How to suppress zeroes when using geom_histogram with scale_y_log10

Question

I'm trying to plot a histogram with a log y scale using ggplot, geom_histogram and scale_y_log10. Most regions (those with counts greater than 1) appear correct: the background is transparent and the histogram bars are filled with the default color black. But at counts of 1, the colors are inverted: black background and transparent fill of the histogram bars. This code (below) generates the example in the graph.

Can anyone explain the cause of this? I understand the problems that come with log scales but I can't seem to find a solution to this. I'm hoping there's a easy fix, or that I overlooked something.

set.seed(1)
df <- data.frame(E=sample(runif(100), 20, TRUE))
ggplot(df,aes(E)) + geom_histogram(binwidth=0.1) + scale_y_log10(limits=c(0.1,100)) + xlim(0,1)

Answer 1

You can add drop=TRUE to the geom_histogram call to drop bins with zero counts (see ?stat_bin for details):

set.seed(1)
df <- data.frame(E=sample(runif(100), 20, TRUE))
ggplot(df,aes(E)) + 
  geom_histogram(binwidth=0.1, drop=TRUE) + 
  scale_y_log10(limits=c(0.1,100)) + 
  xlim(0,1)

EDIT: Since the scale starts at 1, it is impossible to display a bar of height 1. As mentioned in this answer, you can choose to start at different levels, but it may become misleading. Here's the code for this anyway:

require(scales)
mylog_trans <- 
function (base = exp(1), from = 0) 
{
  trans <- function(x) log(x, base) - from
  inv <- function(x) base^(x + from)
  trans_new("mylog", trans, inv, log_breaks(base = base), domain = c(base^from, Inf))
}

ggplot(df,aes(E)) + 
  geom_histogram(binwidth=0.1, drop=TRUE) + 
  scale_y_continuous(trans = mylog_trans(base=10, from=-1), limits=c(0.1,100)) +
  xlim(0,1)