Draw arrow on ggplot with dates as variable, by specifying co-ordinates rather than using the units-CodePudding

I am attempting to plot the blood test results for a patient in a time series. I have managed to do this and included a reference range between two shaded y-intercepts. My problem is that the annotate() or geom_segment() calls want me to specify, in the units of my independent variable, which is, unhelpfully, a date (YYYY-MM-DD).

Is it possible to get R to ignore the units of the x- and y-axis and specify the arrow co-ordinates as if they were on a grid?

result <- runif(25, min = 2.0, max = 3.5)
start_date <- ymd("2021-08-16")
end_date <- ymd("2022-10-29")
date <- sample(seq(start_date, end_date, by = "days"), 25, replace = TRUE)
q <- data.table(numbers, date)
ggplot(q, aes(x = date, y = result))   
  geom_line()   
  geom_point(aes(x = date, y = result), shape = 21, size = 3)  
  scale_x_date(limits = c(min(q$date), max(q$date)), 
               breaks = date_breaks("1 month"),
               labels = date_format("%b %Y"))  
  ylab("Corrected calcium (mmol/L") 
  xlab("Date of blood test")   
  ylim(1,4) 
  geom_ribbon(aes(ymin=2.1, ymax=2.6), fill="grey", alpha=0.2, colour="grey") 
  geom_vline(xintercept=as.numeric(q$date[c(3, 2)]),
             linetype=4, colour="black")  
  theme(axis.text.x = element_text(angle = 45))   theme_prism(base_size = 10)  
  annotate("segment", x = 1, y = 2, xend = 3, yend = 4, arrow = arrow(length = unit(0.15, "cm")))

The error produced is Error: Invalid input: date_trans works with objects of class Date only.

I can confirm that:
> class(q$date)
[1] "Date"

I've just gone with test co-ordinates (1,2,3,4) for the annotate("segment"...), ideally I want to be able to get the arrow to point to a specific data point on the plot to indicate when the patient went on treatment.

Many thanks,
Sandro

CodePudding user response：

You don't need to convert to points or coordinates. Just use the actual values from your data frame. I am just subsetting within annotate using a hard coded index (you can also automate this of course), but you will need to "remind" R that you are dealing with dates - thus the added lubridate::as_date call.

library(ggplot2)
library(lubridate)

result <- runif(25, min = 2.0, max = 3.5)
start_date <- ymd("2021-08-16")
end_date <- ymd("2022-10-29")
date <- sample(seq(start_date, end_date, by = "days"), 25, replace = TRUE)
q <- data.frame(result, date)

## I am arranging the data frame by date
q <- dplyr::arrange(q, date)

ggplot(q, aes(x = date, y = result))   
  geom_line()   
## for start use a random x and y so it starts whereever you want it to start
## for end, use the same row from your data frame, in this case row 20
  annotate(geom = "segment", 
           x = as_date(q$date[2]), xend = as_date(q$date[20]), 
           y = min(q$result), yend = q$result[20], 
           arrow = arrow(),
           size = 2, color = "red")