netbiov (version 1.6.0)

plot.abstract.nodes: Exploratory visualization of information spread of biological networks

Description

Modular layout style:

Visualization of modules in an abstract way. In the function plot.abstract.nodes, nodes in a module are replaced by a single node and the relative size of a node is proportional to the total number of nodes in a module. In the functions plot.abstract.module, plot.abstract.nodes, edges between two modules are replaced by a single edge and the total number of edges between two modules are reflected by the relative edge-width.

Usage

"plot"(x, mod.list=NULL,  rest.module=TRUE, 
color.random=FALSE, nodes.color = NULL, edge.colors=NULL,
layout.function=NULL,tkplot=FALSE,v.sf = 0, e.sf = 0,lab.color=NULL,
lab.cex=NULL, lab.dist=NULL, bg="black", ... )

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

mod.list

mod.list is a list object each components of mod.list consists a vector of module to be plotted.

random

is a logical value, if modules information is not provided then random nodes for the modules are selected.

rest.module

is a logical value, rest of the nodes to be plotted as a one module (if TRUE) or independently (if FALSE)

color.random

is a logical value, if this option is TRUE it will assign random color to each module or nodes.

nodes.color

assigns colors to nodes of recreated graph

edge.colors

is a vector of colors, assigned to color edges depending on their width from small to large width.

layout.function

is a function class, this corrosponds to a layout function given as an input to plot a graph. Input function should return a two column matrix which has same no of rows as the modules in the graph

tkplot

is a boolean variable, if it is true function will use this option to plot a graph, if it is false function will use plot function with a black background.

v.sf

is a numeric value, this option to increase or decrease the size of nodes

e.sf

is a numeric value, this option to increase or decrease width of edges

lab.color

colors the vertices and edge labels

lab.cex

is anumeric value, increase or decrease the font size of labels

lab.dist

is a numeric value, adjust vertex labels

bg

is a color value to adjust background color of the plot.

...

... parameter for other inputs.

References

http://bio-complexity.com/

Examples

  require(igraph)
  data("PPI_Athalina")
  data("modules_PPI_Athalina")
  plot.abstract.nodes(g1, mod.list = lm, 
edge.colors = c("red","green","blue","orange"))