Data Visualization

Andrew Jaffe

January 7, 2016
Basic Plots

We covered some basic plots previously, but we are going to expand

the ability to customize these basic graphics first.
Read in Data
death = read.csv("http://www.aejaffe.com/winterR_2016/data/
as.is=TRUE,header=TRUE, row.names=1)
death[1:2, 1:5]

X1760 X1761 X1762 X1763 X1764

Afghanistan NA NA NA NA NA
Albania NA NA NA NA NA

We see that the column names were years, and R doesn’t necessarily
like to read in a column name that starts with a number and puts
an X there.
We’ll just take off that X and get the years.

library(stringr)
year = names(death) %>% str_replace("X","") %>% as.integer
head(year)

[1] 1760 1761 1762 1763 1764 1765

Basic Plots
> plot(as.numeric(death["Sweden",]) ~ year)

as.numeric(death["Sweden", ])

3.0
2.0
1.0
0.0

1750 1850 1950 2050

Basic Plots
The y-axis label isn’t informative, and we can change the label of the
y-axis using ylab (xlab for x), and main for the main title/label.

> plot(as.numeric(death["Sweden",]) ~ year,

+ ylab = "# of deaths per family", main = "Sweden")

Sweden
3.0
of deaths per family

2.0
1.0
Basic Plots
Let’s drop any of the projections and keep it to year 2012, and
change the points to blue.

plot(as.numeric(death["Sweden",])~year,
ylab = "# of deaths per family", main = "Sweden",
xlim = c(1760,2012), pch = 19, cex=1.2,col="blue")

Sweden
3.0
deaths per family

2.0
1.0
Basic Plots
You can also use the subset argument in the plot() function, only
when using formula notation:

plot(as.numeric(death["Sweden",])~year,
ylab = "# of deaths per family", main = "Sweden",
subset = year < 2015, pch = 19, cex=1.2,col="blue")

Sweden
3.0
deaths per family

2.0
1.0
Basic Plots
Using scatter.smooth plots the points and runs a loess smoother
through the data.

> scatter.smooth(as.numeric(death["Sweden",])~year,span=0.2
+ ylab="# of deaths per family", main = "Sweden",lwd=
+ subset = year < 2015, pch = 19, cex=0.9,col="grey")

Sweden
3.0
deaths per family

2.0
1.0
Basic Plots
par(mfrow=c(1,2)) tells R that we want to set a parameter (par
function) named mfrow (number of plots - 1 row, 2 columns) so we
can have 2 plots side by side (Sweden and the UK)

> par(mfrow=c(1,2))
> scatter.smooth(as.numeric(death["Sweden",])~year,span=0.2
+ ylab="# of deaths per family", main = "Sweden",lwd=
+ xlim = c(1760,2012), pch = 19, cex=0.9,col="grey")
> scatter.smooth(as.numeric(death["United Kingdom",])~year,
+ ylab="# of deaths per family", main = "United Kingd
+ xlim = c(1760,2012), pch = 19, cex=0.9,col="grey")

Sweden United Kingdom

3.0

1.0 1.5 2.0 2.5

eaths per family

eaths per family

2.0
.0
Basic Plots
We can set the y-axis to be the same.

par(mfrow=c(1,2))
yl = range(death[c("Sweden","United Kingdom"),])
scatter.smooth(as.numeric(death["Sweden",])~year,span=0.2,y
ylab="# of deaths per family", main = "Sweden",lwd=3,
xlim = c(1760,2012), pch = 19, cex=0.9,col="grey")
scatter.smooth(as.numeric(death["United Kingdom",])~year,sp
ylab="", main = "United Kingdom",lwd=3,ylim=yl,
xlim = c(1760,2012), pch = 19, cex=0.9,col="grey")

Sweden United Kingdom

3.0

3.0
of deaths per family

2.0

2.0
1.0

1.0
Bar Plots
I Stacked Bar Charts are sometimes wanted to show distributions
of data
## Stacked Bar Charts
cars = read.csv("http://biostat.jhsph.edu/~ajaffe/files/kag
counts <- table(cars$IsBadBuy, cars$VehicleAge)
barplot(counts, main="Car Distribution by Age and Bad Buy S
xlab="Vehicle Age", col=c("darkblue","red"),
legend = rownames(counts))

Car Distribution by Age and Bad Buy Status

15000

1
0
Bar Plots
prop.table allows you to convert a table to proportions (depends
on margin - either row percent or column percent)

## Use percentages (column percentages)

barplot(prop.table(counts, 2), main="Car Distribution by Ag
xlab="Vehicle Age", col=c("darkblue","red"),
legend = rownames(counts))

Car Distribution by Age and Bad Buy Status

0.8

1
0
0.4
Bar Plots
Using the beside argument in barplot, you can get side-by-side
barplots.
# Stacked Bar Plot with Colors and Legend
barplot(counts, main="Car Distribution by Age and Bad Buy S
xlab="Vehicle Age", col=c("darkblue","red"),
legend = rownames(counts), beside=TRUE)

Car Distribution by Age and Bad Buy Status

0
10000

1
0
Graphics parameters

Set within most plots in the base ‘graphics’ package:

I pch = point shape,

http://voteview.com/symbols_pch.htm
I cex = size/scale
I xlab, ylab = labels for x and y axes
I main = plot title
I lwd = line density
I col = color
I cex.axis, cex.lab, cex.main = scaling/sizing for axes marks,
axes labels, and title
Devices

By default, R displays plots in a separate panel. From there, you

can export the plot to a variety of image file types, or copy it to the
clipboard.
However, sometimes its very nice to save many plots made at one
time to one pdf file, say, for flipping through. Or being more precise
with the plot size in the saved file.
R has 5 additional graphics devices: bmp(), jpeg(), png(), tiff(), and
pdf()
Devices

The syntax is very similar for all of them:

pdf("filename.pdf", width=8, height=8) # inches

plot() # plot 1
plot() # plot 2
# etc
dev.off()

Basically, you are creating a pdf file, and telling R to write any
subsequent plots to that file. Once you are done, you turn the
device off. Note that failing to turn the device off will create a pdf
file that is corrupt, that you cannot open.
Boxplots, revisited
These are one of my favorite plots. They are way more informative
than the barchart + antenna. . .

> boxplot(weight ~ Diet, data=ChickWeight, outline=FALSE)

> points(ChickWeight$weight ~ jitter(as.numeric(ChickWeight
350
250
150
Formulas

Formulas have the format of y ~ x and functions taking formulas

have a data argument where you pass the data.frame. You don’t
need to use $ or referencing when using formulas:

boxplot(weight ~ Diet, data=ChickWeight, outline=FALSE)

Colors
R relies on color ‘palettes’.

palette("default")
plot(1:8, 1:8, type="n")
text(1:8, 1:8, lab = palette(), col = 1:8)

gray
yellow
7

magenta
cyan
5
1:8

blue
green3
3

red
Colors
The default color palette is pretty bad, so you can try to make your
own.

palette(c("darkred","orange","blue"))
plot(1:3,1:3,col=1:3,pch =19,cex=2)
1.5 2.0 2.5 3.0
1:3
Colors

It’s actually pretty hard to make a good color palette. Luckily, smart
and artistic people have spent a lot more time thinking about this.
The result is the ‘RColorBrewer’ package
RColorBrewer::display.brewer.all() will show you all of the palettes
available. You can even print it out and keep it next to your monitor
for reference.
The help file for brewer.pal() gives you an idea how to use the
package.
You can also get a “sneak peek” of these palettes at:
www.colorbrewer2.com . You would provide the number of levels or
classes of your data, and then the type of data: sequential,
diverging, or qualitative. The names of the RColorBrewer palettes
are the string after ‘pick a color scheme:’
Colors
palette("default")
plot(weight ~ Time, data= ChickWeight, pch = 19, col = Diet

350
250
weight

150
50
Colors
library(RColorBrewer)
palette(brewer.pal(5,"Dark2"))
plot(weight ~ Time, data=ChickWeight, pch = 19, col = Diet

350
250
weight

150
50
Colors
library(RColorBrewer)
palette(brewer.pal(5,"Dark2"))
plot(weight ~ jitter(Time,amount=0.2),data=ChickWeight,
pch = 19, col = Diet,xlab="Time")
350
250
weight

150
0
Adding legends

The legend() command adds a legend to your plot. There are tons
of arguments to pass it.
x, y=NULL: this just means you can give (x,y) coordinates, or more
commonly just give x, as a character string:
“top”,“bottom”,“topleft”,“bottomleft”,“topright”,“bottomright”.
legend: unique character vector, the levels of a factor
pch, lwd: if you want points in the legend, give a pch value. if you
want lines, give a lwd value.
col: give the color for each legend level
Adding legends
palette(brewer.pal(5,"Dark2"))
plot(weight ~ jitter(Time,amount=0.2),data=ChickWeight,
pch = 19, col = Diet,xlab="Time")
legend("topleft", paste("Diet",levels(ChickWeight$Diet)),
col = 1:length(levels(ChickWeight$Diet)),
lwd = 3, ncol = 2)
350

Diet 1 Diet 3
Diet 2 Diet 4
250
weight

150
Coloring by variable
> circ = read.csv("http://www.aejaffe.com/winterR_2016/data
+ header=TRUE,as.is=TRUE)
> palette(brewer.pal(7,"Dark2"))
> dd = factor(circ$day)
> plot(orangeAverage ~ greenAverage, data=circ,
+ pch=19, col = as.numeric(dd))
> legend("bottomright", levels(dd), col=1:length(dd), pch =

Friday
eAverage

5000

Monday
Saturday
Sunday
Coloring by variable
> dd = factor(circ$day, levels=c("Monday","Tuesday","Wednes
+ "Thursday","Friday","Saturday","Sunday"))
> plot(orangeAverage ~ greenAverage, data=circ,
+ pch=19, col = as.numeric(dd))
> legend("bottomright", levels(dd), col=1:length(dd), pch =

Monday
orangeAverage

5000

Tuesday
Wednesday
Thursday
2000

Friday
Saturday
ggplot2
ggplot2 is a package of plotting that is very popular and powerful.
qplot is a short hand for “quick plot”. We can simply do a boxplot:

> library(ggplot2)
> qplot(factor(Diet), y = weight,
+ data = ChickWeight, geom = "boxplot")

300
weight

200
ggplot2
The generic plotting function is ggplot:

> g = ggplot(aes(x = Diet, y = weight), data = ChickWeight)

> g + geom_boxplot()

300
weight

200

100
Boxplots revisited again
We can do the same plot, by just saying we want a boxplot and
points (and jitter the points)

> qplot( factor(Diet), y = weight, data = ChickWeight,

+ geom = c("boxplot", "jitter"))

300
weight

200
ggplot2: Adding 2 geoms together
To have multiple geometrics, just “add” them

> g + geom_boxplot() + geom_point(position = "jitter")

300
weight

200

100
ggplot2: Adding 2 geoms together
To have multiple geometrics, just “add” them

g + geom_boxplot() + geom_jitter()

300
weight

200

100
Histograms again
We can do histograms again using hist. Let’s do histograms of
weight at all time points for the chick’s weights. We reiterate how
useful these are to show your data.

> hist(ChickWeight$weight, breaks = 20)

Histogram of ChickWeight$weight
Frequency

80
40
Multiple Histograms
> qplot(x = weight,
+ fill = factor(Diet),
+ data = ChickWeight,
+ geom = c("histogram"))

60

40 factor(Diet)
1
count

2
3
20 4
Multiple Histograms
Alpha refers tot he opacity of the color, less is

> qplot(x = weight, fill = Diet, data = ChickWeight,

+ geom = c("histogram"), alpha=I(.7))

60

40 Diet
1
count

2
3
20 4
Multiple Densities
We cold also do densities

> qplot(x= weight, fill = Diet, data = ChickWeight,

+ geom = c("density"), alpha=I(.7))

0.0075

Diet
1
density

0.0050
2
3
4
0.0025
Multiple Densities
> qplot(x= weight, colour = Diet, data = ChickWeight,
+ geom = c("density"), alpha=I(.7))

0.0075

Diet
1
density

0.0050
2
3
4
0.0025
Multiple Densities
> ggplot(aes(x= weight, colour = Diet),
+ data = ChickWeight) + geom_density(alpha=I(.7))

0.0075

Diet
1
density

0.0050
2
3
4
0.0025
Multiple Densities
You can take off the lines of the bottom like this

> ggplot(aes(x = weight, colour = Diet), data = ChickWeight

+ geom_line(stat = "density")

0.0075

Diet
1
density

0.0050
2
3
4
0.0025
Spaghetti plot
We can make a spaghetti plot by telling ggplot we want a “line”,
and each line is colored by Chick.

> qplot(x=Time, y=weight, colour = Chick,

+ data = ChickWeight, geom = "line")
16 14 38
15 7 32
13 24 40
9 30 34
300
20 22 35
10 23 44
weight

8 27 45
200 17 28 43
19 26 41
4 25 47
Spaghetti plot: Facets
In ggplot2, if you want separate plots for something, these are
referred to as facets.

> qplot(x = Time, y = weight, colour = Chick,

+ facets = ~Diet, data = ChickWeight, geom = "line")

16 14 38
1 2
15 7 32

300 13 24 40
9 30 34
200
20 22 35
100 10 23 44
weight

8 27 45
3 4 17 28 43
19 26 41
300
4 25 47
Spaghetti plot: Facets
We can turn off the legend (referred to a “guide” in ggplot2). (Note
- there is different syntax with the +)

> qplot(x=Time, y=weight, colour = Chick,

+ facets = ~ Diet, data = ChickWeight,
+ geom = "line") + guides(colour=FALSE)

1 2

300

200

100
weight

3 4
Spaghetti plot: Facets
> ggplot(aes(x = Time, y = weight, colour = Chick),
+ data = ChickWeight) + geom_line() +
+ facet_wrap(facets = ~Diet) + guides(colour = FALSE)

1 2

300

200

100
weight

3 4

300

200
ggplot2

Let’s try this out on the childhood mortality data used above.
However, let’s do some manipulation first, by using gather on the
data to convert to long.

library(tidyr)
long = death
long$state = rownames(long)
long = long %>% gather(year, deaths, -state)
head(long, 2)

state year deaths

1 Afghanistan X1760 NA
2 Albania X1760 NA
ggplot2

Let’s also make the year numeric, as we did above in the

stand-alone year variable.

library(stringr)
library(dplyr)
long$year = long$year %>% str_replace("^X", "") %>% as.nume
long = long %>% filter(!is.na(deaths))
ggplot2
> qplot(x = year, y = deaths, colour = state,
+ data = long, geom = "line") + guides(colour = FALSE)

4
deaths

2
ggplot2
Let’s try to make it different like base R, a bit. We use tile for the
geometric unit:

qplot(x = year, y = state, colour = deaths,

data = long, geom = "tile") + guides(colour = FALSE)

West Bank Zimbabwe

Yemen,
Western andZambia
Rep.
Sahara
Gaza
Virgin Islands (U.S.)
Vietnam
Venezuela
Vanuatu
Uzbekistan
United
United
United Arab Uruguay
States
Kingdom
Emirates
Ukraine
Uganda
Turkmenistan
Turkey
Tunisia
TrinidadTimor−Leste
andThailand
Tobago
Tonga
Togo
Tanzania
Tajikistan
Taiwan
Syria
Switzerland
Sweden
Swaziland
Suriname
Sri Sudan
Lanka
Spain
South
Solomon
Slovak Africa
Somalia
Islands
Slovenia
Republic
Singapore
Sierra Leone
Serbia
Senegal
Saoand
Saint Vincent TometheSaudi
and Arabia
Principe
Samoa
Grenadines
Saint Lucia
Rwanda
Russia
Romania
Reunion
Puerto Qatar
Rico
Portugal
Poland
Papua New Philippines
Peru
Paraguay
Guinea
Panama
Pakistan
Oman
Norway
Nigeria
Niger
NewNew
Netherlands Nicaragua
Zealand
Caledonia
Antilles
Netherlands
Nepal
Namibia
Myanmar
Mozambique
Morocco
Micronesia, Montenegro
Mongolia
Moldova
Fed. Sts.
Mexico
Mayotte
Mauritius
Mauritania
Martinique
Malta
Maldives
MalaysiaMali
Malawi
state

Madagascar
Macedonia,
Macao, FYR
China
Luxembourg
Lithuania
Libya
Liberia
Lesotho
Lebanon
Latvia
Korea,Korea,
Dem. Laos
Kyrgyzstan
Kuwait
Rep.
Kenya
Kazakhstan
Jordan
Japan
JamaicaItaly
Israel
Ireland
Iraq
Iran
Hong Indonesia
Kong, India
Iceland
Hungary
China
Honduras
Guyana
Guinea−Bissau
GuineaHaiti
Guatemala
Guam
Guadeloupe
Grenada
Greece
Ghana
Germany
Georgia
Gambia
Gabon
French
FrenchPolynesia
Guiana
France
Finland Fiji
Equatorial Ethiopia
Estonia
Eritrea
Guinea
El Salvador
Dominican Egypt
Ecuador
Rep.
ggplot2

Useful links:

I http://docs.ggplot2.org/0.9.3/index.html
I http://www.cookbook-r.com/Graphs/