In-Class Exercise (Lesson 5)

Author

FU YILIN

Load Packages

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

Import Data

kg <- fromJSON("data/MC1_graph.json")

Inspect Structure

str(kg, max.level = 1)

List of 5
 $ directed  : logi TRUE
 $ multigraph: logi TRUE
 $ graph     :List of 2
 $ nodes     :'data.frame': 17412 obs. of  10 variables:
 $ links     :'data.frame': 37857 obs. of  4 variables:

Extract and inspect

nodes_tbl <- as_tibble(kg$nodes)
edges_tbl <- as_tibble(kg$links)

Initial EDA

ggplot(data = edges_tbl,
       aes(y = `Edge Type`)) +
  geom_bar()

ggplot(data = nodes_tbl,
       aes(y = `Node Type`)) +
  geom_bar()

Mapping from node id to row index

id_map <- tibble(id = nodes_tbl$id,
                 index = seq_len(
                   nrow(nodes_tbl)))

Step 2: Map source and target IDs to row indices

edges_tbl <- edges_tbl %>%
  left_join(id_map, by = c("source" = "id")) %>%
  rename(from = index) %>%
  left_join(id_map, by = c("target" = "id")) %>%
  rename(to = index)

Step 3: Filter out any unmatched (invalid) edges

edges_tbl <- edges_tbl %>%
  filter(!is.na(from), !is.na(to))

Step 4: Creating the graph

visualing the knowledge graph

graph <- tbl_graph(nodes = nodes_tbl, 
                   edges = edges_tbl, 
                   directed = kg$directed)

class(graph)

[1] "tbl_graph" "igraph"

set.seed(1234)

Visualizing the whole Graph

ggraph(graph, layout = "fr") +
  geom_edge_link(alpha = 0.3, 
                 colour = "gray") +
  geom_node_point(aes(color = `Node Type`), 
                  size = 4) +
  geom_node_text(aes(label = name), 
                 repel = TRUE, 
                 size = 2.5) +
  theme_void()

Warning: ggrepel: 17411 unlabeled data points (too many overlaps). Consider
increasing max.overlaps

Step 1: Filter edges to only “Memberof”

graph_memberof <- graph %>%
  activate(edges) %>%
  filter(`Edge Type` == "MemberOf")

Step 2: Extract only connected nodes

used_node_indices <- graph_memberof %>%
  activate(edges) %>%
  as_tibble() %>%
  select(from, to) %>%
  unlist() %>%
  unique()

Step 3: Keep only those nodes

used_node_indices <- graph_memberof %>%
  activate(edges) %>%
  as_tibble() %>%
  select(from, to) %>%
  unlist() %>%
  unique()

Plot the sub-graph

ggraph(graph_memberof, 
       layout = "fr") +
  geom_edge_link(alpha = 0.5, 
                 colour = "gray") +
  geom_node_point(aes(color = `Node Type`), 
                  size = 1) +
  geom_node_text(aes(label = name), 
                 repel = TRUE, 
                 size = 2.5) +
  theme_void()

Warning: ggrepel: 17411 unlabeled data points (too many overlaps). Consider
increasing max.overlaps