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

In aiminy/NetPathMiner: NetPathMiner for Biological Network Construction, Path Mining and Visualization

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.

Author(s)

Ahmed Mohamed

See Also

Other Plotting methods: colorVertexByAttr, plotAllNetworks, plotClassifierROC, plotClusterMatrix, 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)

aiminy/NetPathMiner documentation built on May 12, 2019, 3:38 a.m.