breakEdges: Break Cytoscape (or graphNEL) Network Edges

Description

Removes those edges in a graph network with the edge attribute that is "under" or "over" the cutoff value supplied.

Usage

breakEdges(cwObject,cutoff,edgeAtt='weight',valDir='under',layout='force-directed')

Arguments

cwObject

The object returned by ccOutCyt

cutoff

What is the cutoff to select edges

edgeAtt

Which edge attribute should be used for deciding which edges to select

valDir

Select the edge attribute with values "under" (default) or "over" the input value

layout

What type of layout should be used after the edges are broken

Value

The first returns nothing, rather it modifies the network in Cytoscape itself.The second returns a new ccCompareResult object for use by ccOutCyt

Details

When viewing annotations returned by ccCompare, unless a hierarchical view is used, the annotations are linked by edges weighted by how many genes are shared between each annotation. The default cutoff is 0.1, any edges above that are kept. This can result in a big hairy mess when viewing the annotation network in Cytoscape. To help clean up the display and encourage finding functionally related sets of annotations, it is very useful to remove edges with low values of overlap, and re-layout the network. breakEdges does just that.

The other option is to break the highly overlapping edges prior to sending the network to Cytoscape, thereby speeding up the process, as the fewer edges one has to "push" to Cytoscape the faster it will go.

Examples

Run this code

## Not run: 
# 	require(RCytoscape)
# 	g <- makeSimpleGraph()
# 	cw <- CytoscapeWindow('breakEdges',g)
# 	displayGraph(cw)
# 	layout(cw)
# 	redraw(cw)
# 	breakEdges(cw,'score',0,layout=NULL)
# ## End(Not run)