In-class Exercise 5

Author

Lennis

Published

May 13, 2023

Modified

June 18, 2023

Getting Started

Install and launching R packages

The code chunk below uses p_load() of pacman package to check if the relevant packages are installed in the computer. If they are, then they will be launched into R.

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

Importing the data

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

Wrangling time data

GAStech_edges <- GAStech_edges %>%
  mutate(SendDate = dmy(SentDate)) %>%
  mutate(Weekday = wday(SentDate,
                        label = TRUE,
                        abbr = FALSE))

Wrangling other attributes

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

Creating network objects using tidygraph

GAStech_graph <- tbl_graph(nodes = GAStech_nodes,
                           edges = GAStech_edges_aggregated, 
                           directed = TRUE)

Changing the active object

GAStech_graph %>%
  activate(edges) %>%
  arrange(desc(Weight))
# A tbl_graph: 54 nodes and 1372 edges
#
# A directed multigraph with 1 component
#
# A tibble: 1,372 × 4
   from    to Weekday  Weight
  <int> <int> <ord>     <int>
1    40    41 Saturday     13
2    41    43 Monday       11
3    35    31 Tuesday      10
4    40    41 Monday       10
5    40    43 Monday       10
6    36    32 Sunday        9
# ℹ 1,366 more rows
#
# A tibble: 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

Plotting network graphs with ggraph

Plotting a basic graph

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

Changing the theme

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

g + theme_graph()

Changing the plot colour

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

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

Working with ggraph layouts

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

g + theme_graph()

Modifying network nodes

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

g + theme_graph()

Modifying edges

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()

Creating facet graphs

Working with facet_edges()

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)

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)

Framed facet graph

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')

Working with facet_nodes()

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')

Network Metrics Analysis

Visualizing network metrics

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()

Visualizing communities

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()

Plotting an interactive graph

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()
visNetwork(GAStech_nodes, 
           GAStech_edges_aggregated)

Working with layout

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

Working with nodes

Rename group to department

GAStech_nodes <- GAStech_nodes %>%
  rename(group = Department) 
visNetwork(GAStech_nodes,
           GAStech_edges_aggregated) %>%
  visIgraphLayout(layout = "layout_with_fr") %>%
  visLegend() %>%
  visLayout(randomSeed = 123)

Working with edges

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

Interactivity

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

Exploring Vast Challenge Data

Install and launching R packages

The code chunk below uses p_load() of pacman package to check if the relevant packages are installed in the computer. If they are, then they will be launched into R.

pacman::p_load(jsonlite, tidygraph, ggraph, visNetwork, tidyverse)

Importing the data

MC1 <- fromJSON("data/MC1.json")

Creating the graph

MC1_nodes <- as_tibble(MC1$nodes) %>%
  select(id, type, country)
MC1_edges <- as_tibble(MC1$links) %>%
  select(source, target, type, weight, key)