Logarithmic y-axis Tick Marks in R plot() or ggplot2()

Question

I saw the ideal tick-mark structure for a log="y" plot in this paper, Figure 3b 3c 3d.

It has short, log-spaced minor tick marks without labels, plus long, log-spaced major tick marks with labels.

Does anyone know how to achieve this in R?

Answer 1

Here is a ggplot2 solution:

library(ggplot2)

set.seed(20180407)

df = data.frame(x = seq(from = 1, by = 1, length.out = 20),
                y = 2^(seq(to = 1, by = -1, length.out = 20) + rnorm(20, 0, 0.7)))

ggplot(data = df, aes(x = x, y = y)) +
  geom_line() +
  scale_y_log10() +
  annotation_logticks(sides = "l") 

You can make it look even more than the paper you linked to with some theming:

ggplot(data = df, aes(x = x, y = y)) +
  geom_line(colour = "blue") +
  geom_point(colour = "blue") +
  scale_y_log10() +
  annotation_logticks(sides = "l") +
  theme_minimal() +
  theme(panel.grid = element_blank(), 
        axis.line = element_line(),
        axis.ticks.x = element_line())

Answer 2

In base R just build the axes however you want. Something like this could be a start.

set.seed(5)
d <- data.frame(x=1:100, y=rlnorm(100, meanlog=5, sdlog=3))
with(d, {
  plot(x, y, log="y", yaxt="n")
  y1 <- floor(log10(range(y)))
  pow <- seq(y1[1], y1[2]+1)
  ticksat <- as.vector(sapply(pow, function(p) (1:10)*10^p))
  axis(2, 10^pow)
  axis(2, ticksat, labels=NA, tcl=-0.25, lwd=0, lwd.ticks=1)
})

In lattice, the latticeExtra package has the capability:

library(lattice)
library(latticeExtra)
xyplot(y~x, data=d, scales=list(y=list(log=10)),
       yscale.components=yscale.components.log10ticks)