This document discusses basic graphing in R using the base, lattice, and ggplot2 packages. It demonstrates how to create histograms, density plots, scatter plots, box plots, and grouped plots using each graphing system. Examples are provided using the BONEDEN.DAT and BETACAR.DAT datasets to illustrate different types of one-variable and two-variable plots.

1. Graphing
with
2012-11-19 @HSPH
Kazuki Yoshida, M.D.
MPH-CLE student
FREEDOM
TO
KNOW

2. Group Website is at:
http://rpubs.com/kaz_yos/useR_at_HSPH

3. Previously in this group
n Introduction
n Reading Data into R (1)
n Reading Data into R (2)
n Descriptive, continuous
n Descriptive, categorical
Group Website: http://rpubs.com/kaz_yos/useR_at_HSPH

4. Menu
n Basic graphing with R

5. Ingredients
Statistics Programming
n One-variable plot n base, lattice, and ggplot2
n Histogram n hist(), histogram()
n Density plot n densityplot()
n Two-variable plot n plot(Y~X)
n Scatter plot n boxplot(), bwplot()
n Box plot n Conditioning in lattice
n Grouped plot

6. 3 different systems

7. base (traditional)
http://commons.wikimedia.org/wiki/File:Plottype.png

8. lattice package
http://zoonek.free.fr/blosxom/R/2006-08-10_R_Graphics.html

9. ggplot2
http://blog.revolutionanalytics.com/2009/09/ggplot2-and-the-grammar-of-graphics.html

10. Open
R Studio

11. Install and Load
lattice ggplot2

12. Download comma-separated and Excel
Put them in folder
BONEDEN.DAT.txt
BETACAR.DAT.txt
http://www.cengage.com/cgi-wadsworth/course_products_wp.pl?
fid=M20bI&product_isbn_issn=9780538733496

13. Read in BONEDEN.DAT.txt
Name it bone
Bone density in twins with
discordant smoking exposure

14. Read in BETACAR.DAT.txt
Name it vitA
Plasma level of carotene by different
formula of beta-carotene

15. formula
Y-axis ~ X-axis

16. Histogram

17. ## base
hist(bone$age)
## lattice
histogram(bone$age)
## ggplot2
qplot(x = age, data = bone, geom = "Histogram")

18. Density plot

19. ## base
plot(density(bone$age))
## lattice
densityplot(bone$age)
## ggplot2
qplot(x = age, data = bone, geom = "density")

20. Scatter plot

21. ## base
plot(fn1 ~ age, bone)
## lattice
xyplot(fn1 ~ age, bone)
## ggplot2
qplot(age, fn1, data = bone)

22. Box plot

23. ## base
boxplot(Wk12lvl ~ Prepar, vitA)
## lattice
bwplot(Wk12lvl ~ factor(Prepar), vitA)
## ggplot2
qplot(factor(Prepar), Wk12lvl, data = vitA,
geom = "boxplot")

24. Grouped plot

25. ## base
layout(matrix(1:4,ncol = 2))
for (i in 1:4) {
plot(Wk12lvl ~ Base1lvl, subset(vitA, Prepar == i))
title(paste("Prepar = ", i))
}
## lattice
xyplot(Wk12lvl ~ Base1lvl | factor(Prepar), vitA)
## ggplot2
ggplot(vitA, aes(x = Base1lvl, y = Wk12lvl, group = factor(Prepar)))
+ geom_point() + facet_wrap(~Prepar)