subpathwayToGraph: Subpathway To Graph

Description Usage Arguments Value Examples

View source: R/visualizations.R

Description

Subpathway plotting as a graph.

Usage

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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

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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.