Code for N501Y plot

plot.R

library(tidyverse)
library(gganimate)
library(lubridate)
data <-
  read_csv("D:/cases_anim/cog_metadata_microreact_public.csv.txt")
data$sample_date = ymd(data$sample_date)
library(sp)
library('sf')
ltlas <-
  read_sf(
    "D:/cases_anim/Counties_and_Unitary_Authorities__December_2017__Boundaries_in_the_UK__WGS84_-shp/Counties_and_Unitary_Authorities__December_2017__Boundaries_in_the_UK__WGS84_.shp"
  )
data <- filter(data, !is.na(latitude))



pts <-
  st_as_sf(tibble(data$latitude, data$longitude),
           coords = c(2, 1),
           crs  = 4326)

ltlas <- st_transform(ltlas, crs = 3857)
pts <- st_transform(pts, crs = 3857)


a = st_join(pts, ltlas)
data$ltla = a$ctyua17nm



agg = data %>% filter(n501y == "Y") %>% group_by(ltla) %>% summarise(num =
                                                                       n()) %>% arrange(-num)
ggplot(
  data %>% filter(ltla %in% agg$ltla[1:10], epi_week < 50, ltla != "NA"),
  aes(x = epi_week, fill = n501y)
) + geom_bar(position = "fill") + facet_wrap( ~ ltla, scales = "free_y") +
  theme_bw() + scale_fill_manual(values = c("darkgray", "green", "darkblue", "darkred")) +
  labs(fill = "N501Y", y = "Relative frequency") + scale_y_continuous(labels = scales::percent)
ggsave("graph.pdf", width = 6, height = 6)