netbiov (version 1.6.0)

splitg.mst: Network plot

Description

Modular layout style:

A large complex network is plotted by splitting it into its modules. The positions of the vertices in each subnetwork are determined by using the fruchterman-reingold algorithm or the Kamada-kawai algorithm for the minimum spanning tree of each subnetwork. The edges of the minimum spanning tree are shown in black color.

Usage

splitg.mst(x,layout.function=NULL, mod.list=NULL, 
colors=NULL,mst.edge.col="white", 
vertex.color = c("red","green","blue","orange"),
random.v.color=FALSE,in.con.ed.col=NULL,tkplot=FALSE,
v.size=2, e.size=.5, mst.e.size=1, v.lab=FALSE, 
bg="black", v.lab.cex=0.5, e.lab.cex=0.5, 
v.lab.col="skyblue", lab.dist=0, v.sf=4, sf.modules = 5, ...)

Arguments

x

x is a graph object, created using igraph package.

layout.function

is a 'function' class or a vector of functions to plot the layout of each module by a function in 'layout.function'.

mod.list

mod.list is a list object, which provides a modular information about the graph, each components of mod.list contains a vector of nodes to be plotted.

v.size

is a numeric value or a numeric vector which contains values to assign the size of the nodes.

e.size

is a numeric value to assign the width to edges.

e.lab.cex

is a numeric variable; this determines the size of the labels of the vertices or the modules.

lab.dist

is a numeric variable; this adjusts labels of vertices.

sf.modules

is an integer variable is used to scale up or scale down the graph plot.

v.sf

is a numeric value. This is used to adjust vertex size when v.size input is a numeric vector.

mst.edge.col

This option assigns a color to the edges of the minimum spanning tree of each module of graph 'g'. The default color is black for 'tkplot=TRUE'. If 'tkplot=FALSE' it is white.

random

random is a logical value, this option is used to choose nodes of split graphs randomly

colors

colors is a vector of colors. This option is a vector of the edge colors to assign colors to the edges of the graph.

vertex.color

vertex.colors is a vector of colors to assign colors to the vertices of the modules of the graph.

random.v.color

is a logical value, this option is used to assign colors to the vertices colors of the modules, colors for modules are picked randomly.

in.con.ed.col

is a scaler, assign colors to the edges which are showing connections between the modules.

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 a black background.

mst.e.size

is a numeric value which assigns the edge width to the edges of minimum spanning tree of the input graph.

v.lab

is a logical value to show vertex label.

v.lab.cex

is a numerical value to set the font size of vertex labels.

v.lab.col

is a hexadecimal character value to assign colors to vertex labels.

sf

is a numeric value. This is used to adjust vertex size when v.size input is a numeric vector.

bg

is a color value for background.

...

... parameter for other inputs.

Value

This function plots a graph using 'tkplot' function available in the 'igraph'. This function returns a list,first component of list is a graph object, second component of the list contains x and y coordinates, third component of list contains color ids of edges of the graph etc.

Examples

  data("PPI_Athalina")
  data("modules_PPI_Athalina")
        id <- splitg.mst(g1, mod.list=lm, random.v.color=TRUE, tkplot=FALSE )