Creación de gráficos del coronavirus en R

Introducción

Queremos mostrar la evolución de casos de coronavirus en R con gráficos estáticos e interactivos.

Gráficos

Interactivo (escala lineal)

Interactivo (escala logaritmica)

Solución

Usamos los datos del repositorio creado por Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE). Hay tres series de datos temporales: confirmed, deaths y recovered cases. Primero preparamos los datos y creamos el gráfico usando ggplot2 para la versión estática, y plotly para añadir interactividad. Las series de datos incluyen casos de todo el mundo pero en nuestro ejemplo usamos un subconjunto para Alemania, Francia, Italia, España y el Reino Unido.

# Librerias
library(magrittr)
library(lubridate) 
library(tidyverse)
library(plotly)
library(scales)

# Importación de datos
confirmed <- read_csv("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Confirmed.csv")
deaths <- read_csv("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Deaths.csv")
recovered <- read_csv("https://raw.githubusercontent.com/CSSEGISandData/COVID-19/master/csse_covid_19_data/csse_covid_19_time_series/time_series_19-covid-Recovered.csv")

# Data preparation
AppendMe <- function(dfNames) {
  do.call(rbind, lapply(dfNames, function(x) {
    cbind(get(x), source = x)
  }))
}
df <- AppendMe(c("confirmed", "deaths", "recovered"))
data <- df %>%
  rename(province = `Province/State`, country = `Country/Region`) %>% 
  pivot_longer(
    -c(province, country, Lat, Long, source),
    names_to = "date",
    values_to = "count"
  ) %>% 
mutate(date = mdy(date)) 

# Gráfico escala lineal
p <- data %>%
  filter(country %in% c("Germany", "France", "Italy",  "Spain", "United Kingdom")) %>% 
  group_by(country, date, source) %>%
  summarise(n = sum(count)) %>%
  ggplot(aes(date, n, colour = country)) +
  geom_line(linetype = 2) +
  geom_point(size = 1) +
  facet_wrap( ~  source  , scales = "free", nrow = 3) +
  theme_bw()+
  labs(title = "Cumulative Covid-19 cases (linear scale)")+
  ylab("")+
  scale_x_date(date_labels = "%b %d")+
  scale_y_continuous(labels = comma)
p # Estático
ggplotly(p) # Interactivo

# Gráfico escala logaritmica
p <- data %>%
  filter(country %in% c("Germany", "France", "Italy",  "Spain", "United Kingdom")) %>% 
  group_by(country, date, source) %>%
  summarise(n = sum(count)) %>%
  ggplot(aes(date, n, colour = country)) +
  geom_line(linetype = 2) +
  geom_point(size = 1) +
  facet_wrap( ~  source, scales = "free",  nrow = 3) +
  theme_bw()+
  labs(title = "Cumulative Covid-19 cases (log scale)")+
  ylab("")+
  scale_x_date(date_labels = "%b %d")+
  scale_y_log10(breaks = c(1, 10, 100, 10000))
  p 
ggplotly(p) 

Para subrayar una serie al pasar sobre ella usamos la función highlight del paquete plotly.

p <- data %>%
  filter(country %in% c("Germany", "France", "Italy",  "Spain", "United Kingdom")) %>% 
  group_by(country, date, source) %>%
  summarise(cases = sum(count)) %>%
  highlight_key(~ country ) %>% 
  ggplot(aes(date, cases, colour = country)) +
  geom_line(linetype = 2)+
  geom_point(size = 1) +
  facet_wrap(~  source  , scales = "free", nrow = 3)+
  theme_bw()+
  labs(title = "Cumulative Covid-19 cases (linear scale)")+
  ylab("")+
  scale_x_date(date_labels = "%b %d")+
  scale_y_continuous(labels = comma)
ggplotly(p, tooltip = c("country", "date", "cases")) %>% 
highlight(on = "plotly_hover")

Gráficco here. Pantallazo abajo.

Referencias

• csse_covid_19_time_series
• Novel Coronavirus (COVID-19) Cases Data
• Covid-19 Shiny Dashboard