geneVisualization: Gene level visualization

In DEsubs: DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

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)

DEsubs documentation built on Nov. 8, 2020, 8:31 p.m.