Hands-on Exercise 9: Visualising and Analysing Text Data

Published

March 16, 2024

Modified

March 16, 2024

1 Getting Started

1.1 Install and loading R packages.

pacman::p_load(igraph, tidygraph, ggraph, visNetwork, lubridate, clock, tidyverse, graphlayouts,readr,dplyr,ggplot2)

2 Importing Data

GAStech_nodes <- read_csv("../../data/GAStech_email_node.csv")
GAStech_edges <- read_csv("../../data/GAStech_email_edge-v2.csv")

2.1 Wrangling time

Click to view the code.
GAStech_edges <- GAStech_edges %>%
  mutate(SendDate = dmy(SentDate)) %>%
  mutate(Weekday = wday(SentDate,
                        label = TRUE,
                        abbr = FALSE))

2.2 Wrangling attributes

Click to view the code.
GAStech_edges_aggregated <- GAStech_edges %>%
  filter(MainSubject == "Work related") %>%
  group_by(source, target, Weekday) %>%
    summarise(Weight = n()) %>%
  filter(source!=target) %>%
  filter(Weight > 1) %>%
  ungroup()

3 Creating network objects using tidygraph

3.1 Using tbl_graph() to build tidygraph data model

Click to view the code.
GAStech_graph <- tbl_graph(nodes = GAStech_nodes,
                           edges = GAStech_edges_aggregated, 
                           directed = TRUE)

3.2 Reviewing the output tidygraph’s graph object

GAStech_graph
# A tbl_graph: 54 nodes and 1372 edges
#
# A directed multigraph with 1 component
#
# Node Data: 54 × 4 (active)
      id label               Department     Title                               
   <dbl> <chr>               <chr>          <chr>                               
 1     1 Mat.Bramar          Administration Assistant to CEO                    
 2     2 Anda.Ribera         Administration Assistant to CFO                    
 3     3 Rachel.Pantanal     Administration Assistant to CIO                    
 4     4 Linda.Lagos         Administration Assistant to COO                    
 5     5 Ruscella.Mies.Haber Administration Assistant to Engineering Group Mana…
 6     6 Carla.Forluniau     Administration Assistant to IT Group Manager       
 7     7 Cornelia.Lais       Administration Assistant to Security Group Manager 
 8    44 Kanon.Herrero       Security       Badging Office                      
 9    45 Varja.Lagos         Security       Badging Office                      
10    46 Stenig.Fusil        Security       Building Control                    
# ℹ 44 more rows
#
# Edge Data: 1,372 × 4
   from    to Weekday Weight
  <int> <int> <ord>    <int>
1     1     2 星期日       5
2     1     2 星期一       2
3     1     2 星期二       3
# ℹ 1,369 more rows

3.3 Changing the active object

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GAStech_graph %>%
  activate(edges) %>%
  arrange(desc(Weight))
# A tbl_graph: 54 nodes and 1372 edges
#
# A directed multigraph with 1 component
#
# Edge Data: 1,372 × 4 (active)
    from    to Weekday Weight
   <int> <int> <ord>    <int>
 1    40    41 星期六      13
 2    41    43 星期一      11
 3    35    31 星期二      10
 4    40    41 星期一      10
 5    40    43 星期一      10
 6    36    32 星期日       9
 7    40    43 星期六       9
 8    41    40 星期一       9
 9    19    15 星期三       8
10    35    38 星期二       8
# ℹ 1,362 more rows
#
# Node Data: 54 × 4
     id label           Department     Title           
  <dbl> <chr>           <chr>          <chr>           
1     1 Mat.Bramar      Administration Assistant to CEO
2     2 Anda.Ribera     Administration Assistant to CFO
3     3 Rachel.Pantanal Administration Assistant to CIO
# ℹ 51 more rows

4 Plotting Practice - Plotting Static Network Graphs with ggraph package

4.1 Plotting a basic network graph

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ggraph(GAStech_graph) +
  geom_edge_link() +
  geom_node_point()

4.2 Changing the default network graph theme

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g <- ggraph(GAStech_graph) + 
  geom_edge_link(aes()) +
  geom_node_point(aes())

g + theme_graph()

4.3 Changing the coloring of the plot

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g <- ggraph(GAStech_graph) + 
  geom_edge_link(aes(colour = 'grey50')) +
  geom_node_point(aes(colour = 'grey40'))

g + theme_graph(background = 'grey10',
                text_colour = 'white')

4.4 Fruchterman and Reingold layout

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g <- ggraph(GAStech_graph, 
            layout = "fr") +
  geom_edge_link(aes()) +
  geom_node_point(aes())

g + theme_graph()

4.5 Modifying network nodes

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g <- ggraph(GAStech_graph, 
            layout = "nicely") + 
  geom_edge_link(aes()) +
  geom_node_point(aes(colour = Department, 
                      size = 3))

g + theme_graph()

4.6 Modifying edges

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g <- ggraph(GAStech_graph, 
            layout = "nicely") +
  geom_edge_link(aes(width=Weight), 
                 alpha=0.2) +
  scale_edge_width(range = c(0.1, 5)) +
  geom_node_point(aes(colour = Department), 
                  size = 3)

g + theme_graph()

5 Plotting Practice - Creating facet graphs

5.1 Working with facet_edges()

Click to view the code.
set_graph_style()

g <- ggraph(GAStech_graph, 
            layout = "nicely") + 
  geom_edge_link(aes(width=Weight), 
                 alpha=0.2) +
  scale_edge_width(range = c(0.1, 5)) +
  geom_node_point(aes(colour = Department), 
                  size = 2)

g + facet_edges(~Weekday)

5.2 Working with facet_edges()

Click to view the code.
set_graph_style()

g <- ggraph(GAStech_graph, 
            layout = "nicely") + 
  geom_edge_link(aes(width=Weight), 
                 alpha=0.2) +
  scale_edge_width(range = c(0.1, 5)) +
  geom_node_point(aes(colour = Department), 
                  size = 2) +
  theme(legend.position = 'bottom')
  
g + facet_edges(~Weekday)

5.3 A framed facet graph

Click to view the code.
set_graph_style() 

g <- ggraph(GAStech_graph, 
            layout = "nicely") + 
  geom_edge_link(aes(width=Weight), 
                 alpha=0.2) +
  scale_edge_width(range = c(0.1, 5)) +
  geom_node_point(aes(colour = Department), 
                  size = 2)
  
g + facet_edges(~Weekday) +
  th_foreground(foreground = "grey80",  
                border = TRUE) +
  theme(legend.position = 'bottom')

5.4 Working with facet_nodes()

Click to view the code.
set_graph_style()

g <- ggraph(GAStech_graph, 
            layout = "nicely") + 
  geom_edge_link(aes(width=Weight), 
                 alpha=0.2) +
  scale_edge_width(range = c(0.1, 5)) +
  geom_node_point(aes(colour = Department), 
                  size = 2)
  
g + facet_nodes(~Department)+
  th_foreground(foreground = "grey80",  
                border = TRUE) +
  theme(legend.position = 'bottom')

6 Plotting Practice - Network Metrics Analysis

6.1 Computing centrality indices

Click to view the code.
g <- GAStech_graph %>%
  mutate(betweenness_centrality = centrality_betweenness()) %>%
  ggraph(layout = "fr") + 
  geom_edge_link(aes(width=Weight), 
                 alpha=0.2) +
  scale_edge_width(range = c(0.1, 5)) +
  geom_node_point(aes(colour = Department,
            size=betweenness_centrality))
g + theme_graph()

6.2 Visualising network metrics

Click to view the code.
g <- GAStech_graph %>%
  ggraph(layout = "fr") + 
  geom_edge_link(aes(width=Weight), 
                 alpha=0.2) +
  scale_edge_width(range = c(0.1, 5)) +
  geom_node_point(aes(colour = Department, 
                      size = centrality_betweenness()))
g + theme_graph()

6.3 Visualising Community

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g <- GAStech_graph %>%
  mutate(community = as.factor(group_edge_betweenness(weights = Weight, directed = TRUE))) %>%
  ggraph(layout = "fr") + 
  geom_edge_link(aes(width=Weight), 
                 alpha=0.2) +
  scale_edge_width(range = c(0.1, 5)) +
  geom_node_point(aes(colour = community))  

g + theme_graph()

7 Plotting Practice - Building Interactive Network Graph with visNetwork

7.1 Data preparation

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GAStech_edges_aggregated <- GAStech_edges %>%
  left_join(GAStech_nodes, by = c("sourceLabel" = "label")) %>%
  rename(from = id) %>%
  left_join(GAStech_nodes, by = c("targetLabel" = "label")) %>%
  rename(to = id) %>%
  filter(MainSubject == "Work related") %>%
  group_by(from, to) %>%
    summarise(weight = n()) %>%
  filter(from!=to) %>%
  filter(weight > 1) %>%
  ungroup()

7.2 Plotting the first interactive network graph

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visNetwork(GAStech_nodes, 
           GAStech_edges_aggregated)

7.3 Working with layout

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visNetwork(GAStech_nodes,
           GAStech_edges_aggregated) %>%
  visIgraphLayout(layout = "layout_with_fr")

7.4 Working with visual attributes - Nodes

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GAStech_nodes <- GAStech_nodes %>%
  rename(group = Department) 

visNetwork(GAStech_nodes,
           GAStech_edges_aggregated) %>%
  visIgraphLayout(layout = "layout_with_fr") %>%
  visLegend() %>%
  visLayout(randomSeed = 123)

7.5 Working with visual attributes - Edges

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visNetwork(GAStech_nodes,
           GAStech_edges_aggregated) %>%
  visIgraphLayout(layout = "layout_with_fr") %>%
  visEdges(arrows = "to", 
           smooth = list(enabled = TRUE, 
                         type = "curvedCW")) %>%
  visLegend() %>%
  visLayout(randomSeed = 123)

7.6 Interactivity

Click to view the code.
visNetwork(GAStech_nodes,
           GAStech_edges_aggregated) %>%
  visIgraphLayout(layout = "layout_with_fr") %>%
  visOptions(highlightNearest = TRUE,
             nodesIdSelection = TRUE) %>%
  visLegend() %>%
  visLayout(randomSeed = 123)