Adding figure labels (A, B, C, …) in the top left corner of the plotting region

I decided to submit a manuscript using only R with knitr, pandoc and make. Actually, it went quite well. Certainly, revisions of manuscript with complex figures did not require much of manual work once the R code for the figures has been created. The manuscript ended up as a Word file (for the sake of co-authors), looking no different than any other manuscript. However, you can look up precisely how all the figures have been generated and, with a single command, re-create the manuscript (with all figures and supplementary data) after you changed a parameter.

One of the small problems I faced was adding labels to pictures. You know — like A, B, C… in the top right corner of each panel of a composite figure. Here is the output I was striving at:

Doing it proved to be more tedious than I thought at first. By default, you can only plot things in the plotting region, everything else gets clipped — you cannot put arbitrary text anywhere outside the rectangle containing the actual plot:

plot(rnorm(100))
text(-20, 0, "one two three four", cex=2)

This is because the plotting are is the red rectangle on the figure below, and everything outside will not be shown by default:

One can use the function mtext to put text on the margins. However, there is no simple way to say “put the text in the top left corner of the figure”, and the results I was able to get were never perfect. Anyway, to push the label really to the very left of the figure region using mtext, you first need to have the user coordinate of that region (to be able to use option ‘at’). However, if you know these coordinates, it is much easier to achieve the desired effect using text.

First, we need to figure out a few things. To avoid clipping of the region, one needs to change the parameter xpd:

par(xpd=NA)

Then, we need to know where to draw the label. We can get the coordinates of the device (in inches), and then we can translate these to user coordinates with appropriate functions:

plot(rnorm(100))
di <- dev.size("in")
x <- grconvertX(c(0, di[1]), from="in", to="user")
y <- grconvertY(c(0, di[2]), from="in", to="user")

x[1] and y[2] are the coordinates of the top left corner of the device… but not of the figure. Since we might have manipulated the layout, for example, by calling par(mfrow=...) or layout to put multiple plots on the device, and we would like to always label the current plot only (i.e. put the label in the corner of the current figure, not of the whole device), we have to take this into account as well:

fig <- par("fig")
x <- x[1] + (x[2] - x[1]) * fig[1:2]
y <- y[1] + (y[2] - y[1]) * fig[3:4]

Before plotting, we have to adjust this position by half of the text string width and height, respectively:

txt <- "A"
x <- x[1] + strwidth(txt, cex=3) / 2
y <- y[2] - strheight(txt, cex=3) / 2
text(x, y, txt, cex=3)

Looks good! That is exactly what I wanted:

Below you will find an R function that draws a label in one of the three regions — figure (default), plot or device. You specify the position of the label using the labels also used by legend: “topleft”, “bottomright” etc.

First, a few examples how to use it:

Basic use:

par(mfrow=c(2,2))
sapply(LETTERS[1:4], function(x) { 
    plot(rnorm(100))
    fig_label(x, cex=2) 
})

Result:

Plotting at different positions and in different regions:

plot(rnorm(100))
for(i in c("topleft", "topright", "top", 
           "left", "center", "right", 
           "bottomleft", "bottom", "bottomright")) {
    fig_label(i, pos=i, cex=2, col="blue")
    fig_label(i, pos=i, cex=1.5, col="red", region="plot")
}

Result:

All the different regions:

par(mfrow=c(2,2))
sapply(LETTERS[1:4], function(x) { 
    plot(rnorm(100))
    fig_label("figure region", cex=2, col="red") 
    fig_label("plot region", region="plot", cex=2, col="blue")
})
fig_label("device region", cex=2, pos="bottomright", 
  col="darkgreen", region="device")

Result:

And here is the function:

fig_label <- function(text, region="figure", pos="topleft", cex=NULL, ...) {

  region <- match.arg(region, c("figure", "plot", "device"))
  pos <- match.arg(pos, c("topleft", "top", "topright", 
                          "left", "center", "right", 
                          "bottomleft", "bottom", "bottomright"))

  if(region %in% c("figure", "device")) {
    ds <- dev.size("in")
    # xy coordinates of device corners in user coordinates
    x <- grconvertX(c(0, ds[1]), from="in", to="user")
    y <- grconvertY(c(0, ds[2]), from="in", to="user")

    # fragment of the device we use to plot
    if(region == "figure") {
      # account for the fragment of the device that 
      # the figure is using
      fig <- par("fig")
      dx <- (x[2] - x[1])
      dy <- (y[2] - y[1])
      x <- x[1] + dx * fig[1:2]
      y <- y[1] + dy * fig[3:4]
    } 
  }

  # much simpler if in plotting region
  if(region == "plot") {
    u <- par("usr")
    x <- u[1:2]
    y <- u[3:4]
  }

  sw <- strwidth(text, cex=cex) * 60/100
  sh <- strheight(text, cex=cex) * 60/100

  x1 <- switch(pos,
    topleft     =x[1] + sw, 
    left        =x[1] + sw,
    bottomleft  =x[1] + sw,
    top         =(x[1] + x[2])/2,
    center      =(x[1] + x[2])/2,
    bottom      =(x[1] + x[2])/2,
    topright    =x[2] - sw,
    right       =x[2] - sw,
    bottomright =x[2] - sw)

  y1 <- switch(pos,
    topleft     =y[2] - sh,
    top         =y[2] - sh,
    topright    =y[2] - sh,
    left        =(y[1] + y[2])/2,
    center      =(y[1] + y[2])/2,
    right       =(y[1] + y[2])/2,
    bottomleft  =y[1] + sh,
    bottom      =y[1] + sh,
    bottomright =y[1] + sh)

  old.par <- par(xpd=NA)
  on.exit(par(old.par))

  text(x1, y1, text, cex=cex, ...)
  return(invisible(c(x,y)))
}
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10 thoughts on “Adding figure labels (A, B, C, …) in the top left corner of the plotting region

  1. Could you please give me an example in details to show the application of the fig_label <- function, thanks a lot.

    • Nice one. However, pagenum cannot create labels in the figure area, if I am not mistaken — it only draws on the device region (essentially by overlaying a grid viewport). Thus, the first example above will not work — you cannot put four plots on a page (using par(mfrow)) and label each of them separately. Well, you could manually calculate the position of the text in respect to the device region; but then, change the layout and you need to change all your labeling commands. So in my case, I prefer my own solution.

  2. Could you teach me how to use tmod package in the analysis of Arabidopsis thaliana microarray data. Thank you very much!

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