How to build a waffle chart with circle-shaped tiles using {waffle} and {ggplot2} libraries in R?

# Data manipulation
library(tidyverse)

# Waffle chart
library(waffle)

# Visualization extensions for ggplot2
library(paletteer)
library(ggsci)
library(ggtext) 
library(shadowtext)
library(showtext)

# Create styled HTML/LaTeX tables
library(kableExtra)  

outbreaks_year_disease_grouped <- read.csv("outbreaks_year_disease_grouped.csv")

outbreaks_year_disease_grouped |>
  arrange(Year, -freq) |>
  kbl(caption = "Disease outbreaks per disease and year") |>
  kable_paper("hover", full_width = F)

# Add custom font
font_add_google("Atkinson Hyperlegible Next", "Atkinson Hyperlegible Next") 
showtext_auto()

# Custom theme for the waffle chart
theme_waffle_chart <- function() {

  # Introduce the previously selected font
  theme_minimal(base_family = "Atkinson Hyperlegible Next") +

  # Custom theme settings
  theme(
    # Axis settings
    axis.title = element_blank(), # Remove axis titles
    axis.line = element_blank(), # Remove axis lines
      
    # Title settings
    plot.title.position = "plot", # Position of the title
    plot.title = element_textbox(
      color = "black",
      face = "bold",
      size = 24,
      margin = margin(5, 0, 5, 0), # Top, right, bottom, left margins
      width = unit(1, "npc") # Full plot width
    ),

    plot.margin = unit(c(0.25, 0.25, 0.25, 0.25), "cm"),

    # Legend 
    legend.justification = c(1, 1),
    legend.title = element_text(face = "bold", size = 14),
    legend.title.position = "top",
    legend.text = element_text(face = "bold", size = 12),
    legend.direction = "vertical",
    legend.spacing.x = unit(30, "pt"),
    legend.key.size = unit(11, "pt"),
    legend.key.spacing.y = unit(3, "pt"),
    legend.key.spacing.x = unit(10, "pt"),

    # Subtitle settings
    plot.subtitle = element_textbox(
      color = "grey50",
      face = "bold",
      size = 18,
      margin = margin(0, 0, 40, 0), # Top, right, bottom, left margins
      width = unit(1, "npc")
    ),

    # Caption settings
    plot.caption = element_textbox(
      color = "grey70",
      size = 14,
      hjust = 0
    ),
    plot.caption.position = "plot",

    # Background and margins
    plot.background = element_rect(
      color = "white",
      fill = "white"
    ),
    panel.grid = element_blank(), 
    strip.text.x = element_text(face = "bold", margin = margin(t = 10), color = "black", size = 20),

    # Axis
    axis.ticks.y = element_line(linewidth = 1),
    axis.ticks.length.y = unit(5, "pt"),
    axis.text.x = element_text(face = "bold", color = "black", size = 12),
    axis.text.y = element_text(face = "bold", color = "black", size = 15),
    axis.title.x = element_text(face = "bold", margin = margin(t = 10), color = "black", size = 13),
    axis.title.y = element_text(face = "bold", margin = margin(r = 10), color = "black", size = 17)
    )
}

# Title, subtitle, and caption for the waffle chart
title_chart <- "Pandemic- and epidemic-prone disease outbreaks in the world | 2021–2025"
subtitle_chart <- "In 2025, influenza emerged as the most reported disease behind outbreaks, being responsible for 121 events."

caption_chart <- paste0(
  "**Note:** Each circle represents a country.",
  "<br>", 
  "**Data:** A global dataset of pandemic- and epidemic-prone disease outbreaks (DOI: 10.1038/s41597-022-01797-2).",
  "<br>", 
  "**Graphic:** Juan Torres Munguía."
  )

ggplot(outbreaks_year_disease_grouped, 
      aes(fill = icd104n, values = freq)) +
  geom_waffle(size = 0.75, 
              n_rows = 10, 
              flip = TRUE,
              color = "white", 
              make_proportional = FALSE) +
  facet_wrap(~Year, 
             nrow = 1, 
             strip.position = "bottom")

ggplot(outbreaks_year_disease_grouped, 
                aes(fill = icd104n, values = freq)) +
  geom_waffle(size = 0.75, 
              n_rows = 10, 
              flip = TRUE,
              color = "white", 
              make_proportional = FALSE) +
  facet_wrap(~Year, 
             nrow = 1, 
             strip.position = "bottom") +
  scale_fill_manual(values = c(paletteer_d("colorBlindness::paletteMartin"))) +
  scale_x_discrete() +
  scale_y_continuous(labels = function(x) x * 10, 
                     expand = c(0, 0)) +
  coord_equal() +
  labs(
    title = title_chart,
    subtitle = subtitle_chart,
    caption = caption_chart,
    x = "", 
    y = "Frequency of disease outbreaks",
    fill = "Pathogen:") +
  guides(fill = guide_legend(position = "right")) +
  theme_waffle_chart()

ggplot(outbreaks_year_disease_grouped, 
                aes(fill = icd104n, values = freq)) +
  geom_waffle(radius = grid::unit(0.5, "npc"),
              size = 0.75, 
              n_rows = 10, 
              flip = TRUE,
              color = "white", 
              make_proportional = FALSE) +
  facet_wrap(~Year, 
             nrow = 1, 
             strip.position = "bottom") +
  scale_fill_manual(values = c(paletteer_d("colorBlindness::paletteMartin"))) +
  scale_x_discrete() +
  scale_y_continuous(labels = function(x) x * 10, 
                     expand = c(0, 0)) +
  coord_equal() +
  labs(
    title = title_chart,
    subtitle = subtitle_chart,
    caption = caption_chart,
    x = "", 
    y = "Frequency of disease outbreaks",
    fill = "Pathogen:") +
  guides(fill = guide_legend(position = "right")) +
  theme_waffle_chart()

showtext_opts(dpi = 320) # Resolution of 320 dpi for high-quality images ("retina")
ggsave(
  "waffle-pandemics-2026.png",
  dpi = 320,
  width = 14,
  height = 10,
  units = "in"
)
showtext_auto(FALSE)