In jokergoo/spiralize: Visualize Data on Spirals

library(knitr)
knitr::opts_chunk$set(
    error = FALSE,
    tidy  = FALSE,
    message = FALSE,
    warning = FALSE,
    fig.width = 7,
    fig.height = 7,
    fig.align = "center",
    fig.retina = 2
)
knitr::knit_hooks$set(pngquant = knitr::hook_pngquant)
knitr::opts_chunk$set(
  message = FALSE,
  dev = "ragg_png",
  fig.align = "center",
  pngquant = "--speed=10 --quality=30"
)
options(width = 100)

The COVID-19 daily increase is basically a time series data, thus it is natural to visualize it via spirals. As an example, we take the data for the United States and only the number of confirmed cases.

library(COVID19)
x = covid19(country = "United States", verbose = FALSE)
x = x[, c("date", "confirmed")]
x$date = as.Date(x$date)

# remove the leading and ending days with no data
na_range = range(which(!is.na(x$confirmed)))
x = x[seq(na_range[1], na_range[2]), ]
head(x)

Some days have NA values. We assign them with the same value as the most recent days with non-NA values.

for(i in which(is.na(x$confirmed))) {
    x$confirmed[[i]] = x$confirmed[[i-1]]
}

Now we can calculate the daily increase.

x$daily_increased = diff(c(0, x$confirmed))
x$daily_increased[x$daily_increased < 0] = 0
head(x)
range(x$daily_increased)

Making spiral is straightforward. First we initialize the layout with the time ranges, then create a track and draw bars in it. We additionally add the month names to sectors and labels representing the corresponding years.

library(spiralize)
library(lubridate)

spiral_initialize_by_time(xlim = range(x$date), normalize_year = TRUE)

spiral_track(height =  0.8, ylim = c(0, 1.5e6))
spiral_bars(x$date, x$daily_increased, gp = gpar(fill = 2, col = 2))

spiral_yaxis(at = c(0, 5e5, 1e6, 1.5e6), labels = c("0", "500K", "1M", "1.5M"), 
    labels_gp = gpar(fontsize = 7))

# month names
dd = max(x$date)
day(dd) = 15
dd = dd + months(1:12)
spiral_text(dd, y = 1.5, month.name[month(dd)], facing = "inside", nice_facing = TRUE)

# labels of years
for(y in c(2020, 2021, 2022, 2023)) {
    spiral_text(paste0(y, "-01-01"), TRACK_META$ycenter, paste0(y, "-01-01"), 
        gp = gpar(fontsize = 7))
}

We can improve the plot a little bit, such as making the background in gradients and change bars to "lolipops".

spiral_initialize_by_time(xlim = range(x$date), normalize_year = TRUE)

spiral_track(height =  0.8, gradient = 3, background_gp = gpar(fill = "#DDDDDD"),
    ylim = c(0, 1.5e6))

spiral_lines(x$date, x$daily_increased, type = "h", gp = gpar(col = 2))
spiral_points(x$date, x$daily_increased, pch = 16, gp = gpar(col = 2))

spiral_yaxis(at = c(0, 5e5, 1e6, 1.5e6), labels = c("0", "500K", "1M", "1.5M"), 
    labels_gp = gpar(fontsize = 7))

# month names
dd = max(x$date)
day(dd) = 15
dd = dd + months(1:12)
spiral_text(dd, y = 1.5, month.name[month(dd)], facing = "inside", nice_facing = TRUE)

# labels of years
for(y in c(2020, 2021, 2022, 2023)) {
    spiral_text(paste0(y, "-01-01"), TRACK_META$ycenter, paste0(y, "-01-01"), 
        gp = gpar(fontsize = 7))
}

I have implemented it as a Shiny application. The source code for generating this app is avaiable at https://gist.github.com/jokergoo/fa39ee3dcf20cbc13a31bbe93c3498fb. You can run it by:

source("https://gist.githubusercontent.com/jokergoo/fa39ee3dcf20cbc13a31bbe93c3498fb/raw/696f8331075085629a1d2b303c928c1f68249637/spiral_covid19_shiny.R")
shinyApp(ui = ui, server = server)