Question

By default, pairs() puts the axes on all sides of the plot, alternating between the sides. However, I’m putting the correlation between the data sets in the upper triangle, so I want to adjust the axis position like this:

Which parameters do I need to set?

Answer 1

You could custumize the pairs function.
If you look at the code, the axis are drawn within 2 nested for-loops (one for rows and one for colums):

Here is a custimized pairs function, were I just edited the sides in localAxis() within these for-loops:

pairs2 <- 
  function (x, labels, panel = points, ..., lower.panel = panel, 
            upper.panel = panel, diag.panel = NULL, text.panel = textPanel, 
            label.pos = 0.5 + has.diag/3, cex.labels = NULL, font.labels = 1, 
            row1attop = TRUE, gap = 1) 
  {
    textPanel <- function(x = 0.5, y = 0.5, txt, cex, font) text(x, 
                                                                 y, txt, cex = cex, font = font)
    localAxis <- function(side, x, y, xpd, bg, col = NULL, main, 
                          oma, ...) {
      if (side%%2 == 1) 
        Axis(x, side = side, xpd = NA, ...)
      else Axis(y, side = side, xpd = NA, ...)
    }
    localPlot <- function(..., main, oma, font.main, cex.main) plot(...)
    localLowerPanel <- function(..., main, oma, font.main, cex.main) lower.panel(...)
    localUpperPanel <- function(..., main, oma, font.main, cex.main) upper.panel(...)
    localDiagPanel <- function(..., main, oma, font.main, cex.main) diag.panel(...)
    dots <- list(...)
    nmdots <- names(dots)
    if (!is.matrix(x)) {
      x <- as.data.frame(x)
      for (i in seq_along(names(x))) {
        if (is.factor(x[[i]]) || is.logical(x[[i]])) 
          x[[i]] <- as.numeric(x[[i]])
        if (!is.numeric(unclass(x[[i]]))) 
          stop("non-numeric argument to 'pairs'")
      }
    }
    else if (!is.numeric(x)) 
      stop("non-numeric argument to 'pairs'")
    panel <- match.fun(panel)
    if ((has.lower <- !is.null(lower.panel)) && !missing(lower.panel)) 
      lower.panel <- match.fun(lower.panel)
    if ((has.upper <- !is.null(upper.panel)) && !missing(upper.panel)) 
      upper.panel <- match.fun(upper.panel)
    if ((has.diag <- !is.null(diag.panel)) && !missing(diag.panel)) 
      diag.panel <- match.fun(diag.panel)
    if (row1attop) {
      tmp <- lower.panel
      lower.panel <- upper.panel
      upper.panel <- tmp
      tmp <- has.lower
      has.lower <- has.upper
      has.upper <- tmp
    }
    nc <- ncol(x)
    if (nc < 2) 
      stop("only one column in the argument to 'pairs'")
    has.labs <- TRUE
    if (missing(labels)) {
      labels <- colnames(x)
      if (is.null(labels)) 
        labels <- paste("var", 1L:nc)
    }
    else if (is.null(labels)) 
      has.labs <- FALSE
    oma <- if ("oma" %in% nmdots) 
      dots$oma
    else NULL
    main <- if ("main" %in% nmdots) 
      dots$main
    else NULL
    if (is.null(oma)) {
      oma <- c(4, 4, 4, 4)
      if (!is.null(main)) 
        oma[3L] <- 6
    }
    opar <- par(mfrow = c(nc, nc), mar = rep.int(gap/2, 4), oma = oma)
    on.exit(par(opar))
    dev.hold()
    on.exit(dev.flush(), add = TRUE)
    for (i in if (row1attop) 
      1L:nc
         else nc:1L) for (j in 1L:nc) {
           localPlot(x[, j], x[, i], xlab = "", ylab = "", axes = FALSE, 
                     type = "n", ...)
           if (i == j || (i < j && has.lower) || (i > j && has.upper)) {
             box()
             # edited here...
             #           if (i == 1 && (!(j%%2) || !has.upper || !has.lower)) 
             #           localAxis(1 + 2 * row1attop, x[, j], x[, i], 
             #                       ...)
             # draw x-axis
             if (i == nc & j != nc) 
               localAxis(1, x[, j], x[, i], 
                         ...)
             # draw y-axis
             if (j == 1 & i != 1) 
               localAxis(2, x[, j], x[, i], ...)
             #           if (j == nc && (i%%2 || !has.upper || !has.lower)) 
             #             localAxis(4, x[, j], x[, i], ...)
             mfg <- par("mfg")
             if (i == j) {
               if (has.diag) 
                 localDiagPanel(as.vector(x[, i]), ...)
               if (has.labs) {
                 par(usr = c(0, 1, 0, 1))
                 if (is.null(cex.labels)) {
                   l.wid <- strwidth(labels, "user")
                   cex.labels <- max(0.8, min(2, 0.9/max(l.wid)))
                 }
                 text.panel(0.5, label.pos, labels[i], cex = cex.labels, 
                            font = font.labels)
               }
             }
             else if (i < j) 
               localLowerPanel(as.vector(x[, j]), as.vector(x[, 
                                                              i]), ...)
             else localUpperPanel(as.vector(x[, j]), as.vector(x[, 
                                                                 i]), ...)
             if (any(par("mfg") != mfg)) 
               stop("the 'panel' function made a new plot")
           }
           else par(new = FALSE)
         }
    if (!is.null(main)) {
      font.main <- if ("font.main" %in% nmdots) 
        dots$font.main
      else par("font.main")
      cex.main <- if ("cex.main" %in% nmdots) 
        dots$cex.main
      else par("cex.main")
      mtext(main, 3, 3, TRUE, 0.5, cex = cex.main, font = font.main)
    }
    invisible(NULL)
  }
data(iris)
pairs2(iris[1:4], main = "Anderson's Iris Data -- 3 species",pch = 21, bg = c("red", "green3", "blue")[unclass(iris$Species)])

Edit
Changed pairs2(), so that the axis appear only on the lower diagonal.