sidier (version 3.0.1)

simplify.network: Network showing modules as nodes

Description

This function modifies node coordinates to allow a clearer depiction of complex networks. Nodes are moved along the axis connecting the original position to the module centroid. The magnitude of such movement is defined by user.

Usage

simplify.network(node.names=NA,modules=NA,coordinates=NA, network=NA,
shift = 0.5, max.lwd.edge =2, min.lwd.edge =1, max.vertex.size=4, min.vertex.size=2,
label.size=1/2.5, bgcol="white", main="")

Arguments

node.names

a vector containing the names of nodes

modules

a vector containing the module assigned to each node

coordinates

a two columns matrix containing the X and Y coordinates of each node in the original network

network

a matrix describing the original network. Can be either a 0/1 matrix or a weighted matrix. Row names must contain node names.

shift

a numeric defining the magnitude of node shift, limited between 0 (coinciding with the original location) and 1 (coinciding with the module centroid location).

max.lwd.edge

if shift=1, a numeric defining the line width for the maximum number of connections between modules

min.lwd.edge

if shift=1, a numeric defining the line width for the minimum number of connections between modules

max.vertex.size

if shift=1, a numeric defining the size of the node representing the largest module

min.vertex.size

if shift=1, a numeric defining the size of the node representing the smallest module

label.size

a numeric defining the size of node labels, referred to its particular node size

bgcol

a vector of strings representing the background colour for each node

main

a string, the title for the plot (no title by default)

Details

If 'shift=1', all nodes belonging to a module are represented as a single node depicted in the module centroid. In that case, node size is proportional to the number of element in this module and edge widths are proportional to the number of connections found between modules.

Examples

inputMatrix<-matrix(c(1, 1, 1, 1.2,  2, 1, 0.8, 1,    3, 2, 1.2, 1,  4, 2, 2, 2.2,
 5, 3, 1.8, 2,  6, 3, 2.2, 2,  7, 3, 1.7, 2.1,  8, 3, 2.2, 2.2),ncol=4,byrow=TRUE)
colnames(inputMatrix)<-c("node","module","x","y")

network<-matrix(c(1,  1,  0,  0,  1,  1,  0,  0,  1,  1,  1,  0,  0,  0,  0,  0,  0,
  1,  1,  1,  0,  0,  0,  0,  0,  0,  1,  1,  0,  0,  0,  0,  1,  0,  0,  0,  1,  1,
  1,  1,  1,  0,  0,  0,  1,  1,  1,  1,  0,  0,  0,  0,  1,  1,  1,  1, 0,  0,  0,
  0,  1,  1,  1,  1),ncol=8)
colnames(network)<-c(1:8)
row.names(network)<-c(1:8)

i1<-0
simplify.network(node.names=inputMatrix[,1],modules=inputMatrix[,2],
coordinates=inputMatrix[,3:4],network=network,shift = i1,
bgcol=c("red","red","blue","blue","green","green","green","green"),
main=paste("shift=",i1))

i1<-0.5
simplify.network(node.names=inputMatrix[,1],modules=inputMatrix[,2],
coordinates=inputMatrix[,3:4],network=network,shift = i1,
bgcol=c("red","red","blue","blue","green","green","green","green"),
main=paste("shift=",i1))

i1<-1.0
simplify.network(node.names=inputMatrix[,1],modules=inputMatrix[,2],
coordinates=inputMatrix[,3:4],network=network,shift = i1,
bgcol=c("red","red","blue","blue","green","green","green","green"),
main=paste("shift=",i1))

network<-as.matrix(as.dist(matrix(sample(c(1,0),10000,replace=TRUE),ncol=100)))
inputMatrix<-matrix(nrow=100,ncol=4)
inputMatrix[,1]<-1:100
inputMatrix[,2]<-c(rep(1,30),rep(2,20),rep(3,20),rep(4,20),rep(5,10))
inputMatrix[,3]<-c(
sample(seq(-40,0,0.01),30,rep=TRUE),
sample(seq(-40,0,0.01),20,rep=TRUE),
sample(seq(0,40,0.01),20,rep=TRUE),
sample(seq(0,40,0.01),20,rep=TRUE),
sample(seq(-20,20,0.01),10,rep=TRUE))
inputMatrix[,4]<-c(
sample(seq(0,40,0.01),30,rep=TRUE),
sample(seq(-40,0,0.01),20,rep=TRUE),
sample(seq(0,40,0.01),20,rep=TRUE),
sample(seq(-40,0,0.01),20,rep=TRUE),
sample(seq(-20,20,0.01),10,rep=TRUE))
cols<-c("red","green","yellow","blue","turquoise")

simplify.network(node.names=inputMatrix[,1],network=network,shift=0,
coordinates=inputMatrix[,3:4],modules=inputMatrix[,2],bgcol=cols[inputMatrix[,2]])

simplify.network(node.names=inputMatrix[,1],network=network,shift=1,
coordinates=inputMatrix[,3:4],modules=inputMatrix[,2],bgcol=cols[inputMatrix[,2]])