NetPathMiner (version 1.8.0)

layoutVertexByAttr: A graph layout function, which groups vertices by attribute.

Description

This function generates a layout for igraph objects, keeping vertices with the same attribute (ex: in the same pathway, etc) close to each other.

Usage

layoutVertexByAttr(graph, attr.name, cluster.strength = 1, layout = layout.auto)

Arguments

graph

An annotated igraph object.

attr.name

The attribute name by which vertices are laid out.

cluster.strength

A number indicating tie strengths between vertices with the same attribute. The larger it is, the closer the vertices will be.

layout

A layout function, ideally a force-directed layout fuction, such as layout.fruchterman.reingold and layout.kamada.kawai.

Value

A two-column matrix indicating the x and y postions of vertices.

See Also

Other Plotting methods: colorVertexByAttr; plotAllNetworks; plotClassifierROC; plotClusterMatrix, plotClusterProbs, plotClusters; plotCytoscape, plotCytoscapeGML; plotNetwork; plotPathClassifier; plotPaths

Examples

data("ex_kgml_sig")
  v.layout <- layoutVertexByAttr(ex_kgml_sig, "pathway")
  plotNetwork(ex_kgml_sig, vertex.color="pathway", layout=v.layout)

  v.layout <- layoutVertexByAttr(ex_kgml_sig, "pathway", cluster.strength=5)
  plotNetwork(ex_kgml_sig, vertex.color="pathway", layout=v.layout)