organismVisualization: Organism level visualization

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

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)

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