scale_y_continuous and limits not working

Question

[Camila Martínez]

Hello, I don't know how to make a plot and indicate the limits for the y axis. I tried with:

ggplot() +
  geom_step(data = Pcal.msmc2, aes(x = time_scaled, y = Ne_scaled), color = "red") +
  ggtitle(my_title2, subtitle=my_subtitle2) +
  xlab("Years ago") +
  ylab("Number of individuals (Ne)") +
  annotation_logticks(sides = "bl") +
  scale_x_continuous(trans='log10', breaks=trans_breaks('log10', function(x) 10^x),
                     labels=trans_format('log10', math_format(10^.x))) +
  scale_y_continuous(trans='log10', breaks=trans_breaks('log10', function(x) 10^x),
                     labels=trans_format('log10', math_format(10^.x))) +
  expand_limits(x = c(100, 100000), y = c(0,1000))

But it didn't work, I got this image:

I want the plot only to show from 0 to 10000 on the y axis. How can I do that?

[Jesse]

You can't include 0 on a log scale: log10(0) = -infinity (or rather, the limit as you approach 0 is -infinity... you get the idea).

Someone else will probably have a better answer about what you should do, though... use a broken y axis and special handling for zeros? use two panels? rethink using a log scale at all?

Answer 1

[isd1989]

You could try:

+ ylim(c(0, 10000))

However, this effectively truncates the plot, so it will not be representative of the trends in your data.