16 Plots from Scratch

In this chapter we describe one of my favorite graphing approaches to create what I like to call plots from scratch. That is, making a graph in a way that we have full control of all the nitty-gritty details of a plot.

16.1 Making a graphic from scratch

In addition to using plot(), possibly calling one or more low-level functions, you should know that it is also possible to create a plot from scratch. Although this procedure is less documented, it is extremely flexible and powerful. The general recipe to create a plot with this approach is as follows:

call plot.new() to start a new plot frame
call plot.window() to define coordinates
then call low-level functions:
typical options involve axis()
then title() (title, subtitle)
after that call other function: e.g. points(), lines(), etc

plot.new()
plot.window(xlim = c(0, 10), ylim = c(-2, 4), xaxs = "i")
axis(side = 1, col.axis = "grey30")
axis(side = 2, col.axis = "grey30", las = 1)
title(main = "Main Title",
      col.main = "tomato",
      sub = "Plot Subtitle",
      col.sub = "orange",
      xlab = "x-axis", 
      ylab = "y-axis",
      col.lab = "blue", 
      font.lab = 3)
box("figure", col = "grey90")

Here’s another example:

set.seed(5)
x <- rnorm(200)
y <- x + rnorm(200)

plot.new()
plot.window(xlim = c(-4.5, 4.5), xaxs = "i", 
            ylim = c(-4.5, 4.5), yaxs = "i")
z <- lm(y ~ x)
abline(h = -4:4, v = -4:4, col = "lightgrey")
abline(a = coef(z)[1], b = coef(z)[2], lwd = 2, col = "red")
points(x, y)
axis(side = 1)
axis(side = 2, las = 1)
box()
title(main = "A Fitted Regression Line")

16.1.1 How does it work

You start a new plot with plot.new()

plot.new() opens a new (empty) plot frame
plot.new() chooses a default plotting region

After starting with plot.new(), use plot.window() to set up the coordinate system for the plotting frame

# axis limits (0,1)x(0,1)
plot.window(xlim = c(0, 1), ylim = c(0, 1))

By default plot.window() produces axis limits which are expanded by 6% over those actually specified.

The default limits expansion can be turned-off by specifying xaxs = "i" and/or yaxs = "i"

plot.window(xlim, ylim, xaxs = "i")

Aspect Ratio Control

Another important argument is asp, which allows us to specify the aspect ratio

plot.window(xlim, ylim, xaxs = "i", asp = 1)

asp = 1 means that unit steps in the x and y directions produce equal distances in the x and y directions on the plot.

(Important for avoiding distortion of circles that look like ellipses)

Drawing Axes

The axis() function can be used to draw axes at any of the four sides of a plot.

side = 1 below the graph
side = 2 to the left of the graph
side = 3 above the graph
side = 4 to the right of the graph

Axes can be customized via several arguments (see ?axis)

location of tick-marks
labels of axis
colors
sizes
text fonts
text orientation

Plot Annotatiosn

The function title() allows us to include labels in the margins

main main title above the graph
sub subtitle below the graph
xlab label for the x-axis
ylab label for the y-axis

The annotations can be customized with additional arguments for the fonts, colors, and size (expansion)

font.main, col.main, cex.main
font.sub, col.sub, cex.sub
font.lab, col.lab, cex.lab

16.1.2 Drawing Arrows

plot.new()
plot.window(xlim = c(0, 1), ylim = c(0, 1))
arrows(0.05, 0.075, 0.45, 0.9, code = 1)
arrows(0.55, 0.9, 0.95, 0.075, code = 2)
arrows(0.1, 0, 0.9, 0, code = 3)
text(0.5, 1, "A", cex = 1.5)
text(0, 0, "B", cex = 1.5)
text(1, 0, "C", cex = 1.5)

16.1.3 Drawing Rectangles

Rectangles can be drawn with the function:

rect(x0, y0, x1, y1, col = str, border = str)

x0, y0, x1, y1 give the coordinates of diagonally opposite corners of the rectangles/
col specifies the color of the interior.
border specifies the color of the border/

# barplot "manually" constructed
plot.new()
plot.window(xlim = c(0, 5), ylim = c(0, 10))
rect(0:4, 0, 1:5, c(7, 8, 4, 3), 
     col = "turquoise",
     border = "white")
axis(1)
axis(2, las = 1)