2019, 6:19 p.m.