Description Usage Arguments Value Examples
Global layout style:
Large complex networks can be plotted using the fruchtermanreingold algorithm, the Kamadakawai algorithm or any given input function by applying these algorithms to the minimum spanning tree (MST). The edges of the minimum spanning tree are shown in black, all other edges are shown in colors which are a function of the distances between the coordinates of the nodes.
1 2 3 4 5 6 7  mst.plot.mod(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), sf=0,
e.arrow=.2, layout.overall=NULL)

x 

layout.function 

layout.overall 

mst.edge.col 
This option assigns a color to the edges of the minimum spanning tree of graph 'g'. If mst.edge.col = NULL, then 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 a logical value to show vertex label. 
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 value or a character name of a color 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 the vertices. This is used to adjust the vertex size when the option 
sf 
is a numeric value. It is a scaling factor used to scaleup or scaledown the abstract graph. 
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 40 41 42 43 44 45 46 47 48 49 50 51 52  ## Example 1 ####
g < barabasi.game(2000, directed=FALSE)
id < mst.plot.mod(g)
## Example 2 ####
### plotting a graph by combining two algorithms ##%
fn < function(g){layout.reingold.tilford(g,
circular=TRUE, root=which.max(degree(g)))}
id < mst.plot.mod(g, v.size=1, sf=20, layout.function=fn,
layout.overall=layout.fruchterman.reingold, mst.e.size=2,
vertex.color="darkgreen")
data("PPI_Athalina")
id < mst.plot.mod(g1, v.size=1, sf=0, layout.function=fn,
layout.overall=layout.fruchterman.reingold, mst.e.size=1,
vertex.color="magenta", colors=heat.colors(20))
## Example 3 ####
## When expression values of genes or nodes
## are given and to be plotted as a color of vertices ###
id < mst.plot.mod(g1, expression=rnorm(vcount(g1)), v.size=1)
## Example 4 ####
## 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.mod(g1, expression=rnorm(vcount(g1)),
v.size=degree(g1), v.sf=c(1,5))
## Example 5 ####
## 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.mod(g1, mst.edge.col="purple",
colors=heat.colors(20), vertex.color="yellow", v.size=1)
## Example 6 ####
## Plotting a graph with kamadakawai layout algorithm ###
id < mst.plot.mod(g1, mst.edge.col="purple",
colors=heat.colors(20), vertex.color="white", v.size=1,
layout.function=layout.kamada.kawai)
## Example 7 ####
## Plotting a graph with when weights of edges are given ###
id < mst.plot.mod(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)

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