by David Lillis, Ph.D.
Last time we created two variables and added a best-fit regression line to our plot of the variables. Here are the two variables again. (more…)
by David Lillis, Ph.D.
Last time we created two variables and added a best-fit regression line to our plot of the variables. Here are the two variables again. (more…)
Today let’s re-create two variables and see how to plot them and include a regression line. We take height to be a variable that describes the heights (in cm) of ten people. (more…)
In the last lesson, we saw how to use qplot to map symbol colour to a categorical variable. Now we see how to control symbol colours and create legend titles.
M <- structure(list(PATIENT = c("Mary","Dave","Simon","Steve","Sue","Frida","Magnus","Beth","Peter","Guy","Irina","Liz"),
GENDER = c("F","M","M","M","F","F","M","F","M","M","F","F"),
TREATMENT = c("A","B","C","A","A","B","A","C","A","C","B","C"),
AGE =c("Y","M","M","E","M","M","E","E","M","E","M","M"),
WEIGHT_1 = c(79.2,58.8,72.0,59.7,79.6,83.1,68.7,67.6,79.1,39.9,64.7,65.6),
WEIGHT_2 = c(76.6,59.3,70.1,57.3,79.8,82.3,66.8,67.4,76.8,41.4,65.3,63.2),
HEIGHT = c(169,161,175,149,179,177,175,170,177,138,170,165),
SMOKE = c("Y","Y","N","N","N","N","N","N","N","N","N","Y"),
EXERCISE = c(TRUE,FALSE,FALSE,FALSE,TRUE,FALSE,FALSE,TRUE,TRUE,FALSE,FALSE,TRUE),
RECOVER = c(1,0,1,1,1,0,1,1,1,1,0,1)),
.Names = c("PATIENT","GENDER","TREATMENT","AGE","WEIGHT_1","WEIGHT_2","HEIGHT","SMOKE","EXERCISE","RECOVER"),
class = "data.frame", row.names = 1:12)
M
PATIENT GENDER TREATMENT AGE WEIGHT_1 WEIGHT_2 HEIGHT SMOKE EXERCISE RECOVER
1 Mary F A Y 79.2 76.6 169 Y TRUE 1
2 Dave M B M 58.8 59.3 161 Y FALSE 0
3 Simon M C M 72.0 70.1 175 N FALSE 1
4 Steve M A E 59.7 57.3 149 N FALSE 1
5 Sue F A M 79.6 79.8 179 N TRUE 1
6 Frida F B M 83.1 82.3 177 N FALSE 0
7 Magnus M A E 68.7 66.8 175 N FALSE 1
8 Beth F C E 67.6 67.4 170 N TRUE 1
9 Peter M A M 79.1 76.8 177 N TRUE 1
10 Guy M C E 39.9 41.4 138 N FALSE 1
11 Irina F B M 64.7 65.3 170 N FALSE 0
12 Liz F C M 65.6 63.2 165 Y TRUE 1
Now let’s map symbol size to GENDER and symbol colour to EXERCISE, but choosing our own colours. To control your symbol colours, use the layer: scale_colour_manual(values = c()) and select your desired colours. We choose red and blue, and symbol sizes 3 and 7.
qplot(HEIGHT, WEIGHT_1, data = M, geom = c("point"), xlab = "HEIGHT (cm)", ylab = "WEIGHT BEFORE TREATMENT (kg)" , size = factor(GENDER), color = factor(EXERCISE)) + scale_size_manual(values = c(3, 7)) + scale_colour_manual(values = c("red", "blue"))
Here is our graph with red and blue points:
Now let’s see how to control the legend title (the title that sits directly above the legend). For this example, we control the legend title through the name argument within the two functions scale_size_manual() and scale_colour_manual(). Enter this syntax in which we choose appropriate legend titles:
qplot(HEIGHT, WEIGHT_1, data = M, geom = c("point"), xlab = "HEIGHT (cm)", ylab = "WEIGHT BEFORE TREATMENT (kg)" , size = factor(GENDER), color = factor(EXERCISE)) + scale_size_manual(values = c(3, 7), name="Gender") + scale_colour_manual(values = c("red","blue"), name="Exercise")
We now have our preferred symbol colour and size, and legend titles of our choosing.
That wasn’t so hard! In our next blog post we will learn about plotting regression lines in R.
About the Author: David Lillis Ph. D. has taught R to many researchers and statisticians. His company, Sigma Statistics and Research Limited, provides both on-line instruction and face-to-face workshops on R, and coding services in R. David holds a doctorate in applied statistics.
See our full R Tutorial Series and other blog posts regarding R programming.
In this lesson, let’s see how to use qplot to map symbol colour to a categorical variable.
Copy in the following data set (a medical data set relating to patients in a randomised controlled trial):
In this lesson, we see how to use qplot to create a simple scatterplot.
The qplot (quick plot) system is a subset of the ggplot2 (grammar of graphics) package which you can use to create nice graphs. It is great for creating graphs of categorical data, because you can map symbol colour, size and shape to the levels of your categorical variable. To use qplot first install ggplot2 as follows:
(more…)
In this lesson, let’s see how to create mathematical expressions for your graph in R. We’ll use an example of graphing a cosine curve, along with relevant Greek letters as the axis label, and printing the equation right on the graph.
Mathematical expressions, like sine or exponential curves on graphs are made possible through expression(paste()) and substitute().
If you need mathematical symbols as axis labels, switch off the default axes and include Greek symbols by writing them out in English. You can create fractions through the frac() command. Note how we obtain the plus or minus sign through the syntax: %+-%
Here is a nice example. Let’s create a set of 71 values from – 6 to + 6. These values are the horizontal axis values.
x <- seq(-6, 6, len = 71)
Now we plot a cosine function using a continuous curve (using type="l") while suppressing the x axis using the syntax: xaxt="n"
plot(x, cos(x),type="l",xaxt="n",
xlab=expression(paste("Angle ",theta)),
ylab=expression("sin "*theta))
. . . where we have inserted relevant mathematical text for the axis labels using expression(paste()). Here is the graph so far:
Now we create a horizontal axis to our own specifications, including relevant labels:
axis(1, at = c(-2*pi, -1.5*pi, -pi, -pi/2, 0, pi/2, pi, 1.5*pi, 2*pi),
lab = expression(-2*pi, -1.5*pi, -pi, -pi/2, 0, pi/2, pi, 2*pi, 1.5*pi))
Let’s put in some mathematical expressions, centered appropriately. The first argument within each text() function gives the value along the horizontal axis about which the text will be centered.
text(-0.7*pi,0.5,substitute(chi^2=="23.5"))
text(0.1*pi, -0.5, expression(paste(frac(alpha*omega, sigma*phi*sqrt(2*pi)), ” “,
e^{frac(-(5*x+2*mu)^3, 5*sigma^3)})))
text(0.3*pi,0,expression(hat(z) %+-% frac(se, alpha)))
Here is our graph, complete with mathematical expressions:
That wasn’t so hard! In the next lesson we will discuss using qplot in R to create scatterplots.
About the Author: David Lillis has taught R to many researchers and statisticians. His company, Sigma Statistics and Research Limited, provides both on-line instruction and face-to-face workshops on R, and coding services in R. David holds a doctorate in applied statistics.
See our full R Tutorial Series and other blog posts regarding R programming.