Rotate Classification Tree Terminal Barplot axis - R

Question

I have a classification tree analyzed using ctree() was wondering how can one rotate the terminal nodes so that the axes are vertical?

library(party)
data(iris)
attach(iris)
plot(ctree(Species ~ Sepal.Length + Sepel.Width 
     + Petal.Length + Petal.Width, data = iris))

Answer 1

Here is how I would go about it. Not the shortest answer, but I wanted to be as thorough as possible.

Since we are plotting your tree, it's probably a good idea to look at the documentation for the appropriate plotting function:

library(party)
data(iris)
attach(iris)

ctree <- ctree(Species ~ Sepal.Length + Sepal.Width 
               + Petal.Length + Petal.Width, data = iris)

# getting ctree's class

> class(ctree)
[1] "BinaryTree"
attr(,"package")
[1] "party"

Looking at ?'plot.BinaryTree' we see the following description of the terminal_panel argument:

an optional panel function of the form function(node) plotting the terminal nodes. Alternatively, a panel generating function of class "grapcon_generator" that is called with arguments x and tp_args to set up a panel function. By default, an appropriate panel function is chosen depending on the scale of the dependent variable.

Further down in the documentation is a link to ?node_barplot. This is what I guessed was being used as a default, and calling the following proved the guess right:

plot(ctree, terminal_panel = node_barplot(ctree))

(The output is the same as your original graph).

Unfortunately, there's no horizontal or horiz parameters for node_barplot. Looking at the code for this function, by simply typing node_barplot at the prompt, reveals that the graphs are drawn "by hand" using viewports. Unfortunately, the only way I could find to proceed was to edit this function. I tried to make my changes as obvious as possible:

# Note inclusion of horiz = FALSE
alt_node_barplot <- function (ctreeobj, col = "black", fill = NULL, beside = NULL, 
    ymax = NULL, ylines = NULL, widths = 1, gap = NULL, reverse = NULL, 
    id = TRUE, horiz = FALSE)
{
    getMaxPred <- function(x) {
        mp <- max(x$prediction)
        mpl <- ifelse(x$terminal, 0, getMaxPred(x$left))
        mpr <- ifelse(x$terminal, 0, getMaxPred(x$right))
        return(max(c(mp, mpl, mpr)))
    }
    y <- response(ctreeobj)[[1]]
    if (is.factor(y) || class(y) == "was_ordered") {
        ylevels <- levels(y)
        if (is.null(beside)) 
            beside <- if (length(ylevels) < 3) 
                FALSE
            else TRUE
        if (is.null(ymax)) 
            ymax <- if (beside) 
                1.1
            else 1
        if (is.null(gap)) 
            gap <- if (beside) 
                0.1
            else 0
    }
    else {
        if (is.null(beside)) 
            beside <- FALSE
        if (is.null(ymax)) 
            ymax <- getMaxPred(ctreeobj@tree) * 1.1
        ylevels <- seq(along = ctreeobj@tree$prediction)
        if (length(ylevels) < 2) 
            ylevels <- ""
        if (is.null(gap)) 
            gap <- 1
    }
    if (is.null(reverse)) 
        reverse <- !beside
    if (is.null(fill)) 
        fill <- gray.colors(length(ylevels))
    if (is.null(ylines)) 
        ylines <- if (beside) 
            c(3, 2)
        else c(1.5, 2.5)
    # My edit do not work if beside is not true
    #################################################
    if(!beside) horiz = FALSE
    #################################################

    rval <- function(node) {
        pred <- node$prediction
        if (reverse) {
            pred <- rev(pred)
            ylevels <- rev(ylevels)
        }
        np <- length(pred)
        nc <- if (beside) 
            np
        else 1
        fill <- rep(fill, length.out = np)
        widths <- rep(widths, length.out = nc)
        col <- rep(col, length.out = nc)
        ylines <- rep(ylines, length.out = 2)
        gap <- gap * sum(widths)
        #######################################################
        if (!horiz){
            yscale <- c(0, ymax)
            xscale <- c(0, sum(widths) + (nc + 1) * gap)
        } else {
            xscale <- c(0, ymax)
            yscale <- c(0, sum(widths) + (nc + 1) * gap)
        }                    
        #######################################################
        top_vp <- viewport(layout = grid.layout(nrow = 2, ncol = 3, 
            widths = unit(c(ylines[1], 1, ylines[2]), c("lines", 
                "null", "lines")), heights = unit(c(1, 1), c("lines", 
                "null"))), width = unit(1, "npc"), height = unit(1, 
            "npc") - unit(2, "lines"), name = paste("node_barplot", 
            node$nodeID, sep = ""))
        pushViewport(top_vp)
        grid.rect(gp = gpar(fill = "white", col = 0))
        top <- viewport(layout.pos.col = 2, layout.pos.row = 1)
        pushViewport(top)
        mainlab <- paste(ifelse(id, paste("Node", node$nodeID, 
            "(n = "), "n = "), sum(node$weights), ifelse(id, 
            ")", ""), sep = "")
        grid.text(mainlab)
        popViewport()
        plot <- viewport(layout.pos.col = 2, layout.pos.row = 2, 
            xscale = xscale, yscale = yscale, name = paste("node_barplot", 
                node$nodeID, "plot", sep = ""))
        pushViewport(plot)
        if (beside) {
            #############################################################
            if(!horiz){
                xcenter <- cumsum(widths + gap) - widths/2
                for (i in 1:np) {
                    grid.rect(x = xcenter[i], y = 0, height = pred[i], 
                      width = widths[i], just = c("center", "bottom"), 
                      default.units = "native", gp = gpar(col = col[i], 
                        fill = fill[i]))
                }
                if (length(xcenter) > 1) 
                    grid.xaxis(at = xcenter, label = FALSE)
                grid.text(ylevels, x = xcenter, y = unit(-1, "lines"), 
                    just = c("center", "top"), default.units = "native", 
                    check.overlap = TRUE)
                grid.yaxis()
            } else {
                ycenter <- cumsum(widths + gap) - widths/2
                for (i in 1:np) {
                    grid.rect(y = ycenter[i], x = 0, width = pred[i], 
                    height = widths[i], just = c("left", "center"), 
                    default.units = "native", gp = gpar(col = col[i], 
                     fill = fill[i]))
                }
                if (length(ycenter) > 1) 
                    grid.yaxis(at = ycenter, label = FALSE)
                        grid.text(ylevels, y = ycenter, x = unit(-1, "lines"), 
                        just = c("right", "center"), default.units = "native", 
                         check.overlap = TRUE)
                grid.xaxis()
            }
        #############################################################
        }
        else {
            ycenter <- cumsum(pred) - pred
            for (i in 1:np) {
                grid.rect(x = xscale[2]/2, y = ycenter[i], height = min(pred[i], 
                  ymax - ycenter[i]), width = widths[1], just = c("center", 
                  "bottom"), default.units = "native", gp = gpar(col = col[i], 
                  fill = fill[i]))
            }
            if (np > 1) {
                grid.text(ylevels[1], x = unit(-1, "lines"), 
                  y = 0, just = c("left", "center"), rot = 90, 
                  default.units = "native", check.overlap = TRUE)
                grid.text(ylevels[np], x = unit(-1, "lines"), 
                  y = ymax, just = c("right", "center"), rot = 90, 
                  default.units = "native", check.overlap = TRUE)
            }
            if (np > 2) {
                grid.text(ylevels[-c(1, np)], x = unit(-1, "lines"), 
                  y = ycenter[-c(1, np)], just = "center", rot = 90, 
                  default.units = "native", check.overlap = TRUE)
            }
            grid.yaxis(main = FALSE)
        }
        grid.rect(gp = gpar(fill = "transparent"))
        upViewport(2)
    }
    return(rval)
}

And now we can test it!

plot(ctree, terminal_panel = alt_node_barplot(ctree, horiz = TRUE))

Here's the output:

Just a few points:

• I admit that this may not THE solution to your problem. It is merely a way of going about solving this type of problem, when easier options do not exist.

• Don't trust the function I gave above completely. As you can see, the beside parameter disables the horiz parameter automatically (my first edit) since I did not alter the sections of code that deal with beside being true. If you want it to work in this case, you'll have to make those edits yourself - take a look at ?viewport and ?grid.rect to get started. I'm pretty sure the reverse function is also broken, but haven't tested anything. Apologies to the original authors of the function if I butchered it a bit, this was merely meant to be a demonstration.

I hope this helped a bit. Good luck with any further edits you need to make!