Plotting the Epiverse-TRACE interaction network

plot_epiverse_network.R

library(tidyverse)
library(readxl)
library(tidygraph)
library(scico)
library(ggraph)

# read data on connections
df <- read_excel("contact_matrix.xlsx",
  sheet = "matrix"
)
df <- rename(df, name = `...1`)

# read affiliations
affils <- read_excel(
  "contact_matrix.xlsx",
  sheet = "affils"
)

# rename columns
affils <- rename(affils, name = Name, institution = Institution)

# change MRC to MRC-The Gambia
affils <- mutate(
  affils,
  institution = if_else(institution == "MRC", "MRC-The Gambia", institution)
)

# pivot longer to make edgelist
df <- pivot_longer(
  data = df,
  !name,
  names_to = "name2",
  values_to = "weight"
)

# rename for tidygraph and remove last names
df <- rename(df, from = name, to = name2)

# remove NA weights
df <- filter(df, !is.na(weight))

# make graph object
g <- tidygraph::as_tbl_graph(df, directed = TRUE)

# add affiliations
g <- activate(g, "nodes") %>%
  left_join(affils) %>%
  mutate(
    initial_last = str_extract(name, "\\s[^ ]+$") %>%
      str_extract("\\w{1}"),
    name_print = str_replace(
      name, "\\s[^ ]+$", sprintf(" %s.", initial_last)
    )
  )

# calculate centrality
g <- activate(g, "nodes") %>%
  mutate(
    centrality = tidygraph::centrality_betweenness()
  )

# add institution to edges
affils_new <- as_tibble(g) %>%
  mutate(
    from = seq(nrow(affils_new))
  )

g <- activate(g, "edges") %>%
  left_join(
    select(affils_new, from, institution, name)
  ) %>%
  activate("nodes")

# plot with ggraph
plot <-
ggraph(graph = g, layout = "stress") +
  geom_edge_fan(
    aes(
      edge_alpha = as.factor(weight),
      edge_colour = as.factor(institution),
    ),
    edge_width = 0.7,
    lineend = "round"
  ) +
  geom_node_point(
    aes(
      fill = institution,
      size = centrality
    ),
    shape = 21, colour = "white"
  ) +
  geom_node_label(
    aes(
      label = name_print
    ),
    colour = "grey30",
    size = 3,
    fill = alpha("grey", 0.6),
    repel = TRUE
  ) +
  scale_fill_scico_d(
    palette = "hawaii",
    name = "Institution",
    na.value = "grey"
  ) +
  scale_edge_color_manual(
    values = scico(5, palette = "hawaii"),
    name = "Institution",
    na.value = "grey"
  ) +
  scale_size(
    range = c(2, 10)
  ) +
  scale_edge_alpha_manual(
    values = c(
      "1" = 0.1,
      "2" = 0.3,
      "3" = 0.5,
      "4" = 0.8,
      "5" = 1
    ),
    labels = c(
      "1" = "Rarely",
      "2" = "Seldom",
      "3" = "Sometimes",
      "4" = "Often",
      "5" = "Very often"
    )
  ) +
  guides(
    size = "none",
    edge_colour = "none",
    edge_alpha = guide_legend(
      title = "Interactions",
      nrow = 2
    ),
    fill = guide_legend(
      nrow = 2,
      override.aes = list(
        size = 5
      )
    )
  ) +
  theme_void() +
  theme(
    plot.background = element_rect(
      fill = "white"
    ),
    legend.position = "top"
  )

# save plot
ggsave(
  plot,
  filename = "fig_epiverse_network.png",
  dpi = 300,
  width = 8, height = 6
)