CasesAnimation.R

# file is downloaded from covid19.sanger.ac.uk with customised lineage selection
data<- read_csv("C:/Users/Theo/Desktop/Estimated_Cases_in_England (2).csv")
library(gganimate)
data$date


library(MetBrewer)


lookup =c("B"="Other B lineages","B.1.1.529"="Omicron", "B.1.1.7"="Alpha","B.1.617.2"="Delta","B.1.177"="B.1.177","AY.4.2"="AY.4.2")


library(ggrepel)
data$lineage
the_anim<- ggplot(data %>% filter(value>10,!("B.1.1.529"==lineage & date<"2021-10-20")), aes(x = date, color = lookup[lineage], y = value,group=lineage)) +
  geom_line() +
  theme_classic() +
  labs(x = "Specimen date", y = "Estimated cases\n\n") +
  theme_bw() +
  scale_x_date(breaks = scales::pretty_breaks(6), ) + expand_limits(x=lubridate::ymd("2022-03-12"))+
  scale_color_brewer(type="qual") + scale_y_continuous(label=scales::comma) + coord_cartesian(ylim=c(0,NA))+
  labs(color = "", title = "Estimated cases per week in England by variant", caption = "Data: Wellcome Sanger Institute and UKHSA")+scale_color_manual(values=met.brewer("Juarez", 6)) + geom_label(hjust = 0,aes(label=lookup[lineage]),nudge_x=10)+ theme(legend.position = "none")+geom_point()

the_anim

data

anim<- the_anim + transition_reveal(date) +view_follow(fixed_y = c(0,NA),fixed_x=T) +transition_reveal(date)
anim
a <- animate(anim, renderer = file_renderer("c:/desktop/newww/"),height=500,width=800,res=140,nframes = 500,type="cairo")
# generates a step of PNGs that must be stitched, or you could use a different renderer that generates movies directly

I use your code to filter the lineage and date, but not work, please see below, thanks. @theosanderson

subdata <- data %>% dplyr::filter(value > 10, !(lineage == "B.1.1.529" & date < "2021-10-20"))
unique(subdata$lineage); range(subdata$date)
[1] "A" "B.1.177" "B.1.1.7" "B.1.617.2" "AY.4.2" "B.1.1.529"
[1] "2020-09-05" "2022-01-08"

See comment on line 1 @LiXingguangBrandonStark

BTW, why you use transition_reveal(date) twice? @theosanderson

anim<- the_anim + transition_reveal(date) +view_follow(fixed_y = c(0,NA),fixed_x=T) +transition_reveal(date)
anim