Data Visualisation in R with ggplot2

Recommended reading before we begin :

http://byrneslab.net/classes/biol607/readings/wickham_layered-grammar.pdf
What you are NOT expected to gather from the reading :
• Learn ggplot2
• Learn any form of coding
What you ARE expected to gather :
• Understand the layered grammar fundamentals of graphics
I’m assuming once you start reading this you have given at least a cursory reading to the text mentioned
above. You must have realized that layered grammar of graphics is not a complex frame work for statistical
graphics. Instead its an attempt to streamline traditional way of having a distinct name for each kind of
graphics. Basic idea behind this is that almost all kind of graphics are manifestations of different values taken
by underlying layers which are :
• data layer and Aesthetic Mapping
• Geometric Object Layer
• Scales and grouping in the data
• Statistical Transformation
• Coordinate Axes
We’ll start with data layer and aesthetics mapping, subsequent layer discussion will not be discussed under
separate subheadings, rather our discussion will evolve into usage of those layers and we’ll discuss details as
and when we come to it. From your reading of the recommended article, you might have also come across
idea of defaults and their inheritance between layers, we’ll take up that once we are done with basic graphics
in ggplot2. Lets begin.
Before starting the discussion, you need to understand that graphics using ggplot2 are not going to be some
alien plots, they are still going to be same old scatter plots, bar plots , histograms etc, we are still going to
have x -axes , y-axes etc, our plots are going to be two dimensional. Our approach to arrive at those plots
has just become more generic now , that’s all.
All graphics that you generate are made up of some aesthetics and data mapped on to those aesthetics. For
example a scatter plot is nothing but a variable mapped to x axis and another to y axis. Lets define such a
data layer with only these mappings and make a scatter plot.
library(ggplot2)
p=ggplot(mtcars,aes(x=wt,y=mpg))

There are no graphics element yet, we have only created our data layer with some basic aesthetic mapping. If
you simply write p and try to run, you’ll get an appropriate warning stating Error: No layers in plot.
(or a blank plot)
We need to add a geometric object layer on top of this to create a graphic. Lets start with a simple scatter
plot by showing our data using points.
p+geom_point()

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And we have our good old scatter plot. While typing geom_point , you might have got a long list of these
geom options, indeed there are many. But not all of them will make sense with current aesthetic mapping, in
fact in some cases you’ll get error stating some missing aesthetics mapping. Some will produce a plot which
is useless. Lets see more examples of geometric object which make sense [or not] with current aesthetics
mapping.
p+geom_line()

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p+geom_rect()

## Error: geom_rect requires the following missing aesthetics: xmin, xmax, ymin, ymax
p+geom_boxplot()

## Warning: Continuous x aesthetic -- did you forget aes(group=...)?

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Example of boxplot is one which gives you a result which is nonsensical in this context. You can not really
have a boxplot taken two continuous numeric variables mapped to either axes. What did we learn here ?
Although "Colorless green ideas sleep furiously" is grammatically correct sentence , but a useless
nonsense sentence none the less.
You can add multiple kind of geometric object layers at once as well, as long as it makes sense to add them
together.
p=ggplot(mtcars,aes(x=wt,y=mpg))
p+geom_point()+geom_line()+geom_smooth()

## `geom_smooth()` using method = 'loess'

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In addition to x,y axes there are other common aesthetics in a plot:
• Color
• Shape
• Size
Again, these aesthetics are going to be mapped to some data. Lets build on our example of scatter plot.
p=ggplot(mtcars,aes(x=wt,y=mpg,color=vs))
p+geom_point()

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You can see that points have been colored according to value of variable vs. A legend has been added to plot
automatically, which also tells you that variable vs is taken as continuous numeric hence the color scale. We
can convert variable vs to factor type and legend will change.
p=ggplot(mtcars,aes(x=wt,y=mpg,color=factor(vs)))
p+geom_point()

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factor(vs)
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p=ggplot(mtcars,aes(x=wt,y=mpg,color=factor(vs),shape=factor(am),size=cyl))
p+geom_point()

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Now these aesthetic that we see, can be mapped to different geometric objects, few examples of which we
have seen earlier. As you have seen, there are many geometric objects. All of these objects can have there
own aesthetics as well. If you haven’t noticed yet, so-far all geom_* that we have added, had no inputs, they
were inheriting all the aesthetic mapping from the data layer.
I am listing down some aesthetics of the common geometric objects
• points
• – point shape
• – point size
• lines
• – line type
• – line weight
• bars
• – y minimum
• – y maximum
• – fill color
• – outline color
• text
• – label value

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To understand better about inheritance of aesthetics, lets assign color to our data layer add both point and a
smoothing layer to it.
p=ggplot(mtcars,aes(x=wt,y=mpg,color=factor(vs)))
p+geom_point()+geom_smooth()

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factor(vs)
mpg

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You can see that data is automatically grouped according to colors. This grouping is passed to both the
geometric layers by default. If you assign these aesthetics to geometric layers individually in stead putting it
in top layer, data is grouped for those layers only.
p=ggplot(mtcars,aes(x=wt,y=mpg))
p+geom_point(aes(color=factor(vs)))+geom_smooth()

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you can see that points are colored by the groups defined by color aesthetic but there is no grouping in
smoothing layer. Lets look at few more example with bar geometric object using a new data Arthritis
present in package vcd.
## ID Treatment Sex Age Improved
## 1 57 Treated Male 27 Some
## 2 46 Treated Male 29 None
## 3 77 Treated Male 30 None
## 4 17 Treated Male 32 Marked
## 5 36 Treated Male 46 Marked
## 6 23 Treated Male 58 Marked
From here on wards we are not going to define data layer separately, we’ll add it in the same line
ggplot(Arthritis, aes( Improved))+geom_bar()

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None Some Marked

Improved
For geom_bar color only controls color of outline, to change color of the fill, you’ll have to use fill aesthetic.
ggplot(Arthritis, aes(Improved))+geom_bar(aes(color=Treatment))

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Treatment
count

Placebo
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Treated

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None Some Marked

Improved
ggplot(Arthritis, aes(Improved))+geom_bar(aes(fill=Treatment))

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Treatment
count

Placebo
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Treated

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None Some Marked

Improved
We’ll take another example of boxplot. By now you must start to think what aesthetic will map to which
data point in order to generate desired plot. For example to generate a boxplot y axes should map to the
variable in question and x axes should map to the grouping variable .
ggplot(mtcars,aes(y=mpg,x=factor(am)))+geom_boxplot()

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factor(am)
ggplot(mtcars,aes(y=mpg,x=factor(am)))+geom_violin()

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factor(am)
Here violin plots , in addition to your boxplot , provide how dense your points as well. Even better will be to
simply add a point layer and add little jitter to it.
ggplot(mtcars,aes(y=mpg,x=factor(am),color=factor(am)))+geom_point()+geom_jitter()

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Lets see how to make different kind of plots by playing around with coordinate layers. So far the plots that
we have seen , all have simple x-y coordinate system. By adding a polar coordinate system we can convert
our bar plot to pie charts. This makes you realize that , pie charts are nothing but bar charts in a polar
coordinate system. Lets see. We’ll be using dataset diamond here which comes loaded with the package
ggplot2. What you need to remember here is that in the simple bar plot x axis belongs to different values
taken by a categorical variable and y axis belongs to counts of those values in the data. By assigning theta
to y or [count], you are essentially making share of each type in the polar bands getting determined by their
counts.
Always keep in mind , pie chart [ traidition or otherwise ] are just bar chart folded into polar coordinates.
ggplot(diamonds, aes(x = "", fill = clarity)) + geom_bar()

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 clarity
40000
I1
SI2
SI1
count

VS2
VS1

20000 VVS2
VVS1
IF

x
ggplot(diamonds, aes(x = "", fill = clarity)) + geom_bar() + coord_polar(theta = "y")

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clarity
10000 I1
SI2
SI1
VS2
x

40000
VS1
VVS2
VVS1
IF

20000

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count
you can try a different color palette also
ggplot(diamonds, aes(x = "", fill = clarity)) + geom_bar() +
scale_fill_brewer(palette = "Accent")

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 clarity
40000
I1
SI2
SI1
count

VS2
VS1

20000 VVS2
VVS1
IF

x
ggplot(diamonds, aes(x = "", fill = clarity)) + geom_bar() +
coord_polar(theta ="y")+scale_fill_brewer(palette = "Accent")

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clarity
10000 I1
SI2
SI1
VS2
x

40000
VS1
VVS2
VVS1
IF

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count
Now if you map x to clarity , which basically becomes radius in polar coordinates, then instead of equal bar
width ( or equal radius share), it will determined by values of data mapped to x aesthetic. Lets see.
ggplot(diamonds, aes(x = clarity, fill = clarity)) + geom_bar() +
scale_fill_brewer(palette = "Accent")

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 10000 clarity
I1
SI2
SI1
count

VS2
VS1
5000 VVS2
VVS1
IF

I1 SI2 SI1 VS2 VS1 VVS2 VVS1 IF

clarity
ggplot(diamonds, aes(x = clarity, fill = clarity)) + geom_bar() +
coord_polar(theta = "x") + scale_fill_brewer(palette = "Accent")

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10000

7500 clarity
VVS1 SI2 I1
5000
SI2
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count

0 VS2
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IF

VS1 VS2

clarity
Incorporating another variable on fill gives the ‘Wind Rose’ plot:
ggplot(diamonds, aes(x = clarity, fill = cut)) + geom_bar(width = 1) +
scale_fill_brewer(palette = "Accent")

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cut
Fair
Good
count

Very Good
Premium
5000
Ideal

I1 SI2 SI1 VS2 VS1 VVS2 VVS1 IF

clarity
ggplot(diamonds, aes(x = clarity, fill = cut)) + geom_bar(width = 1) +
coord_polar(theta = "x") + scale_fill_brewer(palette = "Accent")

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 IF I1
12500

10000

7500
VVS1 SI2
5000 cut
Fair
2500
Good
count

0
Very Good
Premium
Ideal
VVS2 SI1

VS1 VS2

clarity
Putting theta on ‘Y’ gives a weird sort of bulls-eye plot. Use a width of .9 to produce space between bars.
ggplot(diamonds, aes(x = clarity, fill = clarity)) + geom_bar(width =0.9) +
scale_fill_brewer(palette = "Accent")

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 10000 clarity
I1
SI2
SI1
count

VS2
VS1
5000 VVS2
VVS1
IF

I1 SI2 SI1 VS2 VS1 VVS2 VVS1 IF

clarity
ggplot(diamonds, aes(x = clarity, fill = clarity)) + geom_bar(width =0.9) +
coord_polar(theta = "y") + scale_fill_brewer(palette = "Accent")

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IF
VVS1
VVS2
VS1 clarity
VS2 I1
2500
SI1 SI2
SI2 SI1
10000
clarity

I1 VS2
VS1
VVS2
VVS1
IF

5000

7500

count
This becomes more interesting with a different fill:
ggplot(diamonds, aes(x = clarity, fill = cut)) + geom_bar(width = 0.9) +
scale_fill_brewer(palette = "Accent")

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 10000

cut
Fair
Good
count

Very Good
Premium
5000
Ideal

I1 SI2 SI1 VS2 VS1 VVS2 VVS1 IF

clarity
ggplot(diamonds, aes(x = clarity, fill = cut)) + geom_bar(width = 0.9) +
coord_polar(theta = "y") + scale_fill_brewer(palette = "Accent")

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 0
12500
IF
VVS1
VVS2
VS1
VS2 2500 cut
SI1
Fair
SI2
10000
clarity

I1 Good
Very Good
Premium
Ideal

5000

7500

count
You can also play around with scale layer to transform your axes to log or any other scales. I’ll leave that
for you to explore on your own. Another important visualization that you would like to look at will be
distribution/histogram of your variable. Lets do that. Remember that histogram is nothing but a special
case of bar charts for continuous numeric variables where x axis is made up bins depending on values of the
data mapped to x aesthetic. Y axis still represent counts.
mydata=data.frame(v1=c(rnorm(2000),runif(1000)),
dist=c(rep("Normal",2000),rep("Uniform",1000)))
ggplot(mydata,aes(x=v1))+geom_histogram()

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ggplot(mydata,aes(x=v1,fill=dist))+geom_histogram()

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You can directly plot density curves also.
ggplot(mydata,aes(x=v1,fill=dist))+geom_density()

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you can see that density curves are overlapping. This can be dealt with setting transparency of fill by using
aesthetic alpha which doesnt need to be mapped to data, hence it is specified outside aes .
ggplot(mydata,aes(x=v1,fill=dist))+geom_density(alpha=1/5)

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density

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You can add histogram and density together, but there is an issue which you’ll realize soon.
ggplot(mydata,aes(x=v1,fill=dist))+geom_density(alpha=0.6)+geom_histogram(alpha=0.6)

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density

Normal
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See here, density curves are no where to be seen. Believe me, they are there just that the y axis values
for density are in percentages where as for histogram these are counts which obviously dominate. Hence
your density curves are there but they are merely hugging x axis, this can be taken care of by modifying y
aesthetic of histograms.
ggplot(mydata,aes(x=v1,fill=dist))+geom_density(alpha=0.7)+
geom_histogram(aes(y=..density..),alpha=0.7)

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density

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Uniform

0.5

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Now lets say we wanted to check whether a given data conforms to a normal distribution or not. Clearly
we’d like to plot a normal density curve assuming the data is from normal distribution [ getting µ and σ from
the data] and compare it with the natural density curve of the data. Lets see how we can achieve that.
ggplot(mydata,aes(x=v1))+geom_density(color="red")+
geom_histogram(aes(y=..density..),alpha=0.5)+
stat_function(fun=dnorm,args=list(mean=mean(mydata$v1),sd=sd(mydata$v1)),color="green")

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We’ll conclude here . By now you must understand the layering philosophy of graphics, there is a lot of
option still to try and you can explore that by looking at various examples available on the net. Here are few
sources to look at.
http://r4stats.com/examples/graphics-ggplot2/
http://www.cookbook-r.com/Graphs/Bar_and_line_graphs_(ggplot2)/
A slightly advanced source of examples can be found here :
https://plot.ly/ggplot2/
Few sources that i have provided here, are a good starting point for you to explore , by no means that’s an
exhaustive list. Learn and Explore, Explore and learn.
Prepared By: Lalit Sachan
Contact : lalit.sachan@edvancer.in
In case of any doubts or need for clarification , please take to Q&A forum on LMS.

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