3.9 Plotting Error Bars (base graphics)

Although the focus is mostly put on other packages in this tutorial, it is worth mentioning at this point that R base graphics also offer opportunities to create plots with error bars. For example, plotCI() from plotrix provides an approach that lets us recreate (at least more or less) our lattice-based Figure 3.26.

library(plotrix)

# increase left-side margin for horizontal tick labels to fit on page
par(mar = c(5, 8, 2, 2), las = 1) # see ?par
plotCI(cuts$fit, as.numeric(cuts$cut), uiw = cuts$se.fit, err = "x", yaxt = "n", 
       pch = 21, pt.bg = "black", xlab = "fit", ylab = "")

# add y-axis title
title(ylab = "cut", line = 6) # see ?title

# add y-axis tick labels
lvl = levels(cuts$cut)
axis(side = 2, at = 1:length(lvl), labels = lvl)

Figure 3.30: A base graphics scatter plot with error bars.

invisible(dev.off()) # if not run, edits to par() persist