Labelling logarithmic scale display in R

Question

While plotting histogarm, scatterplots and other plots with axes scaled to logarithmic scale in R, how is it possible to use labels such as 10^-1 10^0 10^1 10^2 10^3 and so on instead of the axes showing just -1, 0, 1, 2, 3 etc. What parameters should be added to the commands such as hist(), plot() etc?

Ity

ggplot2 does this automatically if you do the log transformation within ggplot2. See the examples towards the bottom of this page: had.co.nz/ggplot2/geom_boxplot.html – Vaasta

Thanks, this helped me out. Also, I found something very useful here as well r.789695.n4.nabble.com/log-y-axis-of-histogram-td2399498.html – Ity

Answer 1

Apart from the solution of ggplot2 (see gsk3's comment), I would like to add that this happens automatically in plot() as well when using the correct arguments, eg :

x <- 1:10
y <- exp(1:10)
plot(x,y,log="y")

You can use the parameter log="x" for the X axis, or log="xy" for both.

If you want to format the numbers, or you have the data in log format, you can do a workaround using axis(). Some interesting functions :

• axTicks(x) gives you the location of the ticks on the X-axis (x=1) or Y-axis (x=2)
• bquote() converts expressions to language, but can replace a variable with its value. More information on bquote() in the question Latex and variables in plot label in R? .
• as.expression() makes the language object coming from bquote() an expression. This allows axis() to do the formatting as explained in ?plotmath. It can't do so with language objects.

An example for nice formatting :

x <- y <- 1:10
plot(x,y,yaxt="n")
aty <- axTicks(2)
labels <- sapply(aty,function(i)
            as.expression(bquote(10^ .(i)))
          )
axis(2,at=aty,labels=labels)

Which gives

Unequaled

Thanks, this is quite useful and I think its a general solution. Worked for me just fine – Ity

Answer 2

Here is a different way to draw this type of axis:

plot(NA, xlim=c(0,10), ylim=c(1, 10^4), xlab="x", ylab="y", log="y", yaxt="n")
at.y <- outer(1:9, 10^(0:4))
lab.y <- ifelse(log10(at.y) %% 1 == 0, at.y, NA)
axis(2, at=at.y, labels=lab.y, las=1)

EDIT: This is also solved in latticeExtra with scale.components

Charla

Answer 3

In ggplot2 you just can add a

... + 
scale_x_log10() + 
scale_y_log10(limits = c(1e-4,1), breaks=c(1e-4,1e-3,1e-2,0.1,1)) + ...

to scale your axis, Label them and add custom breaks.

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