geneVisualization: Gene level visualization

Description Usage Arguments Details Value Examples

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

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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

Value

Individual measure results in matrix form.

Examples

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

res <- geneVisualization(  
            DEsubs.out=DEsubs.out, top=10,
            measures.topological=c( 'degree', 'betweenness', 'closeness',
                                    'hub_score', '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', verbose=FALSE)

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