In gastonstat/arcdiagram: Plot pretty arc diagrams

knitr::opts_chunk$set(collapse = T, comment = "#>")
library(igraph)
library(network)
library(arcdiagram)

Introduction

"arcdiagram" is a package for producing pretty arc diagrams of graphs in R. You can think of "arcdiagram" as a plugin of the package "igraph" (by Gabor Csardi and Tamas Nepusz). In this document we will discuss how to use "arcdiagram" to produce arc diagrams of graphs from the package "network" (by Carter Butts, David Hunter, and Mark Handcock).

R package network

R has several packages dedicated to graphs and network analysis. There is even a CRAN Task View for graphical models that you can check at:

http://cran.r-project.org/web/views/gR.html

"arcdiagram" has been designed to fit like a glove for graph edge lists obtained from "igraph". However, graph edge lists can also be obtained using the package "network". Let's see how to play with "arcdiagram" and "network".

Step 1: Load packages

First let's load the packages "arcdiagram" and "network" (I'm assuming you already installed them)

# load 'arcdiagram'
library(arcdiagram)

# load 'network'
library(network)

Step 2: Toy example

Let's start with a very simple example. We will generate a random graph with 7 nodes. One way to do this is by generating an adjacency matrix first and then create the graph with the function network():

# generate a random adjacency matrix
set.seed(95)
toy_matrix <- matrix(rbinom(49,1,.25), 7, 7)
diag(toy_matrix) = 0

# create a graph from the adjacency matrix
toy_graph <- network(toy_matrix, directed = FALSE)

Step 3: Extract edgelist

Once we have the network, we need to extract the edge list which will be used as the main argument for arcplot(). The way to obtain an edge list from a "network" object is with the function as.matrix() and the argument matrix.type = "edgelist"

# edgelist
toy_edges <- as.matrix(toy_graph, matrix.type = "edgelist")

Step 4: Plot arc diagram

The edge list toy_edges is all you need to produce an arc diagram with arcplot():

# plot arc diagram
op <- par(mar = c(1, 0.5, 0.5, 0.5))
arcplot(toy_edges, las=1)
par(op)

Florentine Weddings Network

Let's see another example using a more interesting data set. We will use the data "flo" which is one of the datasets available in "network". This data set consists of weddings among leading Florentine families (in Italy).

Step 1: Data flo

The way to get a graph (i.e. network) from the data "flo" is by using the function network():

# load data 'flo'
data(flo)

# network
netflo <- network(flo)

# what does 'netflo' look like?
netflo

Step 2: Edgelist

Because the main argument for arcplot() is an edge list, we need to use as.matrix() with its argument matrix.type = "edgelist" to get such a list form netflo:

# edgelist
flo_edges <- as.matrix(netflo, matrix.type="edgelist")

Now we can get a first arc diagram:

# second plot
op = par(mar = c(2, 0.5, 1, 0.5))
arcplot(flo_edges, las=1)
par(op)

Step 3: Node Labels

If you inspect either the object netflo or the edgelist flo\_edges, you will see that we have the names of the nodes (i.e. the vertices) as an attribute, for instance:

# print netflo
netflo

As you can see in the last lines of the output, netflo contains the vertex attribute names vertex.names. One way to get these names is by using the function get.vertex.attribute():

# try to get vertex names
get.vertex.attribute(netflo, "vertex.names")

If by any chance you find an error message telling you something like this (don't panic):

Error in get.vertex.attribute(netflo, "vertex.names") : 
  Not a graph object

The cause of the problem is a "compatibility" issue between the packages "igraph" and "network" (remember that "arcdiagram" depends on "igraph"). Both packages have the same name for some of their functions ---get.vertex.attribute() among them---. Actually, since we first load "arcdiagram", this implies that the homonym functions of "network" are masked by those of "igraph". The solution? Use the double colon operator ::. To get the vertex names from netflo we have to specify the namespace under which the required get.vertex.attribute() function is located:

# get vertex names
flo_names <- network::get.vertex.attribute(netflo, "vertex.names")

# show me the names
flo_names

An alternative way to get the vertex names is by extracting them directly from the edge list flo_edges with the function attributes():

# another way to get vertex names
attributes(flo_edges)$vnames

Of course, this a painless way to get the names, but I wanted to show you the hard way in case you find yourself trapped in that quandary.

Step 4: Arc plot attempt

Having extracted the vertex.names, it seems that we are ready to plot an arc diagram with the node labels:

# arc plot with node labels
arcplot(flo_edges, labels=flo_names)

Well, we are not ready yet. The problem is that we have more labels than nodes in the edge list (node 12 does not appear in flo\_edges). The solution is a bit elaborated: first we need to get the node numbers from the edgelist, and then we have to select their corresponding names:

# numeric indices in 'flo_edges'
temp <- unique(as.vector(t(flo_edges)))
temp

# node labels
flo_labels = attributes(flo_edges)$vnames[temp]

# check it
flo_labels

Step 5: Final plot

Now we are ready to produce the desired arc diagram:

# second plot
op = par(mar = c(5, 0, 1, 0))
arcplot(flo_edges, labels=flo_labels)
par(op)

gastonstat/arcdiagram documentation built on April 8, 2022, 5:59 a.m.