A graph layout function, which groups vertices by attribute.

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

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_with_fr and layout_with_kk.

Value

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

See also

Other Plotting methods: colorVertexByAttr(), plotAllNetworks(), plotClassifierROC(), plotClusterMatrix(), plotCytoscapeGML(), plotNetwork(), plotPathClassifier(), plotPaths()

Author

Ahmed Mohamed

Examples

  data("ex_kgml_sig")
  v.layout <- layoutVertexByAttr(ex_kgml_sig, "pathway")
#> This graph was created by an old(er) igraph version.
#> ℹ Call `igraph::upgrade_graph()` on it to use with the current igraph version.
#> For now we convert it on the fly...
  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)