Basic Graphics

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Lecture 5

Arun Kaushik
Dept. of Statistics, BHU
R Graphics High-Level Low-Level Saving Graphs

Outline
1. Overview of R Graphics
2. High-Level Plot Functions
3. Low-Level Plot Functions
4. Saving Graphs

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R Graphics High-Level Low-Level Saving Graphs

R Graphics
 R is capable of creating high quality graphics
 Graphs are typically created using a series of high-level and low-level
plotting commands. High-level functions create new plots and low-level
functions add information to an existing plot.
 Customize graphs (line style, symbols, color, etc) by specifying graphical
parameters
 Specify graphic options using the par() function.
 Can also include graphic options as additional arguments to plotting
functions

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Graphic Parameters, par()

 The function par() is used to set or get graphical parameters.
 This function contains 70 possible settings and allows you to adjust almost
any feature of a graph.
 Graphic parameters are reset to the defaults with each new graphic device.
 To extract a graphic parameter, par("tag ") or par()$tag .
 To set a graphic parameter, par(tag=value ).
 Most elements of par() can be set as additional arguments to a plot
command, however there are some that can only be set by a call to par(),
mar, oma, mfrow, mfcol see the documentation for others.

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High-Level Plot Functions

plot() Scatterplot
hist() Histogram
boxplot() Boxplot
qqplot(), qqnorm(), qqline() Quantile plots
[Link]() Interaction plot
sunflowerplot() Sunflower scatterplot
pairs() Scatter plot matrix
symbols() Draw symbols on a plot
dotchart(), barplot(), pie() Dot chart, bar chart, pie chart
curve() Draw a curve from a given function
image() Create a grid of colored rectangles with
colors based on the values of a third variable
contour(), [Link]() Contour plot
persp() Plot 3-D surface

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Low-Level Plot Functions

points() Add points to a figure

lines() Add lines to a figure
text() Insert text in the plot region
mtext() Insert text in the figure and outer margins
title() Add figure title or outer title
legend() Insert legend
axis(), [Link]() Customize axes
abline() Add horizontal and vertical lines or a single line
box() Draw a box around the current plot
rug() Add a 1-D plot of the data to the figure
polygon() Draw a polygon
rect() Draw a rectangle
arrows() Draw arrows
segments() Draw line segments
trans3d() Add 2-D components to a 3-D plot

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Scatterplot and Line Graphs

 The plot() function is used for producing scatterplots and line graphs
 Common arguments for plot(), see par() for a complete list
type 1-character string denoting the plot type
xlim x limits, c(x1, x2)
ylim y limits, c(y1, y2)
log Character string that contains ”x” if x-axis is log-scale, ”y” if y-axis is log
scale, and ”xy” if both axes are log scale
main Main title for the plot
sub Sub title for the plot
xlab x-axis label
ylab y-axis label
ann Logical, should default annotation appear on plot
axes Logical, should both axes be drawn
col Color for lines and points, either a character string or a number that indexes
the palette()
pch Number referencing a plotting symbol or a character string
cex A number giving the character expansion of the plot symbols
lty Number referencing a line type
lwd Line width
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Example - Scatterplot
x <- rnorm(50); y <- rnorm(50)
group <- rbinom(50, size=1, prob=.5)
# Basic Scatterplot
plot(x, y)
plot(x, y, xlab="X", ylab="Y", main="Y vs X", pch=15, col="red")
# Distinguish between two separate groups
plot(x, y, xlab="X", ylab="Y", main="Y vs X",
pch=ifelse(group==1, 5, 19),
col=ifelse(group==1, "red", "blue"))
# The points argument can be, (1) two separate vectors where one vector
# is the x-coordinates and the other is the y-coordinates (2) a
# two-column matrix or (3) a two-element list with x and y components
plot(x, y, xlab="X", ylab="Y", main="Y vs X", type="n")
points(x[group==1], y[group==1], pch=5, col="red")
points(x[group==0], y[group==0], pch=19, col="blue")

plot(x, y, xlab="X", ylab="Y", main="Y vs X", type="n")

points(cbind(x,y)[group==1,], pch=5, col="red")
points(cbind(x,y)[group==0,], pch=19, col="blue")
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Example - Line Graphs

# Basic Line Graphs
plot(sort(x), sort(y), type="l", lty=2, lwd=2, col="blue")

# Like points, the lines argument can be, (1) two separate vectors
# where one vector is the x-coordinates and the other is the
# y-coordinates (2) a two-column matrix or (3) a two-element list
# with x and y components.
plot(x, y, type="n")
lines(sort(x), sort(y), type="b")
lines(cbind(sort(x),sort(y)), type="l", lty=1, col="blue")

# If there is only one component then the argument is plotted against

# its index (same with plot and points)
plot(sort(x), type="n")
lines(sort(x), type="b", pch=8, col="red")
lines(sort(y), type="l", lty=6, col="blue")

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Histograms and Boxplots

 Use hist() to create histograms and boxplot() for boxplots.
x <- rnorm(50); y <- rnorm(50)
group <- rbinom(50, size=1, prob=.5)

# Basic Histogram
hist(x, main="Histogram of X", col="deeppink4")

# Plot histogram along with a normal density

# Set freq=FALSE, so that the density histogram is plotted (area sums to 1)
hist(x, freq=FALSE, col="red", main="Histogram with Normal Curve")

# Uses the observed mean and standard deviation for plotting the normal curve
xpts <- seq(min(x), max(x), length=50)
ypts <- dnorm(xpts, mean=mean(x), sd=sd(x))
lines(xpts, ypts, lwd=3)

# Basic boxplot
boxplot(x, main="Boxplot of X", border="red", lwd=2)

# Side-by-Side Boxplots
boxplot(x~group, main="Boxplot of X by Group",
names=c("Group 0", "Group 1"), border=c("red", "blue"), lwd=2)
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curve()
 The function curve() draws a curve corresponding to a given function.
 If the function is written within curve() it needs to be a function of x
 If you want to use a multiple argument function, use x for the argument
you wish to plot over.
# Plot a 5th order polynomial
curve(3*x^5-5*x^3+2*x, from=-1.25, to=1.25, lwd=2, col="blue")

# Plot the gamma density

curve(dgamma(x, shape=2, scale=1), from=0, to=7, lwd=2, col="red")

# Plot multiple curves, notice that the first curve determines the x-axis
curve(dnorm, from=-3, to=5, lwd=2, col="red")
curve(dnorm(x, mean=2), lwd=2, col="blue", add=TRUE)

# Add vertical lines at the means

lines(c(0, 0), c(0, dnorm(0)), lty=2, col="red")
lines(c(2, 2), c(0, dnorm(2, mean=2)), lty=2, col="blue")

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outer()
 The outer() function is very useful for contour plots and 3-D surface plots.
 outer() performs a general outer product of two vectors,
   
x1 (y1 y2 y3 ) f (x1 , y1 ) f (x1 , y2 ) f (x1 , y3 )
 x2  =  f (x2 , y1 ) f (x2 , y2 ) f (x2 , y3 ) 
x3 f (x3 , y1 ) f (x3 , y2 ) f (x3 , y3 )
Normally, f (xi , yj ) = xi yj , with outer() f can be any function.
 The function passed to outer() must be a vectorized function
> x <- 1:5
> y <- 1:5
> outer(x, y, FUN=function(row, col) row^col)
[,1] [,2] [,3] [,4] [,5]
[1,] 1 1 1 1 1
[2,] 2 4 8 16 32
[3,] 3 9 27 81 243
[4,] 4 16 64 256 1024
[5,] 5 25 125 625 3125

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R Graphics High-Level Low-Level Saving Graphs

Contour and 3-D Plots

 Contour plots are created using either contour() or [Link]()
 [Link]() accepts a color palette function that is used to assign
colors in the plot
 Built-in color palettes: [Link](), [Link](),
[Link](), rainbow() and [Link]()
 Create your own color palette using colorRampPalette()
 3-D surface plots are created using persp(). Use trans3d() to add 2-D
components to a 3-D surface plot.
 All these functions require a matrix of the z values that correspond to
z = f (x, y ) evaluated on a grid given by x and y , the function outer() is
very useful for creating this matrix.

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Example - Contour and 3-D Plots

library(TeachingDemos) # Contains [Link]()
# Evaluate z on a grid given by x and y
x <- y <- seq(-1, 1, len=25)
z <- outer(x, y, FUN=function(x,y) -x*y*exp(-x^2-y^2))
# Contour plots
contour(x,y,z, main="Contour Plot")
[Link](x,y,z, main="Filled Contour Plot")
[Link](x,y,z, [Link] = [Link])
[Link](x,y,z, [Link] = colorRampPalette(c("red", "white", "blue")))
persp(x,y,z, shade=.75, col="green3") # 3-D Surface Plot
[Link](x,y,z) # Rotate 3-D Surface Plot
# Add 2-D components to a 3-D Surface plot
# view is the "viewing transformation matrix" needed by trans3d
view <- persp(x,y,z, shade=.75, col="green3")
# Point at (x=1, y=1, z=.01)
points(trans3d(1,1,.1, view), cex=2, col="red", pch=19)
text(trans3d(1,1,.1, view), "(1,1,0.1)", pos=1, font=2)
# Line of z vs x, when y=-.5
lines(trans3d(x, y=-.5, z[7,], view), lwd=2, col="red")
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Example - Bivariate Normal

library(TeachingDemos)

# Bivariate Normal Density

# x: 2x1 vector, mu: 2x1 mean vector, Sigma: 2x2 covariance matrix
[Link] <- function(x, mu, Sigma) {
exp(-.5*t(x-mu)%*%solve(Sigma)%*%(x-mu))/sqrt(2*pi*det(Sigma))
}

mu <- c(0,0)
Sigma <- matrix(c(1,.5,.5,1), nrow=2)

x <- y <- seq(-3, 3, len=25)

# Evaluate the bivariate normal density for each value of x and y

z <- outer(x, y,
FUN=function(x, y, ...){
apply(cbind(x,y), 1, [Link], ...)
}, mu=c(0,0), Sigma=Sigma)

# Filled contour and surface plot of the bivariate normal density

[Link](x,y,z, main="Bivariate Normal Density", [Link]=[Link])
persp(x, y, z, shade=.75, col="red", main="Bivariate Normal Density")
[Link](x, y, z)
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Multiple Graphs
 To create a n × m grid of figures use par() with either the mfcol or
mfrow settings.
 mfcol=c(nr, nc) adds figures by column
 mfrow=c(nr, nc) adds figures by row
 To create a more complex arrangement of multiple plots used layout()
 The arguments widths and heights are vectors that specify the relative
widths and heights of the columns and rows, respectively
 [Link]() is used to create multiple plots and allows you to switch
control between plots. After a figure is created you can go back to that
figure and add more information, layout() and par() do not have this
capability.
 However, the documentation warns that returning to an existing screen to
add information results in unpredictable behavior and may lead to problems
that are not readily visible.
 To open a new graphics device,
 windows() on a Windows machine
 quartz() on a Mac machine

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Example - Multiple Graphs

# Figure with two plots side by side
par(mfrow=c(1,2))
plot(rnorm(100), main="Figure 1", pch=19, col="red")
plot(rnorm(100), main="Figure 2", pch=5, col="blue")

# Create layout
layout(matrix(c(1,1,2,3), 2, 2, byrow = TRUE), heights=c(.5,1))
[Link](3) # View layout

# Create layout
layout(matrix(c(2,0,1,3),2,2, byrow=TRUE), widths=c(3,.5), heights=c(.5,3))
[Link](3) # View layout

# Plot scatterplot and boxplots

x <- rnorm(100); y <- rnorm(100)

# Notice that the range of the scatterplot and boxplots have the same limits
par(mar=c(4,4,1,1),oma=c(0,0,1,0), [Link]=2, [Link]=2, [Link]=1.5, [Link]=1.5)
plot(x, y, xlim=c(-3,3), ylim=c(-3,3), xlab="X", ylab="Y", pch=17, col="darkgreen", cex=1.5)
box(lwd=2)
par(mar=c(0,4,0,1))
boxplot(x, horizontal=TRUE, ylim=c(-3,3), axes=FALSE, at=.75, border="red", lwd=3)
par(mar=c(4,0,1,0))
boxplot(y, ylim=c(-3,3), axes=FALSE, at=.75, border="blue", lwd=3)

# Add title in outer margin

title("Scatterplot and Boxplots of X and Y", outer=TRUE, line=-2, [Link]=2)

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Example - Multiple Graphs

# Divide the figure into 3 screens and add scatter plots to each screen
[Link](c(2,1)) # Split display into two screens
[Link](c(1,2), 2) # Split bottom half in two
screen(3) # Select screen 3
plot(1:10) # Draw plot in screen 3
[Link]() # Forgot title, erase screen 3
plot(1:10, main= "Screen 3") # Redraw screen 3
screen(1) # Select screen 1
plot(runif(100), main="Screen 1") # Add plot to screen 1
screen(4) # Select screen 4
plot(0:10, 10:0, main="Screen 4") # Add plot to screen 4
screen(1, FALSE) # Return to screen 1, but do not clear
abline(h=.5, lwd=2, col="red") # Add horizontal line at y=.5 (almost)
[Link](all = TRUE) # Exit split-screen mode

# Proper behavior of abline()

windows() # Start new graphics window
plot(runif(100))
abline(h=.5, lwd=2, col="red")
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Margins
Outer Margin Line 3
par(oma=c(3, 2, 4, 3)) Line 2
Line 1
title('Outer Title', outer=TRUE) Line 0

Line 0
Line 1
Line 2
Figure Margin Figure Margin Line 3
par(mar=c(8, 4, 4, 2)) par(mar=c(5, 4, 4, 2)) Line 2
Line 1
title('Figure Title') title('Figure Title') Line 0
10

10

10
Line 0
Line 1
Plot Region 1 Plot Region 2
8

8
Margin Vectors = c(bottom, left, top, right)

axis(4, outer=TRUE)
6

units are "lines" (can be non−integer)

Y

6
Default Margins
4

Y
par()$oma = c(0, 0, 0, 0)
par()$mar = c(5.1, 4.1, 4.1, 2.1)

4
2

Plot Legend (default)

0

2
0 2 4 6 8 10
text("Plot Region Text")

0
X
0 2 4 6 8 10
Figure Legend (xpd=TRUE)
X
mtext("Figure Margin Text")

Outer Legend (xpd=NA) mtext("Outer Margin Text", outer=TRUE)

 R Graphics consist of a plot region, a figure margin and an outer margin.

 The figure space can be divided into multiple plot regions
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Text
 To add text to the plot region use text() and use mtext() to add text to
the figure and outer margins.
par(mfrow=c(1,2), oma=c(2,2,2,2)) # Add an outer margin to the figure
[Link](123); x <- rnorm(10); y <- rnorm(10)
# Plot 1
plot(x, pch=19, col="red", main="Figure 1")
# Label each point with its index
text(1:10, x, label=1:10, pos=rep(c(4,2), c(2,8)), font=2, cex=1.5)
# Add fancy text to the plot region
text(1, 1, "This is Fancy Plot Text", family="HersheyScript", adj=0, cex=1.5)
# Add text to the margin
mtext("This is Margin Text for Figure 1", side=2, line=4)
# Plot 2
plot(x, pch=15, col="blue", main="Figure 2")
# Add plain text to the plot region
text(1, 1, "This is More Plot Text", family="mono", adj=0, cex=1)
# Add text to the margin
mtext("This is Margin Text for Figure 2", side=3, line=.5)
# Outer Margin, the \n can be include in character strings to add new lines
title("OUTER\nTITLE", outer=TRUE, line=-1)
mtext("This is Outer Margin Text", side=1, outer=TRUE, font=3)
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Math Expressions
 R is capable of adding LATEX like expressions to R graphics
 Use expression() to add math expressions to a figure
 The function bquote() is used to add expressions and values. Terms inside
.() are evaluated, the remaining terms are evaluated as math expressions.
 Math expressions can be used in place of almost any text argument
(cannot be used for axis labels on persp() plots).
 See ?plotmath for a complete list of the syntax used by expression()
and bquote()

plot(1:10, type="n", xlab="X", ylab="Y")

text(5.5, 9, "expression(y==alpha[1]*x+alpha[2]*x^2)", cex=1.5)
text(5.5, 8, expression(y==alpha[1]*x+alpha[2]*x^2), cex=1.5)

theta = 3
text(5.5, 6, "theta=3; bquote(hat(theta)==.(theta))", cex=1.5)
text(5.5, 5, bquote(hat(theta)==.(theta)), cex=1.5)

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Legend
 Legends are added to a figure using legend(), legends can be added to
the plot region, figure margin, or the outer margin
 You are responsible for matching plotting symbols and colors with the
symbols and colors in the legend
 Legend placement is delicate, the location of the legend often changes when
the figure is resized. Fixing the window size before adding legends helps.
 If you are creating one graph the locator() function can be useful for
determining the placement

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Example - Legend
windows(width=9, height=6) # Fix window size
par(mfrow=c(1,2), oma=c(3,0,2,0)) # Add an outer margin to the figure
[Link](789)
x1 <- rnorm(10); x2 <- rnorm(10, mean=2)
y1 <- rnorm(10); y2 <- rnorm(10, mean=2)
# PLOT 1, Use range to determine a plot region that is large enough for all the points
plot(range(x1,x2), range(y1,y2), main="Figure 1", type="n", xlab="X", ylab="Y")
points(x1, y1, col="red", pch=19) # Group 1
points(x2, y2, col="blue", pch=0) # Group 2
legend("topleft", c("Group 1","Group 2"), pch=c(19,0), col=c("red", "blue"),
horiz=TRUE, bty="n")
legend(locator(1), c("Group 1","Group 2"), pch=c(19,0), col=c("red", "blue"), title="Legend")

# PLOT 2
plot(range(x1,x2), range(y1,y2), main="Figure 2", type="n", xlab="X", ylab="Y")
lines(sort(x1), sort(y1), col="red", type="o", pch=19) # Group 1
lines(sort(x2), sort(y2), col="blue", type="o", pch=0) # Group 2
legend(-2, 2.5, c("Group 1", "Group 2"), pch=c(19,0), col=c("red", "blue"),
horiz=TRUE, bty="n", lty=1)

# Legend in figure margin

legend(1.5, -2.25, c("Group 1", "Group 2"), pch=c(19,0), col=c("red", "blue"), lty=1,
bty="n", xpd=TRUE)
# Legend in outer margin
legend(-5.25, -3, c("Group 1", "Group 2"), pch=c(19,0), col=c("red", "blue"), lty=1,
horiz=TRUE, xpd=NA)
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Axis
 In a high-level plot function, if the argument axes=FALSE then the plot
axes will be omitted.
 The functions axis() and [Link]() are used create custom axes.
# Plot with no axes
par(mar=c(5,5,5,5))
plot(1:10, axes=FALSE, ann=FALSE)

# Add an axis on side 2 (left)

axis(2)

# Add an axis on side 3 (top), specify tick mark location, and add labels
axis(3, at=seq(1,10,by=.5), labels=format(seq(1,10,by=.5), nsmall=3))

# Add an axis on side 4 (right), specify tick mark location and rotate labels
axis(4, at=1:10, las=2)

# Add axis on side 1 (bottom), with labels rotated 45 degrees

tck <- axis(1, labels=FALSE)
text(tck, par("usr")[3]-.5, labels=paste("Label", tck), srt=45, adj=1, xpd=TRUE)

box() # Add box aroung plot region

mtext(paste("Side", 1:4), side=1:4, line=3.5, font=2) # Add axis labels
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Example - [Link]()

dates <- [Link]([Link](),by="3 day", [Link]=25)

y <- sort(rexp(length(dates)))

plot(dates, y, xlab="Date", ylab="Y", main="Y vs Date",

axes=FALSE, type="o", pch=18, col="darkorange4", cex=1.5)

# Y-axis
axis(2, at=seq(0, max(y), by=.5))

# X-axis
[Link](1, at=[Link](min(dates), max(dates), "week"),
format="%b %d\n%Y", padj=.5)
[Link](1, at=[Link](min(dates), max(dates), "day"),
labels=FALSE, tcl=-.25)

box()

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Colors
 The function colors() returns a vector of built-in color names.
 grep() can be used to help find colors
 Earl Glynn, has create a very nice PDF color chart of all the built-in colors,
there is a link on the class homepage.
 To create your own color use, rgb(), hsv() or hcl(), depending on what
method of color specification you prefer
 Create a personal color palette using, palette(). When the argument
col=number, R uses the color in the palette that is indexed by number.
# Create and use a custom color
[Link] <- rgb(red=204, green=85, blue=0, max=255)
plot(1:10, pch=15, col=[Link], cex=3)
palette() # Current palette()
plot(1:10, pch=15, col=5, cex=3)
# Custom palette()
palette(c("red", "darkorange", "gold", "green3", "blue", "magenta3"))
plot(c(1,10), c(-3,3), type="n")
for(i in 1:length(palette())) points(rnorm(10), col=i, pch=18, cex=1.5)
palette("default") # Return to default, here "default" is a keyword
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Saving Graphs
 Graphs can be saved using several different formats, such as PDFs, JPEGs,
and BMPs, by using pdf(), jpeg() and bmp(), respectively.
 Graphs are saved to the current working directory.
 In my opinion, pdf() produces the highest quality graphics and are easy to
include in LATEXdocuments if you use a PDF compiler.
# Create a single pdf of figures, with one graph on each page
pdf("[Link]", width=7, height=5) # Start graphics device
x <- rnorm(100)
hist(x, main="Histogram of X")
plot(x, main="Scatterplot of X")

[Link]() # Stop graphics device

# Create multiple pdfs of figures, with one pdf per figure

pdf(width=7, height=5, onefile=FALSE)
x <- rnorm(100)
hist(x, main="Histogram of X")
plot(x, main="Scatterplot of X")

[Link]() # Stop graphics device

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