03 Lab Igraph1

Introducing the igraph library
Course: Complex Network Analysis mit GNU R

Prof. Dr. Claudia Mller-Birn
Institute for Computer Science, Networked Information Systems
February 22, 2012
This chapter is mainly based on the documentation written by Gbor Csrdi, Tams Nepusz: The
igraph software package for complex network research. InterJournal Complex Systems, 1695, 2006.
February 2012 Claudia Mller-Birn, Lecture: Complex Network Analysis mit R
igraph is a free software package for creating and manipulating
undirected and directed graphs
Contains the implementation of a lot graph algorithms
Provides a platform for the developing and/or implementing graph
algorithms
Website with documentation and download
http://cneurocvs.rmki.kfki.hu/igraph/index.html
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Introduction
Installation igraph R package
A recent GNU R version is recommended
To compile the R package from source, you'll need a C and C++
compiler
Optional
- libxml2 library, for reading GraphML files (included in Windows builds).
- GMP library, graph automorphisms (not included in Windows builds).
Suggested packages:
- stats4, rgl, tcltk, RSQLite, digest, graph, Matrix
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Data model
igraph graph is either directed or undirected and it cannot handle
mixed graphs (no direct support for bipartite (two-mode) graphs)
Directed graphs
- An ordered multiset of directed edges and additional meta dat
- |V| is the number of vertices, therefore the number of vertices is an integer number
between zero and |V|-1
- Edge ids are integer numbers between zero and |E|-1, |E| is the number of edges
Undirected graphs
- Undirected graph is an ordered multiset of undirected edges, plus the meta data
- Undirected igraph edge is a two-element (non-loop) or one-element (loop) set of vertex
ids
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Data model (cont.)
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Example directed graph Example undirected graph
Graph objects
igraph uses graph objects to represent graphs and provides functions
to create and manipulate these objects
Graph objects have a R class igraph
Check that an R object is an igraph graph object with the is.igraph
function
Some available functions to create graph objects
Example
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graph()
graph.star()
graph.tree()
graph.adjacency()
> g <- graph( c(0,1, 1,2, 3,4, 5,6))
Claudia Mller-Birn, Lecture: Complex Network Analysis mit R February 2012
Graph structures, edge lists and adjacency matrices
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Generating graph structures
Empty graphs
Full graphs
Stars and Rings
Other structures
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> e <- graph.empty()
> e <- graph.empty(n=10)
> f <- graph.full(15)
> f <- graph.full(15, directed=TRUE)
> s <- graph.star(10, mode = "in")
> s <- graph.star(10, mode = "out")
> s <- graph.star(10, mode = "undirected")
> r <- graph.ring(10, directed=TRUE)
> r <- graph.ring(10, mutual=TRUE)
> r <- graph.ring(10, circular=TRUE)
> graph.lattice()
> graph.tree()
Edge lists and adjacency matrices
Edge list
> g1 <- graph( c( 0,1, 1,2, 2,2, 2,3 ), directed=FALSE )
If you have an edge list of a graph in a two-column matrix, then create an
igraph graph by simply giving the transposed matrix to graph()
> edgelist <- matrix(c( 0,1, 1,2, 2,2, 2,3 ), nrow=2)
> graph(t(edgelist))
inverse operation:
> get.edgelist()
Create adjacency matrix from igraph graph
> g <- erdos.renyi.game(200, 1/30)
> get.adjacency(g)
Create igraph graph from adjacency matrix
> graph.adjacency(g)
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Real world example
Situation: your data are not in an graph format
Edit data
> dat <- edit(data.frame())
Create graph
> g <- graph.data.frame(dat, directed=FALSE)
Check first basic properties
> V(g)$name
> E(g)$weight
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Real world example (cont.)
Your data are saved in CSV format
Import your data
> traits <- read.csv("traits.csv", head=FALSE)
> rel <- read.csv("relations.csv", head=FALSE)
Create empty graph
> g <- graph.empty()
Add vertex attributes
> g <- add.vertices(g, nrow(traits), name=as.character(traits[,1]))
> V(g)$name #check
Reveal names
> names <- sapply(strsplit(V(g)$name, " "), "[",1)
> ids <- 1:length(names)-1
> names(ids) <- names
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Basic measures
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February 2012 Claudia Mller-Birn, Lecture: Complex Network Analysis mit R 13
Functions for exploring the basic structure of a
network
Number of vertices in the graph
vcount(g)
List of all nodes
V(g)
Access the first node
V(g)[0]
List of all vertex attributes names
list.vertex.attributes(g)
Access the attribute 'id' for the first node
V(g)[0]$id
Number of edges in the graph
ecount()
List of all edges/arcs
E(g)
Checks if the graph is directed
is.directed()
Shortest Path
Shortest Path
> shortest.paths(graph, v=V(graph))
- Arguments
- mode: Character constant, gives whether the shortest paths to or from the given vertices should
be calculated for directed graphs. If out then the shortest paths from the vertex, if in then to it will
be considered. If all, the default, then the corresponding undirected graph will be used, ie. not
directed paths are searched. This argument is ignored for undirected graphs.
- from: Numeric constant, the vertex from or to the shortest paths will be calculated. Note that
right now this is not a vector of vertex ids, but only a single vertex.
- to: Numeric vector, only the shortest paths to these vertices will be calculated. De- faults to all
vertices.
- directed: Whether to consider directed paths in directed graphs, this argument is ignored for
undirected graphs.
- unconnected: What to do if the graph is unconnected (not strongly connected if directed paths
are considered). If TRUE only the lengths of the existing paths are considered and averaged; if
FALSE the length of the missing paths are counted having length vcount(graph), one longer than
the longest possible geodesic in the network.
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Degree and degree distribution
Degree
> degree(g)
Degree distribution
> degree.distribution(graph, cumulative = FALSE, ...)
> plot(degree.distribution(graph), xlab="degree", ylab="frequency", log="xy", pch=3, col=3)
Arguments
- v: The ids of vertices of which the degree will be calculated.
- mode: Character string, out for out-degree, in for in-degree or total for the sum of
the two. For undirected graphs this argument is ignored.
- loops: Logical; whether the loop edges are also counted.
- cumulative: Logical; whether the cumulative degree distribution is to be calculated.
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Closeness and Betweenness measure
Closeness
> closeness(graph, v=V(graph), mode = "all")
- Arguments:
- v: The vertices for which closeness will be calculated.
- mode: Character string, defined the types of the paths used for measuring the distance in
directed graphs. in measures the paths to a vertex, out measures paths from a vertex, all
uses undirected paths. This argument is ignored for undirected graphs.
Betweeness
> betweenness(graph, v=V(graph), directed = TRUE)
- Arguments:
- v: The vertices for which the vertex betweenness will be calculated.
- directed: Logical, whether directed paths should be considered while determining the shortest
paths.
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Homework assignment 3
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Homework assignment 3: Basic network measures
1. Install igraph library
2. Apply the during class learned basic measures on the provided data
set. (Please consider the following measures: number of vertices,
number of edges, average path length, mean degree). What can you
say about the network? Please provide your results in a table.
Import the file by using the following function:
g <- read.graph(file="SmallW.net", format="pajek")
3. Write three functions that allow you to calculate the centralization
measures for the whole network (we discussed these measures during
the lecture). Apply your functions on the network and interprete your
results.
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Introducing the igraph library

Course: Complex Network Analysis mit GNU R

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