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Last data update: 2014.03.03

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

layoutVertexByAttr

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.fruchterman.reingold` and `layout.kamada.kawai`.

Value

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

Author(s)

Ahmed Mohamed

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(NetPathMiner)
Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/NetPathMiner/layoutVertexByAttr.Rd_%03d_medium.png", width=480, height=480)
> ### Name: layoutVertexByAttr
> ### Title: A graph layout function, which groups vertices by attribute.
> ### Aliases: layoutVertexByAttr
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>