Description Usage Arguments Value Examples
Large complex networks can be plotted using the fruchtermanreingold algorithm or the Kamadakawai algorithm or any given input function on minimum spanning tree of each network. The edges of the minimum spanning tree (MST) are shown in black color, the rest of the edges are shown in a different colors which are a function of distances between the coordinates of the nodes.
1 2 3 4 5 6  mst.plot(x, layout.function=NULL,colors=NULL,mst.edge.col="white",
vertex.color = "skyblue",tkplot=FALSE,expression=NULL, v.size=FALSE,
e.size=FALSE, mst.e.size=1, edge.col.wt=NULL, v.lab=FALSE,
e.lab=NULL, bg="black",v.lab.cex=0.5, e.lab.cex=0.5,
v.lab.col="blue",lab.dist=0, e.lab.col="blue",
v.sf=c(3,12),e.arrow=.2)

x 

layout.function 

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

vertex.color 

expression 

tkplot 

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 or a numeric vector which contains values to assign the width of edgesother than the minimum spanning tree edges of the graph. 
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 logical value to show vertex labels. 
e.lab 
is logical value to show edge labels. 
bg 
is a character value to color the background. 
v.lab.cex 
is a numerical value to set the font size of the vertex labels. 
e.lab.cex 
is a numerical value to set the font size of the edge labels. 
lab.dist 
is a numerical value to adjust the distance of labels from the nodes. 
v.lab.col 
is a hexadecimal character value to assign colors to the vertex labels. 
e.lab.col 
is a hexadecimal character value to assign colors to the edge labels. 
e.arrow 
is a inumerical value to set the arrow width in a directed network. 
v.sf 
is a 2 dimensional numeric vector, which represents the minimum and maximum limits of the size of vertices. This is used to adjust the vertex size when the 
edge.col.wt 
is a vector of numeric values provided for each edge. This is used to color the edges from blue to red from high to low values. 
... 

This function plots the graph object given as an input using 'tkplot' or 'plot' function available in 'igraph' package.
This function returns a netbiov
class object.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39  data("PPI_Athalina")
## Example 1 ####
kk < mst.plot(g1)
## Example 2 ####
## When expression values of genes or nodes are given and
## to be plotted as ai color of vertices ###
id < mst.plot(g1, expression=rnorm(vcount(g1)), v.size=1)
## Example 3 ####
## When expression values of genes or nodes are given and to be
## plotted as a
##color of vertices, also the degree of nodes to be shown
## as their vertexsize ###
id < mst.plot(g1, expression=rnorm(vcount(g1)),
v.size=degree(g1), v.sf=c(1,5))
## Example 4 ####
## When MST edges are highlighted in purple color
## and rest of the edges are plotted with a range of
## heat colors depending on the distance between nodes ###
id < mst.plot(g1, mst.edge.col="purple",
colors=heat.colors(20), vertex.color="yellow",
v.size=1)
## Example 5 ####
## Plotting a graph with kamadakawai layout algorithm ###
id < mst.plot(g1, mst.edge.col="purple",
colors=heat.colors(20), vertex.color="white", v.size=1,
layout.function=layout.kamada.kawai)
## Example 6 ####
## Plotting a graph with when weights of edges are given ###
id < mst.plot(g1, mst.edge.col="purple", edge.col.wt =
runif(ecount(g1), min=1, max=10), vertex.color="yellow",
v.size=1, layout.function=layout.kamada.kawai)

Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.