layoutVertexByAttr {NetPathMiner} | R Documentation

## 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_with_fr` and `layout_with_kk`.

### 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)

[Package NetPathMiner version 1.23.0 Index]