Histogram with Logarithmic Scale and custom breaks

user_101927 0
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I'm trying to generate a histogram in R with a logarithmic scale for y. Currently I do:

hist(mydata$V3, breaks=c(0,1,2,3,4,5,25))

This gives me a histogram, but the density between 0 to 1 is so great (about a million values difference) that you can barely make out any of the other bars.

Then I've tried doing:

mydata_hist <- hist(mydata$V3, breaks=c(0,1,2,3,4,5,25), plot=FALSE)
plot(rpd_hist$counts, log="xy", pch=20, col="blue")

It gives me sorta what I want, but the bottom shows me the values 1-6 rather than 0, 1, 2, 3, 4, 5, 25. It's also showing the data as points rather than bars. barplot works but then I don't get any bottom axis.

histogram logarithm r
7 Answers

A histogram is a poor-man's density estimate. Note that in your call to hist() using default arguments, you get frequencies not probabilities -- add ,prob=TRUE to the call if you want probabilities.

As for the log axis problem, don't use 'x' if you do not want the x-axis transformed:

plot(mydata_hist$count, log="y", type='h', lwd=10, lend=2)

gets you bars on a log-y scale -- the look-and-feel is still a little different but can probably be tweaked.

Lastly, you can also do hist(log(x), ...) to get a histogram of the log of your data.

user_1433050

Another option would be to use the package ggplot2.

ggplot(mydata, aes(x = V3)) + geom_histogram() + scale_x_log10()
user_1426510

It's not entirely clear from your question whether you want a logged x-axis or a logged y-axis. A logged y-axis is not a good idea when using bars because they are anchored at zero, which becomes negative infinity when logged. You can work around this problem by using a frequency polygon or density plot.

hadley_166320

Here's a pretty ggplot2 solution:

library(ggplot2)
library(scales)  # makes pretty labels on the x-axis

breaks=c(0,1,2,3,4,5,25)

ggplot(mydata,aes(x = V3)) + 
  geom_histogram(breaks = log10(breaks)) + 
  scale_x_log10(
    breaks = breaks,
    labels = scales::trans_format("log10", scales::math_format(10^.x))
  )

Note that to set the breaks in geom_histogram, they had to be transformed to work with scale_x_log10

user_81957670
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