How to suppress zeroes when using geom_histogram with scale_y_log10
Joseph Kreke
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)
shadow
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)
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