From the documentation of ggplot2::scale_size_area(), I read that

scale_size_area() ensures that a value of 0 is mapped to a size of 0.

However, in this simple example, I still see points where there zeros are. Is this a bug or am I interpreting this wrong?

library(ggplot2)

table(1:3, 1:3) |>
  as.data.frame() |>
  ggplot() +
  aes(x=Var1, y=Var2, size=Freq) +
  geom_point() +
  scale_size_area()

Data

table(1:3, 1:3) |>
  as.data.frame() |>
print()

  Var1 Var2 Freq
1    1    1    1
2    2    1    0
3    3    1    0
4    1    2    0
5    2    2    1
6    3    2    0
7    1    3    0
8    2    3    0
9    3    3    1

Result

>Solution :

I think the issue here is that ggplot2 is drawing a point with zero area but non-zero stroke, so it is effectively drawing a tiny circle around nothing.

The shapes in geom_point() typically have both an outline and a fill; shapes 19-25 give you separate control of these, but they all have a stroke parameter to control how heavy the outline appears (if at all).

Compare

ggplot(data.frame(a = 0:5), aes(a, a, size = a)) +
  geom_point() +
  scale_size_area()

ggplot(data.frame(a = 0:5), aes(a, a, size = a)) +
  geom_point(stroke = 0) +
  scale_size_area()