subpathwayToGraph: Subpathway To Graph

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

Description

Subpathway plotting as a graph.

Usage

subpathwayToGraph( DEsubs.out, submethod, subname, colors, size, export, 
                    width, height, outfile, verbose )

Arguments

DEsubs.out	Return value from DEsubs
submethod	Subpathway extraction type selection (get all availiable options from subpathwayTypes)
subname	Subpathway name as contained in DEsubs return value, i.e. 'sub1'.
colors	A custom color mode which overrides the default settings.
size	A vector storing width and height of the barplot visualization.
export	A set of options for exporting subpathway data. Possible options are 'plot', 'pdf', 'edgelist', 'json', 'gml', 'ncol', 'lgl', 'graphml','dot'.
width	The width of the printable area (pdf)
height	The height of the printable area (pdf)
outfile	Output file name of the visualization. If multiple export types have been selected, the outfile should have an extension '.*'
verbose	TRUE to display informative messages, FALSE to hide.

Value

No value is returned.

Examples

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

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

res <- subpathwayToGraph( 
                DEsubs.out=DEsubs.out, 
                submethod='community.walktrap', 
                subname=paste0('sub', 6),
                size=c(10,10),
                export='pdf',
                outfile=outfile )

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