Error: No summary function supplied, defaulting to `mean_se()`

Question

I'm working in ggplot and I have a plot with the following code:

plot <- ggplot(data, aes(x=Site, y=ratio, colour = Site)) +
  geom_point(stat="summary", fun.y= "mean", size = 4) +
  geom_point (size = 1, alpha = .3) +
  stat_summary(fun.data= mean_se, geom = "errorbar", width = .2, linewidth = 0.3) +
  theme(legend.position = "none") 

I'm receiving the following error message:

Warning in geom_point(stat = "summary", fun.y = "mean", size = 4) :
  Ignoring unknown parameters: `fun.y`
No summary function supplied, defaulting to `mean_se()`

I'm not sure what the issue is. Thanks for any advice.

I tried replacing mean_se with mean_se() and that didn't work.

Answer 1

According to the docs, fun.y is deprecated as an argument to stat_summary, which is where the fun.y argument inside your first geom_point call is passed. As Onyambu says, you need to change this to fun. You also need to change the fun = mean_se to fun.data = mean_se inside your direct stat_summary call.

You haven't included your data in the question, so we have to assume that Site is categorical and ratio is numeric, as in the following sample:

set.seed(123)

data <- data.frame(Site  = rep(LETTERS[1:3], each = 100),
                   ratio = runif(300, 0.5, 1) / runif(300, 0.5, 1))

Now the code could be something like:

library(ggplot2)

ggplot(data, aes(x = Site, y = ratio, colour = Site)) +
  geom_point (size = 1, alpha = 0.3,  position = position_jitter(0.1)) +
  stat_summary(fun.data = mean_se, geom = "errorbar", width = 0.2, 
               color = "black") +
  geom_point(stat = "summary", fun = mean, size = 4) +
  theme_minimal(base_size = 16) +
  theme(legend.position = "none")