Networks

Can you introduce me to Phoebe?

Published

June 21, 2022

Modified

June 20, 2025

Abstract

How one thing connects to another

“The beginnings and endings of all human undertakings are untidy.”

— John Galsworthy, author, Nobel laureate (14 Aug 1867-1933)

Setting up R Packages

# Fonts
# Run these next few commands IN YOUR CONSOLE once.
# install.packages("extrafontdb")
# library(extrafont)
# extrafont::font_import(paths = NULL, recursive = TRUE, prompt = TRUE,pattern = NULL)

########################################
# For General Data Manipulation
library(tidyverse)

########################################
# Network Analysis Library (Handle data and Viz)
library(igraph)

########################################
# For Network "Manipulation"
library(tidygraph)

# For Network Visualization
library(ggraph)
library(graphlayouts)
library(visNetwork)

# For "Network" Datasets
library(igraphdata)
library(sand) # Statistical Analysis of Networks Data

# Fonts
library(ggtext) # Claus Wilke's package
library(showtext)
library(fontawesome)
# For repeatable layouts, some can be random!!
set.seed(12345)

Introduction

Network graphs show relationships between entities: what sort they are, how strong they are, and even of they change over time.

We will examine data structures pertaining both to the entities and the relationships between them and look at the data object that can combine these aspects together. Then we will see how these are plotted, what the structure of the plot looks like. There are also metrics that we can calculate for the network, based on its structure. We will of course examine geometric metaphors that can represent various classes of entities and their relationships.

Network graphs can be rendered both as static and interactive and we will examine R packages that render both kinds of plots.

There is a another kind of structure: one that combines spatial and network data in one. We will defer that for a future module !

What kind Network graphs will we make?

Here is a network map of the characters in Victor Hugo’s Les Miserables:

And this: the well known Zachary’s Karate Club dataset visualized as a network

Goals

At the end of this Lab session, we should:

know the types and structures of network data and be able to work with them
understand the basics of modern network packages in R
be able to create network visualizations using tidygraph, ggraph( static visualizations ) and visNetwork (interactive visualizations)
see directions for how the network metaphor applies in a variety of domains (e.g. biology/ecology, ideas/influence, technology, transportation, to name a few)

Pedagogical Note

The method followed will be based on PRIMM:

PREDICT Inspect the code and guess at what the code might do, write predictions
RUN the code provided and check what happens
INFER what the parameters of the code do and write comments to explain. What bells and whistles can you see?
MODIFY the parameters code provided to understand the options available. Write comments to show what you have aimed for and achieved.
MAKE : take an idea/concept of your own, and graph it.

Graph Metaphors

Network graphs are characterized by two key terms: nodes and edges

Nodes : Entities
- Metaphors: Individual People? Things? Ideas? Places? to be connected in the network.
- Synonyms: vertices. Nodes have IDs.
Edges: Connections
- Metaphors: Interactions? Relationships? Influence? Letters sent and received? Dependence? between the entities.
- Synonyms: links, ties.

In R, we create network representations using node and edge information. One way in which these could be organized are:

Node list: a data frame with a single column listing the node IDs found in the edge list. You can also add attribute columns to the data frame such as the names of the nodes or grouping variables. ( Type? Class? Family? Country? Subject? Race? )

Node Table
ID	Node Name	Attribute? Qualities?Categories? Family? Country?Planet?
1	Ned	Nursery School Teacher
2	Jaguar Paw	Main Character, Apocalypto
3	John Snow	Epidemiologist

Edge list: data frame containing two columns: source node and destination node of an edge. Source and Destination have node IDs.
Weighted network graph: An edge list can also contain additional columns describing attributes of the edges such as a magnitude aspect for an edge. If the edges have a magnitude attribute the graph is considered weighted.

Edges Table
From	To	Relationship	Weightage
1	3	Financial Dealings	6
2	1	History Lessons	2
2	3	Vaccination	15

Layout: A geometric arrangement of nodes and edges.
- Metaphors: Location? Spacing? Distance? Coordinates? Colour? Shape? Size? Provides visual insight due to the arrangement.
Layout Algorithms : Method to arranges nodes and edges with the aim of optimizing some metric .
- Metaphors: Nodes are masses and edges are springs. The Layout algorithm minimizes the stretching and compressing of all springs.(BTW, are the Spring Constants K the same for all springs?…)
Directed and undirected network graph: If the distinction between source and target is meaningful, the network is directed. If the distinction is not meaningful, the network is undirected. Directed edges represent an ordering of nodes, like a relationship extending from one node to another, where switching the direction would change the structure of the network. Undirected edges are simply links between nodes where order does not matter.

Examples

The World Wide Web is an example of a directed network because hyperlinks connect one Web page to another, but not necessarily the other way around.
Co-authorship networks represent examples of un-directed networks, where nodes are authors and they are connected by an edge if they have written a publication together
When people send e-mail to each other, the distinction between the sender (source) and the recipient (target) is clearly meaningful, therefore the network is directed.

Connected and Disconnected graphs: If there is some path from any node to any other node, the Networks is said to be Connected. Else, Disconnected.

Predict/Run/Infer-1

Using `tidygraph` and `ggraph`

tidygraph and ggraph are modern R packages for network data. Graph Data setup and manipulation is done in tidygraph and graph visualization with ggraph.

tidygraph Data -> “Network Object” in R.
ggraph Network Object -> Plots using a chosen layout/algo.

Both leverage the power of igraph, which is the Big Daddy of all network packages. We will be using the Grey’s Anatomy dataset in our first foray into networks.

Step1. Read the data

Download these two datasets into your current project-> data folder.

grey_nodes <- read_csv("files/data/grey_nodes.csv")
grey_edges <- read_csv("files/data/grey_edges.csv")

grey_nodes
grey_edges

ABCDEFGHIJ0123456789

name <chr>	sex <chr>	race <chr>	birthyear <dbl>	position <chr>	season <dbl>	sign <chr>
Addison Montgomery	F	White	1967	Attending	1	Libra
Adele Webber	F	Black	1949	Non-Staff	2	Leo
Teddy Altman	F	White	1969	Attending	6	Pisces
Amelia Shepherd	F	White	1981	Attending	7	Libra
Arizona Robbins	F	White	1976	Attending	5	Leo
Rebecca Pope	F	White	1975	Non-Staff	3	Gemini
Jackson Avery	M	Black	1981	Resident	6	Leo
Miranda Bailey	F	Black	1969	Attending	1	Virgo
Ben Warren	M	Black	1972	Other	6	Aquarius
Henry Burton	M	White	1972	Non-Staff	7	Cancer

ABCDEFGHIJ0123456789

from <chr>	to <chr>	weight <dbl>	type <chr>
Leah Murphy	Arizona Robbins	2	friends
Leah Murphy	Alex Karev	4	benefits
Lauren Boswell	Arizona Robbins	1	friends
Arizona Robbins	Callie Torres	1	friends
Callie Torres	Erica Hahn	6	friends
Callie Torres	Alex Karev	12	benefits
Callie Torres	Mark Sloan	5	professional
Callie Torres	George O'Malley	2	professional
George O'Malley	Izzie Stevens	3	professional
George O'Malley	Meredith Grey	4	friends

Questions and Inferences #1

Look at the output thumbnails. What attributes (i.e. extra information) are seen for Nodes and Edges?

Step 2.Create a network object using tidygraph:

Key function:

tbl_graph(): (aka “tibble graph”). Key arguments: nodes, edges and directed. Note this is a very versatile command and can take many input forms, such as data structures that result from other packages. Type ?tbl_graph in the Console and see the Usage section.

ga <- tbl_graph(
  nodes = grey_nodes,
  edges = grey_edges,
  directed = FALSE
)
ga

# A tbl_graph: 54 nodes and 57 edges
#
# An undirected simple graph with 4 components
#
# Node Data: 54 × 7 (active)
   name               sex   race  birthyear position  season sign    
   <chr>              <chr> <chr>     <dbl> <chr>      <dbl> <chr>   
 1 Addison Montgomery F     White      1967 Attending      1 Libra   
 2 Adele Webber       F     Black      1949 Non-Staff      2 Leo     
 3 Teddy Altman       F     White      1969 Attending      6 Pisces  
 4 Amelia Shepherd    F     White      1981 Attending      7 Libra   
 5 Arizona Robbins    F     White      1976 Attending      5 Leo     
 6 Rebecca Pope       F     White      1975 Non-Staff      3 Gemini  
 7 Jackson Avery      M     Black      1981 Resident       6 Leo     
 8 Miranda Bailey     F     Black      1969 Attending      1 Virgo   
 9 Ben Warren         M     Black      1972 Other          6 Aquarius
10 Henry Burton       M     White      1972 Non-Staff      7 Cancer  
# ℹ 44 more rows
#
# Edge Data: 57 × 4
   from    to weight type    
  <int> <int>  <dbl> <chr>   
1     5    47      2 friends 
2    21    47      4 benefits
3     5    46      1 friends 
# ℹ 54 more rows

Questions and Inferences #2

What information does the graph object contain? What attributes do the nodes have? What about the edges?

Step 3. Plot using `ggraph`

3a. Quick Plot: autograph() This is to check quickly is the data is imported properly and to decide upon going on to a more elaborate plotting.

autograph(ga)

Questions and Inferences #3

Describe this graph, in simple words here. Try to use some of the new domain words we have just acquired: nodes/edges, connected/disconnected, directed/undirected.

3b. More elaborate plot

Key functions:

ggraph(layout = "......"): Create classic node-edge diagrams; i.e. Sets up the graph. Rather like ggplot for networks!

Two kinds of geom: one set for nodes, and another for edges

geom_node_point(aes(.....)): Draws node as “points”. Alternatives are circle / arc_bar / tile / voronoi. Remember the geoms that we have seen before in Grammar of Graphics!
geom_edge_link0(aes(.....)): Draws edges as “links”. Alternatives are arc / bend / elbow / hive / loop / parallel / diagonal / point / span /tile.
geom_node_text(aes(label = ......), repel = TRUE): Adds text labels (non-overlapping). Alternatives are label /...
labs(title = "....", subtitle = "....", caption = "...."): Change main titles, axis labels and legend titles. We know this from our work with ggplot.

# Write Comments next to each line
# About what that line does for the overall graph

ggraph(graph = ga, layout = "kk") +
  #
  geom_edge_link0(width = 2, color = "pink") +
  #
  geom_node_point(
    shape = 21, size = 8,
    fill = "blue",
    color = "green",
    stroke = 2
  ) +

  labs(
    title = "Whoo Hoo! My First Silly Grey's Anatomy graph in R!",
    subtitle = "Why did I ever get in this course...",
    caption = "Bro, they are doing cool things in the other classes...\n And the show is even more cool!"
  ) +

  set_graph_style(family = "Roboto")

Questions and Inferences #4:

What parameters have been changed here, compared to the earlier graph? Where do you see these changes in the code above?

Let us Play with this graph and see if we can make some small changes. Colour? Fill? Width? Size? Stroke? Labs? Of course!

# Change the parameters in each of the commands here to new ones
# Use fixed values for colours or sizes...etc.

ggraph(graph = ga, layout = "kk") +
  geom_edge_link0(width = 2) +
  geom_node_point(
    shape = 21, size = 4,
    fill = "moccasin",
    color = "firebrick",
    stroke = 2
  ) +
  labs(
    title = "Whoo Hoo! My next silly Grey's Anatomy graph in R!",
    subtitle = "Why did I ever get in this course...",
    caption = "Bro, they are doing cool things in the other classes..."
  ) +
  set_graph_style(family = "Roboto")

Questions and Inferences #5

What did the shape parameter achieve? What are the possibilities with shape? How about including alpha?

3c. Aesthetic Mapping from Node and Edge attribute columns

Up to now, we have assigned specific numbers to geometric aesthetics such as shape and size. Now we are ready ( maybe ?) change the meaning and significance of the entire graph and each element within it, and use aesthetics / metaphoric mappings to achieve new meanings or insights. Let us try using aes() inside each geom to map a variable to a geometric aspect.

Don’t try to use more than 2 aesthetic mappings simultaneously!!

The node elements we can tweak are:

Types of Nodes: geom_node_****()
Node Parameters: inside geom_node_****(aes(...............))
-aes(alpha = node-variable) : opacity; a value between 0 and 1
-aes(shape = node-variable) : node shape
-aes(colour = node-variable) : node colour
-aes(fill = node-variable) : fill colour for node
-aes(size = node-variable) : size of node

The edge elements we can tweak are:

Type of Edges” geom_edge_****()
Edge Parameters: inside geom_edge_****(aes(...............))
-aes(colour = edge-variable) : colour of the edge
-aes(width = edge-variable) : width of the edge
-aes(label = some_variable) : labels for the edge

Type ?geom_node_point and ?geom-edge_link in your Console for more information.

ggraph(graph = ga, layout = "fr") +
  geom_edge_link0(aes(width = weight)) + # change variable here

  geom_node_point(aes(color = race), size = 6) + # change variable here

  labs(
    title = "Whoo Hoo! Yet another Grey's Anatomy graph in R!",
    subtitle = "Colouring Nodes by Attribute",
    caption = "Grey's Anatomy"
  ) +

  scale_edge_width(range = c(0.2, 2)) +
  set_graph_style(family = "roboto")

Questions and Inferences #6

Describe some of the changes here. What types of edges worked? Which variables were you able to use for nodes and edges and how? What did not work with either of the two?

# Arc diagram

ggraph(ga, layout = "linear") +
  geom_edge_arc0(aes(width = weight), alpha = 0.8) +
  scale_edge_width(range = c(0.2, 2)) +
  geom_node_point(size = 2, colour = "red") +
  labs(edge_width = "Weight", title = "Grey's Anatomy", subtitle = "Arc Layout") +
  set_graph_style(family = "Roboto")

Questions and Inferences #7

How does this graph look “metaphorically” different? Do you see a difference in the relationships between people here? Why?

# Coord diagram, circular
ggraph(ga, layout = "linear", circular = TRUE) + # Note the layout!
  geom_edge_arc0(aes(width = weight), alpha = 0.8) +
  scale_edge_width(range = c(0.2, 2)) +

  geom_node_point(size = 3, colour = "red") +
  geom_node_text(aes(label = name),
    repel = TRUE, size = 2, check_overlap = TRUE,
    max.overlaps = 25
  ) +
  labs(edge_width = "Weight") +
  theme(aspect.ratio = 1) +
  set_graph_style(family = "Roboto")

Questions and Inferences #8

How does this graph look “metaphorically” different? Do you see a difference in the relationships between people here? Why?

Hierarchical layouts

These provide for some alternative metaphorical views of networks. Note that not all layouts are possible for all datasets!!

# set_graph_style()

# This dataset contains the graph that describes the class
# hierarchy for the Flare visualization library.
# Type ?flare in your Console
head(flare$vertices)

ABCDEFGHIJ0123456789

	name <chr>	size <dbl>	shortName <chr>
1	flare.analytics.cluster.AgglomerativeCluster	3938	AgglomerativeCluster
2	flare.analytics.cluster.CommunityStructure	3812	CommunityStructure
3	flare.analytics.cluster.HierarchicalCluster	6714	HierarchicalCluster
4	flare.analytics.cluster.MergeEdge	743	MergeEdge
5	flare.analytics.graph.BetweennessCentrality	3534	BetweennessCentrality
6	flare.analytics.graph.LinkDistance	5731	LinkDistance

head(flare$edges)

ABCDEFGHIJ0123456789

	from <chr>	to <chr>
1	flare.analytics.cluster	flare.analytics.cluster.AgglomerativeCluster
2	flare.analytics.cluster	flare.analytics.cluster.CommunityStructure
3	flare.analytics.cluster	flare.analytics.cluster.HierarchicalCluster
4	flare.analytics.cluster	flare.analytics.cluster.MergeEdge
5	flare.analytics.graph	flare.analytics.graph.BetweennessCentrality
6	flare.analytics.graph	flare.analytics.graph.LinkDistance

# flare class hierarchy
graph <- tbl_graph(edges = flare$edges, nodes = flare$vertices)

##
set_graph_style(family = "Roboto")
##

# dendrogram
ggraph(graph, layout = "dendrogram") +
  geom_edge_diagonal() +
  labs(title = "Dendrogram")

# circular dendrogram
ggraph(graph, layout = "dendrogram", circular = TRUE) +
  geom_edge_diagonal0() +
  geom_node_point(aes(filter = leaf)) +
  coord_fixed() +
  labs(title = "Circular Dendrogram")

# rectangular tree map
ggraph(graph, layout = "treemap", weight = size) +
  geom_node_tile(aes(fill = depth), size = 0.25) +
  scale_fill_distiller(palette = "Pastel1") +
  labs(title = "Rectangular Tree Map")


# circular tree map
ggraph(graph, layout = "circlepack", weight = size) +
  geom_node_circle(aes(fill = depth), size = 0.25, n = 50) +
  scale_fill_distiller(palette = "Accent") +
  coord_fixed() +
  labs(title = "Circular Tree Map")


# icicle
ggraph(graph, layout = "partition") +
  geom_node_tile(aes(y = -y, fill = depth)) +
  scale_fill_distiller(palette = "Set3") +
  labs(title = "Icicle Chart")

# sunburst (circular icicle)
ggraph(graph, layout = "partition", circular = TRUE) +
  geom_node_arc_bar(aes(fill = depth)) +
  scale_fill_distiller(palette = "Spectral") +
  coord_fixed() +
  labs(title = "Circular Icicle")

Questions and Inferences #9

How do graphs look “metaphorically” different? Do they reveal different aspects of the group? How?

Faceting

Faceting allows to create sub-plots according to the values of a qualitative attribute on nodes or edges.

##
set_graph_style(family = "Roboto", size = 8)
##
# facet edges by type
ggraph(ga, layout = "linear", circular = TRUE) +
  geom_edge_link0(aes(color = type)) +
  geom_node_point() +
  facet_edges(~type) +
  th_foreground(border = TRUE) +
  theme(aspect.ratio = 1)
# facet nodes by sex
ggraph(ga, layout = "linear", circular = TRUE) +
  geom_edge_link0() +
  geom_node_point() +
  facet_nodes(~race) +
  th_foreground(border = TRUE) +
  theme(aspect.ratio = 1)
# facet both nodes and edges
ggraph(ga, layout = "linear", circular = TRUE) +
  geom_edge_link0(aes(color = type)) +
  geom_node_point() +
  facet_graph(type ~ race) +
  th_foreground(border = TRUE) +
  theme(aspect.ratio = 1, legend.position = "right")

Questions and Inferences #10

Does splitting up the main graph into sub-networks give you more insight? Describe some of these.

Network analysis with tidygraph

The data frame graph representation can be easily augmented with metrics or statistics computed on the graph. Remember how we computed counts with the penguin dataset in Grammar of Graphics.

Before computing a metric on nodes or edges use the activate() function to activate either node or edge data frames. Use dplyr verbs (filter, arrange, mutate) to achieve your computation in the proper way.

Network Centrality: Go-To and Go-Through People!

Centrality is a an “ill-defined” metric of node and edge importance in a network. It is therefore calculated in many ways. Type ?centrality in your Console.

Let’s add a few columns to the nodes and edges based on network centrality measures:

ga %>%
  activate(nodes) %>%
  # Node with  the most connections?
  mutate(degree = centrality_degree(mode = c("in"))) %>%
  filter(degree > 0) %>%
  activate(edges) %>%
  # "Busiest" edge?
  mutate(betweenness = centrality_edge_betweenness())

# A tbl_graph: 54 nodes and 57 edges
#
# An undirected simple graph with 4 components
#
# Edge Data: 57 × 5 (active)
    from    to weight type         betweenness
   <int> <int>  <dbl> <chr>              <dbl>
 1     5    47      2 friends             20.3
 2    21    47      4 benefits            44.7
 3     5    46      1 friends             39  
 4     5    41      1 friends             66.3
 5    18    41      6 friends             39  
 6    21    41     12 benefits            91.5
 7    37    41      5 professional       164. 
 8    31    41      2 professional        98.8
 9    20    31      3 professional        47.2
10    17    31      4 friends            102. 
# ℹ 47 more rows
#
# Node Data: 54 × 8
  name               sex   race  birthyear position  season sign   degree
  <chr>              <chr> <chr>     <dbl> <chr>      <dbl> <chr>   <dbl>
1 Addison Montgomery F     White      1967 Attending      1 Libra       3
2 Adele Webber       F     Black      1949 Non-Staff      2 Leo         1
3 Teddy Altman       F     White      1969 Attending      6 Pisces      4
# ℹ 51 more rows

Packages tidygraph and ggraph can be pipe-lined to perform analysis and visualization tasks in one go.

##
set_graph_style(family = "Roboto")
##
ggraph(ga, layout = "nicely") +
  geom_edge_link0(aes(alpha = centrality_edge_betweenness())) +

  geom_node_point(aes(
    colour = centrality_degree(),
    size = centrality_degree()
  )) +

  geom_node_text(aes(label = name), repel = TRUE, size = 1.5) +

  scale_size(name = "Degree", range = c(0.5, 5)) +

  scale_color_gradient(
    name = "Degree", # SAME NAME!!
    low = "blue", high = "red",
    aesthetics = c("colour", "fill"),
    guide = guide_legend(reverse = FALSE)
  ) +

  scale_edge_alpha(name = "Betweenness", range = c(0.05, 1)) +
  labs(
    title = "Grey's Anatomy",
    subtitle = "Nodes Scaled by Degree, Edges shaded by Betweenness"
  )

Questions and Inferences #11

How do the Centrality Measures show up in the graph? Would you “agree” with the way we have done it? Try to modify the aesthetics by copy-pasting this chunk below and see how you can make an alternative representation.

Analysis and Visualizing Network Communities

Who is close to whom? Which are the groups you can see?

##
set_graph_style(family = "Roboto")
##
# visualize communities of nodes
ga %>%
  activate(nodes) %>%
  mutate(community = as.factor(group_louvain())) %>%
  ggraph(layout = "graphopt") +
  geom_edge_link0() +
  geom_node_point(aes(color = community), size = 3) +
  labs(title = "Grey's Anatomy", subtitle = "Nodes Coloured by Community Detection Algorithm (Louvain)")

Questions and Inferences #12

Is the Community depiction clear? How would you do it, with which aesthetic? Copy Paste this chunk below and try.

Interactive Graphs with `visNetwork`

Exploring the VisNetwork package. Make graphs wiggle and shake using tidy commands! The package implements interactivity using the physical metaphor of weights and springs we discussed earlier.

The visNetwork() function uses a nodes list and edges list to create an interactive graph. The nodes list must include an “id” column, and the edge list must have “from” and “to” columns. The function also plots the labels for the nodes, using the names of the cities from the “label” column in the node list.

library(visNetwork)

# Prepare the data for plotting by visNetwork
grey_nodes
grey_edges
# Relabel greys anatomy nodes and edges for VisNetwork
grey_nodes_vis <- grey_nodes %>%
  rowid_to_column(var = "id") %>%
  rename("label" = name) %>%
  mutate(sex = case_when(
    sex == "F" ~ "Female",
    sex == "M" ~ "Male"
  )) %>%
  replace_na(., list(sex = "Transgender?")) %>%
  rename("group" = sex)
grey_nodes_vis
grey_edges_vis <- grey_edges %>%
  select(from, to) %>%
  left_join(., grey_nodes_vis,
    by = c("from" = "label")
  ) %>%
  left_join(., grey_nodes_vis,
    by = c("to" = "label")
  ) %>%
  select("from" = id.x, "to" = id.y)
grey_edges_vis

ABCDEFGHIJ0123456789

name <chr>	sex <chr>	race <chr>	birthyear <dbl>	position <chr>
Addison Montgomery	F	White	1967	Attending
Adele Webber	F	Black	1949	Non-Staff
Teddy Altman	F	White	1969	Attending
Amelia Shepherd	F	White	1981	Attending
Arizona Robbins	F	White	1976	Attending
Rebecca Pope	F	White	1975	Non-Staff
Jackson Avery	M	Black	1981	Resident
Miranda Bailey	F	Black	1969	Attending
Ben Warren	M	Black	1972	Other
Henry Burton	M	White	1972	Non-Staff

ABCDEFGHIJ0123456789

from <chr>	to <chr>	weight <dbl>
Leah Murphy	Arizona Robbins	2
Leah Murphy	Alex Karev	4
Lauren Boswell	Arizona Robbins	1
Arizona Robbins	Callie Torres	1
Callie Torres	Erica Hahn	6
Callie Torres	Alex Karev	12
Callie Torres	Mark Sloan	5
Callie Torres	George O'Malley	2
George O'Malley	Izzie Stevens	3
George O'Malley	Meredith Grey	4

ABCDEFGHIJ0123456789

id <int>	label <chr>	group <chr>	race <chr>	birthyear <dbl>
1	Addison Montgomery	Female	White	1967
2	Adele Webber	Female	Black	1949
3	Teddy Altman	Female	White	1969
4	Amelia Shepherd	Female	White	1981
5	Arizona Robbins	Female	White	1976
6	Rebecca Pope	Female	White	1975
7	Jackson Avery	Male	Black	1981
8	Miranda Bailey	Female	Black	1969
9	Ben Warren	Male	Black	1972
10	Henry Burton	Male	White	1972

ABCDEFGHIJ0123456789

from <int>	to <int>
47	5
47	21
46	5
5	41
41	18
41	21
41	37
41	31
31	20
31	17

Using fontawesome icons

grey_nodes_vis %>%
  visNetwork(nodes = ., edges = grey_edges_vis) %>%
  visNodes(font = list(size = 40)) %>%
  # Colour and icons for each of the gender-groups
  visGroups(
    groupname = "Female", shape = "icon",
    icon = list(code = "f182", size = 75, color = "tomato"),
    shadow = list(enabled = TRUE)
  ) %>%
  visGroups(
    groupname = "Male", shape = "icon",
    icon = list(code = "f183", size = 75, color = "slateblue"),
    shadow = list(enabled = TRUE)
  ) %>%
  visGroups(
    groupname = "Transgender?", shape = "icon",
    icon = list(code = "f22c", size = 75, color = "fuchsia"),
    shadow = list(enabled = TRUE)
  ) %>%
  # visLegend() %>%
  # Add the fontawesome icons!!
  addFontAwesome(version = "4.7.0") %>%
  # Add Interaction Controls
  visInteraction(
    navigationButtons = TRUE,
    hover = TRUE,
    selectConnectedEdges = TRUE,
    hoverConnectedEdges = TRUE,
    zoomView = TRUE
  )

There is another family of icons available in visNetwork, called ionicons. Let’s see how they look:

grey_nodes_vis %>%
  visNetwork(nodes = ., edges = grey_edges_vis, ) %>%
  visLayout(randomSeed = 12345) %>%
  visNodes(font = list(size = 50)) %>%
  visEdges(color = "green") %>%
  visGroups(
    groupname = "Female",
    shape = "icon",
    icon = list(
      face = "Ionicons",
      code = "f25d",
      color = "fuchsia",
      size = 125
    )
  ) %>%
  visGroups(
    groupname = "Male",
    shape = "icon",
    icon = list(
      face = "Ionicons",
      code = "f202",
      color = "green",
      size = 125
    )
  ) %>%
  visGroups(
    groupname = "Transgender?",
    shape = "icon",
    icon = list(
      face = "Ionicons",
      code = "f233",
      color = "dodgerblue",
      size = 125
    )
  ) %>%
  visLegend() %>%
  addIonicons() %>%
  visInteraction(
    navigationButtons = TRUE,
    hover = TRUE,
    selectConnectedEdges = TRUE,
    hoverConnectedEdges = TRUE,
    zoomView = TRUE
  )

Some idea of interactivity and controls with visNetwork:

# let's look again at the data
starwars_nodes <- read_csv("files/data/star-wars-network-nodes.csv")
starwars_edges <- read_csv("files/data/star-wars-network-edges.csv")

# We need to rename starwars nodes dataframe and edge dataframe columns for visNetwork
starwars_nodes_vis <-
  starwars_nodes %>%
  rename("label" = name)

# Convert from and to columns to **node ids**
starwars_edges_vis <-
  starwars_edges %>%
  # Matching Source <- Source Node id ("id.x")
  left_join(., starwars_nodes_vis, by = c("source" = "label")) %>%
  # Matching Target <- Target Node id ("id.y")
  left_join(., starwars_nodes_vis, by = c("target" = "label")) %>%
  # Select "id.x" and "id.y" ONLY
  # Rename them as "from" and "to"
  # keep "weight" column for aesthetics of edges
  select("from" = id.x, "to" = id.y, "value" = weight)

# Check everything once
starwars_nodes_vis
starwars_edges_vis

ABCDEFGHIJ0123456789

label <chr>	id <dbl>
R2-D2	0
CHEWBACCA	1
C-3PO	2
LUKE	3
DARTH VADER	4
CAMIE	5
BIGGS	6
LEIA	7
BERU	8
OWEN	9

ABCDEFGHIJ0123456789

from <dbl>	to <dbl>	value <dbl>
2	0	17
3	0	13
10	0	6
7	0	5
13	0	5
1	0	3
16	0	1
1	10	7
2	1	5
1	3	16

Ok, let’s make things move and shake!!

visNetwork(
  nodes = starwars_nodes_vis,
  edges = starwars_edges_vis
) %>%
  visNodes(font = list(size = 30)) %>%
  visEdges(color = "red")

visNetwork(
  nodes = starwars_nodes_vis,
  edges = starwars_edges_vis
) %>%
  visNodes(
    font = list(size = 30), shape = "icon",
    icon = list(code = "f1e3", size = 75)
  ) %>%
  visEdges(color = list(color = "red", hover = "green", highlight = "black")) %>%
  visInteraction(hover = TRUE) %>%
  addFontAwesome(version = "4.7.0")

Your Turn

Airline Data:

Start with this bit of code in your second chunk, after set up

```{r}
#| label: start up code for Airlines
#| eval: false ## remove this!!
airline_nodes <-
  read_csv("./mydatafolder/AIRLINES-NODES.csv") %>%
  mutate(Id = Id + 1)

airline_edges <-
  read_csv("./mydatafolder/AIRLINES-EDGES.csv") %>%
  mutate(Source = Source + 1, Target = Target + 1)
```

The Famous Zachary Karate Club dataset

Start with pulling this data into your Quarto:

```{r}
#| eval: false ## remove this!
data("karate", package = "igraphdata")
karate
```

Try ?karate in the console
Note that this is not a set of nodes, nor edges, but already a graph-object!
So no need to create a graph object using tbl_graph.
You will need to just go ahead and plot using ggraph.

Game of Thrones:

Start with pulling this data into your Rmarkdown:

```{r}
#| label: start-up code for GoT
#| eval: false ## remove this!!

GoT <- read_rds("data/GoT.RDS")
```

Note that this is a list of 7 graphs from Game of Thrones.
Select one using GoT[[index]] where index = 1…7 and then plot directly.
Try to access the nodes and edges and modify them using any attribute data

Other Datasets

Choose any other graph dataset from igraphdata
(type ?igraphdata in console)
Ask me for help if you need any

Make-2: Literary Network with TV Show / Book / Story / Play

You need to create a Network Graph for your favourite Book, play, TV serial or Show. (E.g. Friends, BBT, or LB or HIMYM, B99, TGP, JTV…or Hamlet, Little Women , Pride and Prejudice, or LoTR)

Step 1. Go to: Literary Networks for instructions.
Step 2. Make your data using the instructions.
- In the nodes excel, use id and names as your columns. Any other details in other columns to the right.
- In your edges excel, use from and to as your first columns.
- Entries in these columns can be names or ids but be consistent and don’t mix.
Step 3. Decide on 3 answers that you to seek and plan to make graphs for.
Step 4. Create graph objects. Say 3 visualizations.
Step 5. Write comments/answers in the code and narrative text. Add pictures from the web using Markdown syntax.
Step 6. Write Reflection ( ok, a short one!) inside your Quarto document. Make sure it renders !!
Step 7. Group Submission: Submit the render-able .qmd file AND the data. Quarto Markdown with joint authorship. Each person submits on their Assignments. All get the same grade on this one.

Ask me for clarifications on what to do after you have read the Instructions in your group.

References

Hadley Wickham, Danielle Navarro, and Thomas Lin Pedersen, ggplot2: Elegant Graphics for Data Analysis. https://ggplot2-book.org/networks
Omar Lizardo and Isaac Jilbert, Social Networks: An Introduction. https://bookdown.org/omarlizardo/_main/
Mark Hoffman, Methods for Network Analysis. https://bookdown.org/markhoff/social_network_analysis/
Statistical Analysis of Network Data with R, 2nd Edition.https://github.com/kolaczyk/sand
Thomas Lin Pedersen - 1 giraffe, 2 giraffe,GO!
Tyner, Sam, François Briatte, and Heike Hofmann. 2017. “Network Visualization with ggplot2.” The R Journal 9 (1): 27–59. https://journal.r-project.org/archive/2017/RJ-2017-023/index.html
Network Datasets https://icon.colorado.edu/#!/networks
Yunran Chen, Introduction to Network Analysis Using R

R Package Citations

Package	Version	Citation
ggraph	2.2.1	Pedersen (2024a)
ggtext	0.1.2	Wilke and Wiernik (2022)
graphlayouts	1.2.2	David Schoch (2023)
igraph	2.1.4	Csardi and Nepusz (2006); Csárdi et al. (2025)
igraphdata	1.0.1	Csardi (2015)
sand	2.0.0	Kolaczyk and Csárdi (2020)
showtext	0.9.7	Qiu and See file AUTHORS for details. (2024)
tidygraph	1.3.1	Pedersen (2024b)
visNetwork	2.1.2	Almende B.V. and Contributors and Thieurmel (2022)

Almende B.V. and Contributors, and Benoit Thieurmel. 2022. visNetwork: Network Visualization Using “vis.js” Library. https://doi.org/10.32614/CRAN.package.visNetwork.

Csardi, Gabor. 2015. igraphdata: A Collection of Network Data Sets for the “igraph” Package. https://doi.org/10.32614/CRAN.package.igraphdata.

Csardi, Gabor, and Tamas Nepusz. 2006. “The Igraph Software Package for Complex Network Research.” InterJournal Complex Systems: 1695. https://igraph.org.

Csárdi, Gábor, Tamás Nepusz, Vincent Traag, Szabolcs Horvát, Fabio Zanini, Daniel Noom, and Kirill Müller. 2025. igraph: Network Analysis and Visualization in r. https://doi.org/10.5281/zenodo.7682609.

David Schoch. 2023. “graphlayouts: Layout Algorithms for Network Visualizations in r.” Journal of Open Source Software 8 (84): 5238. https://doi.org/10.21105/joss.05238.

Kolaczyk, Eric, and Gábor Csárdi. 2020. sand: Statistical Analysis of Network Data with r, 2nd Edition. https://doi.org/10.32614/CRAN.package.sand.

Pedersen, Thomas Lin. 2024a. ggraph: An Implementation of Grammar of Graphics for Graphs and Networks. https://doi.org/10.32614/CRAN.package.ggraph.

———. 2024b. tidygraph: A Tidy API for Graph Manipulation. https://doi.org/10.32614/CRAN.package.tidygraph.

Qiu, Yixuan, and authors/contributors of the included software. See file AUTHORS for details. 2024. showtext: Using Fonts More Easily in r Graphs. https://doi.org/10.32614/CRAN.package.showtext.

Wilke, Claus O., and Brenton M. Wiernik. 2022. ggtext: Improved Text Rendering Support for “ggplot2”. https://doi.org/10.32614/CRAN.package.ggtext.

Citation

BibTeX citation:

@online{2022,
  author = {},
  title = {\textless Iconify-Icon Icon=“bx:network-Chart” Width=“1.2em”
    Height=“1.2em”\textgreater\textless/Iconify-Icon\textgreater{}
    {Networks}},
  date = {2022-06-21},
  url = {https://av-quarto.netlify.app/content/courses/Analytics/Descriptive/Modules/100-Networks/},
  langid = {en},
  abstract = {How one thing connects to another}
}

For attribution, please cite this work as:

“<Iconify-Icon Icon=‘bx:network-Chart’ Width=‘1.2em’ Height=‘1.2em’></Iconify-Icon> Networks.” 2022. June 21, 2022. https://av-quarto.netlify.app/content/courses/Analytics/Descriptive/Modules/100-Networks/.

Setting up R Packages

Introduction

What kind Network graphs will we make?

Goals

Pedagogical Note

Graph Metaphors

Predict/Run/Infer-1

Using tidygraph and ggraph

Step1. Read the data

Step 2.Create a network object using tidygraph:

Step 3. Plot using ggraph

Hierarchical layouts

Faceting

Network analysis with tidygraph

Network Centrality: Go-To and Go-Through People!

Analysis and Visualizing Network Communities

Interactive Graphs with visNetwork

Your Turn

Make-2: Literary Network with TV Show / Book / Story / Play

References

R Package Citations

Citation

Using `tidygraph` and `ggraph`

Step 3. Plot using `ggraph`

Interactive Graphs with `visNetwork`