Displaying minor logarithmic ticks in x-axis in R

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 t开发者_运维问答he 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?

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 :

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:

Try magaxis in package magicaxis.

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

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:

Use "" for the labels of the minor ticks.

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)
}

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