subpathwayVisualization: Subpathway level visualization

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

Description

Circular diagrams containing subpathways enrichment in potential key regulators (miRNAs, TFs) and biological, biomedical and pharmacological issues.

Usage

subpathwayVisualization( DEsubs.out, references, submethod, subname, colors, 
                        scale, shuffleColors, outfiles, export, verbose )

Arguments

DEsubs.out	Return value from DEsubs.
references	Topological references include degree, betweeness centrality, closeness centrality, hub_score, eccentricity and page_rank. The corresponding options are 'degree', 'betweenness', 'closeness', 'hub_score', 'eccentricity' and 'page_rank'. Functional references include (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'.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.
submethod	Subpathway extraction type selection (see all 124 options along with their R commands in supplementary document)
subname	Subpathway name as contained in DEsubs return value, i.e. 'sub1'
colors	A custom color mode which overrrides the default settings.
scale	A value in (0,1] used to scale the visualization. Useful in the case of long labels which are trimmed by default.
shuffleColors	TRUE to shuffle user defined or default colors. Defaults to FALSE.
outfiles	Output filenames of the visualizations. If the argument is not specified, default filenames are used ('DEsubs/Output').
export	Export type of visualizations ('plot', 'pdf')
verbose	TRUE to display informative messages, FALSE to hide.

Details

The associations of subpathways with various biological and pharmacologicalfeatures are estimated through a hypergeometric test. The enriched associations of a subpathway to each feature are illustrated through circular diagrams.

Value

A list of matrices, each containing the P-Value of enrichment between the terms for a specific reference (rows) and each of the subpathway genes (columns). If there is no enrichment, the value is NA.

Examples

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

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

res <- subpathwayVisualization( 
                DEsubs.out=DEsubs.out,  
                references=c('TF'), 
                submethod='community.walktrap',
                subname='sub1', 
                scale=c(1.0), 
                export='pdf',
                outfile=outfile )

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