#### parallelCoord.R  : parallel coordinate plot

## Jonathan Rougier

## create a parallel coordinate plot where the user can specify the
## colouring of the objects.  There is a similar function in the MASS
## library, parcoord

parallelCoord <- function(X, col = "black", labels = colnames(X),
                          lab.side = c("bottom", "top", "none"), lab.pos = NA) {

  lab.side <- match.arg(lab.side)
  
  X <- as.matrix(X)
  stopifnot(is.numeric(X))
  p <- ncol(X)
  labels # force evaluations of labels

  pp <- tapply(X, col(X), pretty, min.n = 3, eps.correct = 1, simplify = FALSE)
  rng <- sapply(pp, range)
  mins <- rng[1, ]
  scales <- rng[2, ] - rng[1, ]
  X <- (t(X) - mins) / scales # transposed, as used in matlines

  plot.new()
  plot.window(xlim = c(1, p), ylim = c(0, 1))
  for (j in 1:p) {
    axis.labels <- pp[[j]]
    axis(2, at = (axis.labels - mins[j]) / scales[j], labels = axis.labels,
         pos = j, lwd = 2, las = 1, xpd = NA)
  }

  matlines(1:p, X, lty = 1, pch = NA, col = col)

  if (!is.null(labels) && lab.side != "none")
    axis(switch(lab.side, bottom = 1, top = 3), at = 1:p, labels = labels,
         tick = FALSE, pos = lab.pos)

  invisible()
}

## little example using the iris dataset.  This dataset is available
## in R as iris, but I'm loading it from a webpage here to show how
## this is done, and how names and factor levels are assigned

if (FALSE) {

  iris <- read.table("http://www.maths.leeds.ac.uk/~charles/mva-data/iris.dat",header = TRUE)
  names(iris) <- c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width", "Species")
  spnms <- c("setosa", "versicolour", "virginica")
  iris$Species <- factor(spnms[iris$Species], spnms)
  
  parallelCoord(iris[, 1:4], col = as.numeric(iris$Species) + 1)

  ## Can soup this up a bit

  oo <- c(2, 1, 4, 3)

  parallelCoord(iris[, oo],
                col = as.numeric(iris$Species) + 1,
                labels = gsub("\\.", " ", names(iris)[oo]))
  title(main = "Parallel coordinate plot, Fisher's Iris data")
  legend(1, -0.15, paste(levels(iris$Species), "   "), col = seq(along = levels(iris$Species)) + 1,
         lty = 1, lwd = 2, pch = NA, bty = "n", horiz = TRUE, xpd = NA)
}