Displaying minor logarithmic ticks in x-axis in R - r

Question

I have a normal distribution plot and a histogram plot with x axis in log scale displaying 0, 10^0, 10^1 ... I want to include minor ticks between the major ones. Actually I was able to change the major ticks format from 1, 2, 3 and so on to 10^0, 10^1, 10^2, 10^3 using the solution given to me in my previous question. I used the following code for the major ticks :
major.ticks <- axTicks(1)
labels <- sapply(major.ticks,function(i)
as.expression(bquote(10^ .(i)))
)
axis(1,at=major.ticks,labels=labels)
Can this be edited to just mark the minor ticks without labeling them?

Answer 1

There is a function minor.tick in the package Hmisc, but that one deals poorly with logarithmical scales. I use the following function for getting minor ticks that follow the logarithmical scale. ax is the axis you use it on (same as for the function axis), n is the number of minor ticks (default to 9), t.ratio is the ratio between the major and the minor ticks, and with ... you can pass extra parameters to axis
edit : Nice idea in the comments, so I edited my function. There are two extra parameters, mn and mx for the minimum and the maximum on the logarithmic scale (mn=0 thus means the minimum is 10^0 or 1 !)
The function:
minor.ticks.axis <- function(ax,n,t.ratio=0.5,mn,mx,...){
lims <- par("usr")
if(ax %in%c(1,3)) lims <- lims[1:2] else lims[3:4]
major.ticks <- pretty(lims,n=5)
if(missing(mn)) mn <- min(major.ticks)
if(missing(mx)) mx <- max(major.ticks)
major.ticks <- major.ticks[major.ticks >= mn & major.ticks <= mx]
labels <- sapply(major.ticks,function(i)
as.expression(bquote(10^ .(i)))
)
axis(ax,at=major.ticks,labels=labels,...)
n <- n+2
minors <- log10(pretty(10^major.ticks[1:2],n))-major.ticks[1]
minors <- minors[-c(1,n)]
minor.ticks = c(outer(minors,major.ticks,`+`))
minor.ticks <- minor.ticks[minor.ticks > mn & minor.ticks < mx]
axis(ax,at=minor.ticks,tcl=par("tcl")*t.ratio,labels=FALSE)
}
This can be applied as follows :
x <- 10^(0:8)
y <- 1:9
plot(log10(x),y,xaxt="n",xlab="x",xlim=c(0,9))
minor.ticks.axis(1,9,mn=0,mx=8)
Gives :

Answer 2

Here is a simple function to to this:
log10.axis <- function(side, at, ...) {
at.minor <- log10(outer(1:9, 10^(min(at):max(at))))
lab <- sapply(at, function(i) as.expression(bquote(10^ .(i))))
axis(side=side, at=at.minor, labels=NA, tcl=par("tcl")*0.5, ...)
axis(side=side, at=at, labels=lab, ...)
}
Here is an example:
x <- exp(rnorm(200, 5))
hist(log(x), 20, xaxt="n", xlim=c(0, 8))
log10.axis(1, at=seq(0, 8, 2))
Gives:

Answer 3

Try magaxis in package magicaxis.

Answer 4

In ggplot2, we can use annotation_logticks together with scales::trans_breaks and scales::trans_format. Below is an example taken from the link above.
library(ggplot2)
a <- ggplot(msleep, aes(bodywt, brainwt)) +
geom_point(na.rm = TRUE) +
scale_x_log10(
breaks = scales::trans_breaks("log10", function(x) 10^x),
labels = scales::trans_format("log10", scales::math_format(10^.x))
) +
scale_y_log10(
breaks = scales::trans_breaks("log10", function(x) 10^x),
labels = scales::trans_format("log10", scales::math_format(10^.x))
) +
theme_bw()
a + annotation_logticks() # Default: log ticks on bottom and left

Answer 5

There is the minorAxis function in the StratigrapheR package, that can be used for any kind of minor ticks. It can be used with the seq_log function to make logarithmic ticks:
library(StratigrapheR)
x <- exp(rnorm(200, 5))
hist(log10(x), 20, xaxt="n", xlim=c(0, 4), xlab = "x", main = "Logarithmic Histogram of x")
ticks <- seq_log(10^0,10^4, divide = T)
lab <- sapply(0:4, function(i) as.expression(bquote(10^ .(i))))
minorAxis(1, at.maj = log10(ticks[[1]]), at.min = log10(ticks[[2]]), labels = lab)
Gives:

Answer 6

Use "" for the labels of the minor ticks.

Answer 7

There was a small error,
lims<-lims[3:4] was missing
minor.ticks.axis <- function(ax,n,t.ratio=0.5,mn,mx,...){
lims <- par("usr")
if(ax %in%c(1,3)) lims <- lims[1:2] else lims <- lims[3:4]
major.ticks <- pretty(lims,n=5)
if(missing(mn)) mn <- min(major.ticks)
if(missing(mx)) mx <- max(major.ticks)
major.ticks <- major.ticks[major.ticks >= mn & major.ticks <= mx]
labels <- sapply(major.ticks,function(i)
as.expression(bquote(10^ .(i)))
)
axis(ax,at=major.ticks,labels=labels,...)
n <- n+2
minors <- log10(pretty(10^major.ticks[1:2],n))-major.ticks[1]
minors <- minors[-c(1,n)]
minor.ticks = c(outer(minors,major.ticks,`+`))
minor.ticks <- minor.ticks[minor.ticks > mn & minor.ticks < mx]
axis(ax,at=minor.ticks,tcl=par("tcl")*t.ratio,labels=FALSE)
}

Answer 8

The x axis labels in the first plot on this page is in error.
The minor ticks are not properly distributed.