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Last data update: 2014.03.03

R: Exploratory visualization of information spread of biological...

plot.spiral.graph

R Documentation

Exploratory visualization of information spread of biological networks

Description

Plots a graph in a spirical fashion, highly connected nodes are placed at center.

Usage


## S3 method for class 'spiral.graph'
plot(x, tp=61, vertex.color=NULL, 
color.random=FALSE, rank.function=NULL,tkplot=FALSE,
v.size=2, e.size=.5,e.curve=.5, v.lab=FALSE, bg="black",
e.col="grey", skip=0, ...)

Arguments

`x`	`x` is a graph object created from an adjacency matrix or from a tabular data of two columns using `graph()` function available in `igraph`
`tp`	is a numeric value, a tuning parameter to get different spirical shapes.
`color.random`	is alogical value, if TRUE, picks colors randomly and assign to nodes depending on their degree
`rank.function`	is a 'function' class returns a two column matrix with number of rows equal to the total nodes in the graph.
`tkplot`	it is a boolean variable, if it is true, function will use 'tkplot' function to plot a graph, if it is false function will use plot function with the black background.
`v.size`	is a numeric value or a numeric vector which contains numeric values to assign the size of nodes.
`e.size`	is a numeric value to assign the width to edges.
`e.curve`	is a positive numeric value that adjusts the curvature of the edges.
`v.lab`	is a logical value to show vertex label.
`bg`	name of a color or a hexadecimal code of a color. This option is used to color the background of the plot. The default option is "black".
`e.col`	is a character or a hexadecimal color value to set the color of edges.
`vertex.color`	is a vector of colors assign colors to nodes depending on their degree, from high to low.
`skip`	is an integer value to plot nodes away from the center.
`...`	`...` parameter for other inputs.

Details

This layout function plots network in a spiral fashion.

Value

returns a list object of 'netbiov' class

Author(s)

Shailesh Tripathi, Frank Emmert-Streib

References

http://bio-complexity.com/

Examples

  g <- barabasi.game(500)
  x <- plot.spiral.graph(g, 121 )
  x <- plot.spiral.graph(g, 120,rank.function=layout.reingold.tilford,
vertex.color="red", e.col="green")

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.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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(netbiov)
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/netbiov/plot.spiral.graph.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.spiral.graph
> ### Title: Exploratory visualization of information spread of biological
> ###   networks
> ### Aliases: plot.spiral.graph
> 
> ### ** Examples
> 
>   g <- barabasi.game(500)
>   x <- plot.spiral.graph(g, 121 )
>   x <- plot.spiral.graph(g, 120,rank.function=layout.reingold.tilford,
+ vertex.color="red", e.col="green")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>