Network Data and Visualization

WEN, Tzai-Hung (NTU Geography)

0. Load packages for network analysis

library(sna)
library(igraph)

1. Import from csv file: Matrix format

(using sna package)

setwd("D:/R_Labs")
data<- "sample_adjmatrix.csv"
el<-read.table(data, header=T, row.names=1, sep=",")
m=as.matrix(el)
m

##       X23732 X23778 X23824 X23871 X58009 X58098 X58256
## 23732      0      1      0      1      0      1      0
## 23778      1      0      1      1      0      1      0
## 23824      0      1      0      0      0      0      0
## 23871      1      1      0      0      1      1      0
## 58009      0      0      0      1      0      1      0
## 58098      1      1      0      1      1      0      1
## 58256      0      0      0      0      0      1      0

gplot(m, displaylabels=TRUE)

(using igraph package)

#igraph object
g1=graph.adjacency(m,mode="undirected",weighted=NULL)
class(g1); plot(g1)

## [1] "igraph"

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2. Import from csv file: edge-list format

(using sna package)

setwd("D:/R_Labs")
data2<- "n2.csv"
(el2<-read.table(data2, header=T, sep=","))

##    V1 V2 V3
## 1   1  2  1
## 2   1  3  1
## 3   1  5  1
## 4   2  6  1
## 5   2  7  1
## 6   2  5  1
## 7   3  4  1
## 8   3  5  1
## 9   4  5  1
## 10  5  7  1

(m2=as.matrix(el2))

##       V1 V2 V3
##  [1,]  1  2  1
##  [2,]  1  3  1
##  [3,]  1  5  1
##  [4,]  2  6  1
##  [5,]  2  7  1
##  [6,]  2  5  1
##  [7,]  3  4  1
##  [8,]  3  5  1
##  [9,]  4  5  1
## [10,]  5  7  1

attr(m2,"n")<-7 # number of nodes
attr(m2,"vnames")<-letters[1:7] # names of each node
gplot(m2,displaylabels=TRUE)

(using igraph package)

setwd("D:/R_Labs")
data3<- "sample_edgelist.csv"
(el3<-read.table(data3, header=T, sep=","))

##    Source Target
## 1   23732  23778
## 2   23732  23871
## 3   23732  58098
## 4   23778  23824
## 5   23778  23871
## 6   23778  58098
## 7   23871  58009
## 8   23871  58098
## 9   58009  58098
## 10  58098  58256

# read from data.frame  (--> list)
g3=graph.data.frame(el3,directed=FALSE) 
class(g3); plot(g3)

## [1] "igraph"

plot(g3, vertex.color="red",  edge.color="black", edge.arrow.size=.3, 
     vertex.size=10, main='My Graph')

igraph plot parameters

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3. Manipulating the graph

# igraph --> matrix
(m3<-get.adjacency(g3))

## 7 x 7 sparse Matrix of class "dgCMatrix"
##       23732 23778 23871 58009 58098 23824 58256
## 23732     .     1     1     .     1     .     .
## 23778     1     .     1     .     1     1     .
## 23871     1     1     .     1     1     .     .
## 58009     .     .     1     .     1     .     .
## 58098     1     1     1     1     .     .     1
## 23824     .     1     .     .     .     .     .
## 58256     .     .     .     .     1     .     .

class(m3) # dgMatrix

## [1] "dgCMatrix"
## attr(,"package")
## [1] "Matrix"

(m3<-as.matrix(m3)) # convert to regular matrix

##       23732 23778 23871 58009 58098 23824 58256
## 23732     0     1     1     0     1     0     0
## 23778     1     0     1     0     1     1     0
## 23871     1     1     0     1     1     0     0
## 58009     0     0     1     0     1     0     0
## 58098     1     1     1     1     0     0     1
## 23824     0     1     0     0     0     0     0
## 58256     0     0     0     0     1     0     0

class(m3)

## [1] "matrix"

V(g3) # vertex

## + 7/7 vertices, named:
## [1] 23732 23778 23871 58009 58098 23824 58256

E(g3) # edge

## + 10/10 edges (vertex names):
##  [1] 23732--23778 23732--23871 23732--58098 23778--23824 23778--23871
##  [6] 23778--58098 23871--58009 23871--58098 58009--58098 58098--58256

vcount(g3); ecount(g3) # counts of vertex and edges

## [1] 7

## [1] 10

# graph attribute
V(g3)$name

## [1] "23732" "23778" "23871" "58009" "58098" "23824" "58256"

V(g3)$name <- c("Tom", "Mary","John","Amy","Eric","Sam","Jack")
V(g3)$name

## [1] "Tom"  "Mary" "John" "Amy"  "Eric" "Sam"  "Jack"

# weighted graph
is.weighted(g3)

## [1] FALSE

E(g3)$weight<-runif(ecount(g3) )
is.weighted(g3)

## [1] TRUE

E(g3)$weight

##  [1] 0.77965655 0.06086829 0.99097351 0.05464308 0.40371985 0.08755811
##  [7] 0.28608251 0.75620541 0.72238959 0.79841096

plot(g3, vertex.color="red",  edge.color="black", edge.width=E(g3)$weight*10, vertex.size=10, main='My Weighted Graph')

# Types of graphs
g.full<- graph.full(7)
g.ring<- graph.ring(7)
g.tree<-graph.tree(7, children = 3, mode= "undirected")
g.star<-graph.star(7, mode= "undirected" )
par(mfrow=c(2,2))
plot(g.full, main="full");plot(g.ring, main="ring");plot(g.tree, main="tree");plot(g.star, main="star")

dev.off()

## null device 
##           1