Plot negative on logarithmic axis in ggplot

Question

I followed this example and it works great for my data (https://r-graphics.org/recipe-axes-axis-log). Except I am also trying to add standard deviations and for one of the variables, the standard deviation is bigger than the mean. The figure just plots the top error bar but not the bottom. How can I add the error bar for Sample 5?

 Sample <- c(1, 2, 3, 4, 5)
 Fe <- c(418, 592, 228, 351, 23880)
 sd <- c(269, 538, 187, 236, 36577)

 df <- data.frame(Sample, Fe, sd)
 df

 (plot <- ggplot(df, aes(x = Sample, y = Fe, ymin = Fe - sd, ymax = Fe + sd)) + theme_bw() +
  geom_point(size=3, stat = "identity") + 
 geom_errorbar(aes(width = 0.1), stat = "identity") +
 scale_y_continuous(trans = log10_trans(),
                   breaks = trans_breaks("log10", function(x) 10^x),
                   labels = trans_format("log10", math_format(10^.x))) +
  annotation_logticks(sides = "l"))

Answer 1

You can pmax(0, .) it:

library(ggplot2)
library(scales)

ggplot(df, aes(x = Sample, y = Fe, ymin = pmax(0, Fe - sd), ymax = Fe + sd)) +
  theme_bw() +
  geom_point(size=3, stat = "identity") + 
  geom_errorbar(aes(width = 0.1), stat = "identity") +
  scale_y_continuous(trans = log10_trans(),
                     breaks = trans_breaks("log10", function(x) 10^x),
                     labels = trans_format("log10", math_format(10^.x))) +
  annotation_logticks(sides = "l")

Or you can use a smaller number and see the lower end of that error bar, though that might suggest a present value that isn't ...

ggplot(df, aes(x = Sample, y = Fe, ymin = pmax(1, Fe - sd), ymax = Fe + sd)) +
  theme_bw() +
  geom_point(size=3, stat = "identity") + 
  geom_errorbar(aes(width = 0.1), stat = "identity") +
  scale_y_continuous(trans = log10_trans(),
                     breaks = trans_breaks("log10", function(x) 10^x),
                     labels = trans_format("log10", math_format(10^.x))) +
  annotation_logticks(sides = "l")

Using much smaller values will continue to squish the other errors a little tighter as the y-axis tries to adjust.