visualization: Network visualization

In ProNet: Biological Network Construction, Visualization and Analyses

Description

This function takes an igraph formatted network as input and exports a picture of the visulization. Mode of the layout, and size, color, shape of the nodes, edges and labels can be set according to the experiment data.

Usage

visualization(graph, layout = c("reingold.tilford", "circle", "random",
  "fruchterman.reingold", "sphere", "kamada.kawai", "lgl"),
  node.fill.color = "SkyBlue2", node.border.color = "Black",
  node.shape = c("circle", "square", "sphere", "csquare", "rectangle",
  "crectangle", "vrectangle", "none", "pie", "raster"), node.size = 15,
  node.label = "name", node.label.color = 1, node.label.size = 0.8,
  node.label.position = 0, edge.shape = 1, edge.width = 1,
  edge.color = "gray1", ...)

Arguments

graph	An igraph object.
layout	Mode of the layout, possible values are fruchterman.reingold, reingold.tilford, random, circle, kamada.kawai, lgl and sphere. See igraph for more information.
node.fill.color	The fill color of the vertex. Default value is SkyBlue2.
node.border.color	Border color the the vertex. Default value is Black.
node.shape	Shape of the vertex. currently circle, square, csquare, rectangle, crectangl, vrectangle and none are supported.
node.size	Size of the vertex. Default value is 15.
node.label	Label of the vertex. Specify NA to omit vertex labels. Default value is the vertex name.
node.label.color	Color of labels of the vertex. Default value is 1.
node.label.size	Font size of the vertex label. Default value is 0.8.
node.label.position	Positon of the vertex label. Default value is 0.
edge.shape	Shape of the edge. Default value is 1.
edge.width	Width of the edge. Default value is 1.
edge.color	Color of the edge. Default value is gray1.
...	Other arguments.

Value

A plot of the network.

Examples

local<-data.frame(1:5,2:6)
attribute<-data.frame(node=1:6,value=c(2.2,5.3,1.2,4.5,6.2,0.6))
net<-construction(input=local,local.net=TRUE,node.attribute=attribute)
visualization(net,layout="reingold.tilford")
visualization(net,layout="reingold.tilford",node.size=V(net)$value)

Example output

Loading required package: Rcpp
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

Loading required package: MCL
Loading required package: linkcomm
Loading required package: RColorBrewer

Welcome to linkcomm version 1.0-11

For a step-by-step guide to using linkcomm functions:
   > vignette(topic = "linkcomm", package = "linkcomm")
To run an interactive demo:
   > demo(topic = "linkcomm", package = "linkcomm")
To cite, see:
   > citation("linkcomm")
NOTE: To use linkcomm, you require read and write permissions in the current directory (see: help("getwd"), help("setwd"))

ProNet documentation built on May 30, 2017, 2:02 a.m.