Key Concepts
In this chapter, we’ll explore the following key concepts:
Exploratory Data Analysis (EDA)
Exploratory Data Visualization (EDV)
Explanatory vs. Explanatory Plots
The Grammar of Graphics
Data & Non-Data Ink
Aesthetic Mappings
Attributes
Overplotting
Faceting
New Packages
This chapter uses the following packages:
ggplot2
GGally
scales
plotly
library ( datasets )library ( ggplot2 )library ( GGally )
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
library ( scales )library ( plotly )
Attaching package: 'plotly'
The following object is masked from 'package:ggplot2':
last_plot
The following object is masked from 'package:stats':
filter
The following object is masked from 'package:graphics':
layout
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.4 ✔ readr 2.1.5
✔ forcats 1.0.0 ✔ stringr 1.5.1
✔ lubridate 1.9.3 ✔ tibble 3.2.1
✔ purrr 1.0.2 ✔ tidyr 1.3.1
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ readr::col_factor() masks scales::col_factor()
✖ purrr::discard() masks scales::discard()
✖ dplyr::filter() masks plotly::filter(), stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Key Takeaways
Too long; didn’t read? Here’s what you need to know:
We visualize data to:
Submit, Publish, Teach (“Explanatory Viz”)
Explore, Learn, Share (“Exploratory Viz”)
Exploratory viz is a key part of any data analysis
“Grammar of Graphics” framework inspired “ggplot2”
“Layers” are like visual parts of speech
There are 7 layers - 3 are essential
Each layer has a family of functions
Essential layers include:
Data: Intakes data frame/tibble
Aesthetic: Maps variables to axes, color, etc.
Geometry: Specifies the shape of your data
Nonessential layers include:
Statistics: Modeling and computation
Coordinates: Zooming in and modifying scales
Facets: Small multiples, a.k.a. trellis plots
Themes: Overall style - grid lines, text, etc.
Variety of ggplot2 extensions (see resources)
Use package “plotly” to make ggplot2 interactive
Why Visualize Data?
We visualize data for two principal reasons. We want to:
Learn about our data, i.e. exploratory data visualization
Tell our data’s stories to others, i.e. explanatory data visualization
Explanatory Visualization
Explanatory visualization is polished, publication-quality, and interpretable:
Meant to be consumed by broad, non-specialist audiences
Takes significant time and iterations to perfect
Conveys one or two “big ideas”, each
Just note the length of the code and its result. What idea does this plot convey?
library (ggplot2)ggplot (read_csv (url), aes (x = val, y = myr)) + geom_jitter (alpha = 0.3 , color = "tomato" ) + geom_smooth (method = "lm" , se = FALSE , color = "grey50" , lwd = 1 , alpha = 0.3 ) + facet_wrap (~ elm) + labs (title = "Annual income vs. Holland personality scores" , x = "Personality Score" ,y = "Income (K)" ,caption = "Sources: US DOL O*NET & BLS" ) + scale_y_continuous (labels = c ("0" , "50" , "100" , "150" , "$200" )) + theme_minimal ()
To experiment with Holland codes and predicted income, check it out in Shiny .
Exploratory Visualization
Exploratory visualization is “quick and dirty” and intends to discover.
Meant to be consumed by yourself, colleagues, or other specialists
Created quickly, with no polish, refinement, or audience in mind
Can convey many ideas, or none - that’s why you do it!
This code is manageable! Observe a simple call to ggpairs() and the iris dataset.
library ( ggplot2 )library ( GGally )ggpairs ( data= iris, aes ( color= Species ) )
With just a little code, pairs plots visualize every variable against the other.
Hopefully, you wouldn’t publish this. But we can quickly find patterns in a pairs plot:
We can see positive correlations between sepal and petals for two species
We observe that “Setosa” have thinner, longer sepals compared to others
We also observe that “Versicolor” has the least variation in size
Such visual exploration can help refine hypotheses before analysis begins!
YOUR TURN: EXPLORATORY VIZ WITH PAIRS PLOTS
Load the necessary packages with library().
Then, call ggpairs() on the economics dataset from ggplot2.
dc_light_exercise_example-01
Do I have to Visualize?
Exploratory viz is a key component in exploratory data analysis , or EDA .
Failing to visually explore your data can get you in hot water. Let’s try it!
Observe the following data frame containing four data sets.
Variable x1 corresponds to y1, x2 to y2, and so forth:
library (datasets)
x1 x2 x3 x4 y1 y2 y3 y4
1 10 10 10 8 8.04 9.14 7.46 6.58
2 8 8 8 8 6.95 8.14 6.77 5.76
3 13 13 13 8 7.58 8.74 12.74 7.71
4 9 9 9 8 8.81 8.77 7.11 8.84
5 11 11 11 8 8.33 9.26 7.81 8.47
6 14 14 14 8 9.96 8.10 8.84 7.04
7 6 6 6 8 7.24 6.13 6.08 5.25
8 4 4 4 19 4.26 3.10 5.39 12.50
9 12 12 12 8 10.84 9.13 8.15 5.56
10 7 7 7 8 4.82 7.26 6.42 7.91
11 5 5 5 8 5.68 4.74 5.73 6.89
At a glance, they look like the have some similarities!
Check It: Let’s perform a few statistical EDA functions on each subset, 1-4.
What do you notice when we figure out and organize:
Average of all X and Y values with mean()
Variance of all X and Y values with var()
Correlation between X and Y for all sets with cor()
Linear regression coefficients between X and Y with lm()
x_mean y_mean x_var y_var correl coeff
Set 1 9 7.500909 11 4.127269 0.8164205 0.5000909
Set 2 9 7.500909 11 4.127629 0.8162365 0.5000000
Set 3 9 7.500000 11 4.122620 0.8162867 0.4997273
Set 4 9 7.500909 11 4.123249 0.8165214 0.4999091
Heavens to Murgatroyd! These are practically the same sets!
The mean and variance of X is the exact same across sets
The mean and variance of Y is almost exactly the same across sets
The correlation between X & Y is extremely close across sets
The coefficient of determination is also extremely close
Once visualized, all four linear relationships appear to be exactly the same:
Well, that settles that. Pack it up, folks - the data are the same.
Hold up.
Wait a minute.
Something ain’t right.
Let’s try replotting the actual datasets and not just their linear models.
Boom! Not the same datasets at all .
Despite having the same mean, variance, correlations, and coefficients:
Dataset 1 is a normally distributed linear relationship
Dataset 2 is a parabolic curve
Dataset 3 is a perfect linear relationship with a high-leverage outlier
Dataset 4 shows absolutely no relationship but again has an outlier
Conclusion: Always conduct exploratory visualization as a staple of any analysis.
FUN FACT:
You just got Anscombe’d. Francis John “Frank” Anscombe was an English statistician who helped pioneer the field in the twentieth century. He wrote:
“…a computer should make both calculations and graphs…”
To demonstrate, Anscombe invented these datasets: Anscombe’s Quartet .
The Grammar of Graphics
We’ve compared human language and programming languages in the past.
Let’s take the analogy further. Observe the following sentence:
Source: Chionetti, A. (2013)
Recall that language consists of nouns, verbs, adjectives, articles, prepositions, etc.
If we change any part of speech , we change the meaning of our sentence. Observe:
The quick brown fox jumps off the lazy dog.
Now the fox has escalated things, opting to use the poor dog as a springboard.
The quick brown fox runs over the lazy dog.
Well this is just getting graphic.
The decrepit brown fox jumps over the lazy dog.
He’s a good dog.
Parts of Speech: Every part of speech (like adjectives, e.g. “quick”, “lazy”) has a function.
Nouns describe things, verbs describe actions, adjectives describe qualities, etc.
Parts of Viz: Like language, there are parts of visualization . Each part has a function.
A chart’s data could be anything, like quarterly revenues or ELA scores
A chart’s geometry could represent the data as bars, points, lines, or shapes
A chart’s theme could use different fonts, gridlines, transparencies, etc.
These are just some parts of viz in a larger framework: The Grammar of Graphics .
A Brief Overview
In 1999, statistician Leland Wilkinson published The Grammar of Graphics
This framework allows us to dissect and alter plots in the same way we would a sentence.
Let’s begin with parts of viz , or layers .
Layers: Parts of Viz
In the grammar of graphics framework, each visualization is comprised of layers .
Each layer performs a unique function in a visualization
Like parts of speech , a layer can perform one function in infinite ways
For example, the data layer functions to input your data
A noun can be “fox” or “dog; a dataset can be”DOL” or “TSA”
Essential Layers: Data, Mappings, & Shapes
Like human sentences , every complete visualization has 3 essential layers:
The Data Layer
The data layer conveys the dataset informing the visualization.
The data layer inputs a dataset, but doesn’t specify the variables you show
Visualizations can have more than one data layer, e.g. overlay plots
The data layer in everyday conversation:
“Are you pulling occupations from O*NET or BLS? We only need SOC-level.”
Intepretation: Your data layer is comprised of your data source.
Observe the same plot - the only difference is the data layer . What changes?
The Aesthetics Layer
The aesthetics layer conveys which variables to visualize.
Aesthetics refers to the visual ways to represent variablesAesthetics include size, shape, color, fill, line type, transparency, etc.
The most common aesthetic mapping is using x- and y-axes to show quantities
Aesthetics adjust dynamically with your data - they are not static
The aesthetics layer in everyday conversation:
“Can you color-code the datapoints by gender?”
Intepretation: Aesthetics use visual elements like color to convey more data.
Observe the same plot - the only difference is the aesthetics layer . What changes?
The Geometry Layer
The geometry layer conveys the shape your variables use to visualize data.
Geometries include scatter plots, bar charts, line graphs, etc.Some geometries are only compatible with certain variables
Geometries can also take attributes , like size, shape, color, etc.
Geometry attributes do not adjust dynamically with data - they are static
The geometry layer in everyday conversation:
“I’m trying to emphasize the increase in elevated blood lead levels over time.”
Intepretation: It sounds like they’d want a line graph or bar chart to show change.
Observe the same plot - the only difference is the geometry layer . What changes?
PRO TIP
It seems like a small distinction, but the difference is critical:
Both “Attributes” and “Aesthetics” use color, size, line width, fill, etc.
“Attributes” are static and unchanging
“Aesthetics” are dynamic and change with your data
All “aesthetics” are specified in the “aesthetics” layer.
All “attributes” are specified in the “geometries” layer.
Remaining Layers
The 4 remaining layers in the grammar of graphics include:
The coordinates layer modifies plot zoom, truncation, and labeling
The statistics layer performs statistical transformations like lines of best fit
The facets layer creates multiple comparison plots, a.k.a. small multiples
The themes layer modifies font, gridlines, and other “non-data ink” polish
We’ll explore some key functions from these layers in the following sections.
Download the Practice Data
Our practice data are public consruction project worker records in Syracuse, NY.
They were collected for a racial equity impact statement
Download: You can download the practice data here
To Follow Along: Run this code in your R console:
library (readr)<- paste0 ("https://raw.githubusercontent.com/DS4PS/" ,"dp4ss-textbook/master/tables/hancock.csv" )<- read_csv (url)rm (url)
Package “ggplot2”
Package “ggplot2” is a popular, powerful package for data visualization in R.
Authored by Hadley Wickham; maintained by RStudio
An implementation of the “Grammar of Graphics” framework (hence “gg”)
Has a series of function families, each corresponding to a different layer
Expressions in “ggplot2” use a particular syntax. Note that + connects the layers .
Let’s look at a “complete” graph:
library (ggplot2)ggplot (data = hancock) + # Data layer aes (x = net) + # Aesthetics layer geom_histogram () # Geometry layer
Note that the preferred “ggplot2” format is as follows (both do the same thing):
ggplot (data = hancock,aes (x = net)) + # "aes()" is nested in "ggplot()" geom_histogram ()
Let’s break it down. Here are the three layers of a “ggplot2” graphic and how they work:
YOUR TURN: A BASIC GGPLOT
Load the necessary packages with library()
Call ggplot() on the economics dataset from ggplot2
In aes(), map x = to date and y = to unemploy
Call geom_line()
A call to theme_classic() has been added for panache.
dc_light_exercise_example-02
Adding Aesthetics: Let’s plot the same data, except with:
aes() argument x = mapped to netaes() argument y = mapped to grossgeom_histogram() changed to geom_point()
ggplot (data = hancock,aes (x = net,y = gross)) + # Now mapping "gross" to y-axis geom_point () # Changed from geom_histogram()
Modifying Attributes: We can change attributes (non-data ink) in the geom_*() call.
Modify transparency with argument alpha =
Modify color and fill with color = and fill = , respectively
ggplot (data = hancock,aes (x = net,y = gross)) + geom_point (alpha = 0.35 , # Modify transparency between 0 & 1 color = "tomato" ) # Modify color; some colors are known
Modify Labels: We can add function labs() with + to modify labels and titles:
ggplot (data = hancock,aes (x = net,y = gross)) + geom_point (alpha = 0.35 ,color = "tomato" ) + labs (title = "Weekly gross v. net incomes in public construction" ,subtitle = "Hancock Airport, 2018" ,x = "Net Earnings" ,y = "Gross Earnings" ,caption = "Source: Syracuse Regional Airport Authority" )
Premade Themes: Add premade themes with + and theme_ functions:
ggplot (data = hancock,aes (x = net,y = gross)) + geom_point (alpha = 0.35 ,color = "tomato" ) + labs (title = "Weekly gross v. net by public construction workers" ,subtitle = "Hancock Airport, 2018" ,x = "Net Earnings" ,y = "Gross Earnings" ,caption = "Source: Syracuse Regional Airport Authority" ) + theme_minimal () # New theme
Conclusions: In package “ggplot2”, we build on these three essential layers .
The data layer, the aesthetics layer, and the geometry layer
Call data, aesthetics, and geometry in ggplot(), aes(), and geom*() functions
Once you’ve build an initial plot, you can add new layers to enhance it, like themes
Each addition makes plots more decodable and better emphasizes big ideas
YOUR TURN: AESTHETICS & ATTRIBUTES
A basic ggplot has been prepared for you.
Load the necessary packages with library().
Modify geom_point() with the following:
Set size to 2.75 (size = )
Set transparency to 0.15 (alpha = )
Set color to “darkslateblue” (color = )
A theme_minimal() is provided for panache.
dc_light_exercise_example-03
Notable Layer Functions
Each layer in “ggplot2” has an astounding number of functions. Let’s check some out.
The Aesthetics Layer
We’ve seen the principal function of the aesthetics layer , aes().
Most importantly, you should some arguments to which you can map variables:
x = maps to the x-axisy = maps to the y-axisz = maps to the z-axis (3-dimensional, typically)color = maps to colors of points and linesfill = maps to colors of shapes, e.g. barssize = maps to the size of pointslabels = maps to the labels of points, lines, and shapeswidth = maps to the width of linestype = maps to the line type
Read more about aesthetics in the “ggplot2” vignette .
Take the following scatter plot of U.S. unemployed against total population since 1970:
library (ggplot2)ggplot (data = economics, aes (x = unemploy,y = pop)) + geom_point () + theme_minimal ()
We can convey additional information by mapping aesthetics to other variables.
The following maps point size to psavert, or the personal savings rate.
library (ggplot2)ggplot (data = economics, aes (x = unemploy,y = pop,size = psavert)) + # Map personal savings rate to size geom_point (alpha = 0.2 ) + # Set transparency to 20% theme_minimal ()
We can see that regardless of unemployment, savings dwindle as populations grow.
(Population, by the way, is practically interchangeable with date).
CAUTION: OVERPLOTTING & OVERMAPPING
It’s tempting to map many variables to different aesthetics, so be careful to not:
“Overplot”, or obfuscate clarity with too many mappings
“Overmapping”, or mapping a variable to two or more aesthetics
For example, don’t map “population”, e.g. to both color and the y-axis.
As datapoints move upward on the y-axis, the color changes
It may make your plot pretty, but it makes it harder to decode
What’s more, color is redundant and pointless - axes are more decodable
In effect, this is known in data visualization as “belt-and-suspenders design”
Belts or suspenders… you don’t need both!
The Geometry Layer
Each shape your data takes in the geometry layer has an associated function.
View all geometries on the “ggplot2” reference page
Notably, every geometry function begins with geom_
Some statistical functions have equivalents that begin with stat_
You can combine more than one geom function in a singple visual
Rectangular Geoms: When using geoms with rectangular shapes, set stat = to “identity”.
options (scipen = 999 ) # Disable scientific notation ggplot (data = hancock, aes (x = reorder (ethnicity, - net), # Reorder ethnicities by "net" y = net)) + geom_bar (stat = "identity" ) + # Specify stat = "identity" labs (x = NULL ,y = "Weekly Net" ) + theme_minimal ()
Use Fill to Modify Geoms: Map aes() argument fill = to a categorical variable:
ggplot (data = hancock, aes (x = reorder (ethnicity, - net), y = net,fill = reorder (class, - net))) + # Add fill = and reorder() on "net" geom_bar (stat = "identity" ) + labs (x = NULL ,y = "Weekly Net" ,fill = "Class" ) + # Use labs() and fill= to title legend theme_minimal ()
Fill to 100%: With a fill = asthetic, set position = to “fill”:
ggplot (data = hancock, aes (x = reorder (ethnicity, - net), y = net,fill = reorder (class, - net))) + geom_bar (stat = "identity" ,position = "fill" ) + # Set position = to "fill" labs (x = NULL ,y = "Weekly Net" ,fill = "Class" ) + theme_minimal ()
New Geoms with New Positions: With a fill = asthetic, set position = to “dodge”:
ggplot (data = hancock, aes (x = reorder (ethnicity, - net), y = net,fill = reorder (class, - net))) + geom_bar (stat = "identity" ,position = "dodge" ) + # Set position = to "dodge" labs (x = NULL ,y = "Weekly Net" ,fill = "Class" ) + theme_minimal ()
Overlapping Barplots: Set position = to position_dodge() and set width = :
ggplot (data = hancock, aes (x = reorder (ethnicity, - net), y = net,fill = reorder (class, - net))) + geom_bar (stat = "identity" ,position = position_dodge (width = 0.5 )) + # Control the dodge! labs (x = NULL ,y = "Weekly Net" ,fill = "Class" ) + theme_minimal ()
FUN FACT
Many ggplot2 color functions contain brewer in the name. That’s because, by default, ggplot2 uses color palettes based on the research of Dr. Cynthia Brewer .
Dr. Brewer’s premade palettes, all recognized in ggplot2, are available in Color Brewer 2 .
Overlap & Transparency: When multiple points overlap, use transparency (alpha = ).
ggplot (data = hancock, aes (x = reorder (ethnicity, - net), y = net)) + geom_point (alpha = 0.10 ) + # Set transparency to 10% labs (x = NULL ,y = "Weekly Net" ) + theme_minimal ()
Overlapping & Jittering: In combination with transparency, you can “jitter” your points.
“Jittering” adds random horizontal and vertical noise to break up points
In function geom_point(), set position = to “jitter”
Arguments height = and width = controls jitter
Alternatively, use function geom_jitter()
ggplot (data = hancock, aes (x = reorder (ethnicity, - net), y = net)) + geom_jitter (alpha = 0.15 , # Change geom to geom_jitter() width = 0.25 ) + # Set "jitter" width to 0.25 labs (x = NULL ,y = "Weekly Net" ) + theme_minimal ()
YOUR TURN: JITTER & TRANSPARENCY
Load the necessary packages with library().
Then, call ggplot() on the midwest dataset from ggplot2.
Change geom_point() to geom_jitter()
In geom_jitter(), set argument alpha = 0.25
Also in the geom, set argument width = 0.15
dc_light_exercise_example-04
The Statistics Layer
The statistics layer is where data undergo statistical transformations under the hood.
All stat layer functions begin with stat_
Many geometries already use stats, like geom_smooth()
Argument method = can use different models with “lm”, “glm”, “rlm”, etc.
Stat functions typically not called directly, but run within geom functions
Smoothers: Function stat_smooth() adds a LOESS line and standard error area.
ggplot (hancock, aes (x = net,y = gross)) + geom_point () + stat_smooth () + # Function stat-smooth(), same as geom_smooth() theme_minimal ()
Remove Standard Error: Set argument se = to FALSE to disable standard error.
ggplot (hancock, aes (x = net,y = gross)) + geom_point () + stat_smooth (se = FALSE ) + # Argument se = controls standard error theme_minimal ()
Chane Modeling Method: Set argument method = to “lm” for linear models, etc.
ggplot (hancock, aes (x = net,y = gross)) + geom_point () + stat_smooth (se = FALSE ,method = "lm" ) + # Argument method = changes your model theme_minimal ()
The Coordinates Layer: Planes
The coordinates layer ultimately controls the limits and labels of your axes.
All coordinates functions begin with coord_
Most common is coord_cartesian(), which modifies a plot’s Cartesian plane
Flipping Coordinates! No, we’re not cursing out coordinates .
However, you can reverse the x- and y-axes by using function coord_flip():
options (scipen = 999 ) # Disable scientific notation ggplot (data = hancock, aes (x = reorder (ethnicity, net), y = net)) + geom_bar (stat = "identity" ) + labs (title = "Flipped!" ,x = NULL ,y = "Weekly Net" ) + theme_minimal () + coord_flip () # coord_flip() !
Zooming or Filtering: Modifying coordinates typically goes one of two ways:
Zoom in on some specified coordinates
Zoom in and filter out data that are no longer visible
Zoom with coord_cartesian().
Filter with lims().
The Whole Plot (Before): Observe the entirety of the plot without zooming in:
ggplot (hancock,aes (x = net,y = gross)) + geom_point () + geom_smooth () + theme_minimal ()
Zoomed In: We can zoom, without affecting our data, with coordcartesion().
Note the direction and standard error of the LOESS line from geom_smooth().
ggplot (hancock,aes (x = net,y = gross)) + geom_point () + geom_smooth () + theme_minimal () + coord_cartesian (xlim = c (0 , 1250 ), ylim = c (0 , 2000 )) # Zoom in and keep your data!
Filtered: We can use lims() to zoom in and filter data no longer plotted.
Now note how the LOESS line and standard error have changed per this “new” dataset.
ggplot (hancock,aes (x = net,y = gross)) + geom_point () + geom_smooth () + theme_minimal () + lims (x = c (0 , 1250 ), y = c (0 , 2000 )) # Zoom in and filter your data!
QUESTION
Why do the LOESS curves and standard errors change between plots?
The Coordinates Layer: Scales
Scales in “ggplot2” affect your axis gridlines, ticks, breaks, and labels.
Scale functions begin with scale_
Specify which axis with scale_x_ or scale_y_
Also specify discrete, continuous, or another variable type
Example: A discrete (categorical) variable on the y-axis is scale_y_discrete()
Axis Titles: Change (or remove) axis titles with argument name = :
ggplot (hancock,aes (x = net,y = gross)) + geom_point (alpha = 0.05 ) + geom_smooth (color = "grey80" , alpha = 0.1 ) + theme_minimal () + scale_x_continuous (name = "Weekly Net" ) + # Axis? Continuous or discrete? scale_y_continuous (name = "Weekly Gross" ) # Argument name = for axis titles
Breaks: Specify axes’ major label and tick marks with argument breaks = and c():
ggplot (hancock,aes (x = net,y = gross)) + geom_point (alpha = 0.05 ) + geom_smooth (color = "grey80" , alpha = 0.1 ) + theme_minimal () + scale_x_continuous (name = "Weekly Net" ,breaks = c (0 , 1250 , 2500 )) + scale_y_continuous (name = "Weekly Gross" ,breaks = c (0 , 1500 , 3000 )) # Even breaks
Labels: Customize individual labels with argument labels = (ojo - can get lengthy):
ggplot (hancock,aes (x = net,y = gross)) + geom_point (alpha = 0.05 ) + geom_smooth (color = "grey80" , alpha = 0.1 ) + theme_minimal () + scale_x_continuous (name = "Net" ,breaks = c (0 , 1250 , 2500 ),labels = c ("$ 0" , "1.25" , "2.5 K" )) + scale_y_continuous (name = "Gross" ,breaks = c (0 , 1500 , 3000 ),labels = c ("$ 0" , "1.5" , "3 K" )) # Labels in quotes
Pretty Breaks: Package “scales” allows us to more easily format scale_*() functions.
Format breaks automatically (pretty-like)
Label dollar amounts and percentages with ease
Pretty Names: With “scales”, argument name = accepts new standards:
library (scales)ggplot (hancock,aes (x = net,y = gross)) + geom_point (alpha = 0.05 ) + geom_smooth (color = "grey80" , alpha = 0.1 ) + theme_minimal () + scale_x_continuous (name = "Net" ,breaks = c (0 , 1250 , 2500 ),labels = dollar) + # Auto-labeling: Good scale_y_continuous (name = "Gross" ,breaks = c (0 , 1500 , 3000 ),labels = dollar) # Less flexibility: Bad
Pretty Breaks: With “scales”, argument breaks = accepts pretty_breaks():
library (scales)ggplot (hancock,aes (x = net,y = gross)) + geom_point (alpha = 0.05 ) + geom_smooth (color = "grey80" , alpha = 0.1 ) + theme_minimal () + scale_x_continuous (name = "Net" ,breaks = pretty_breaks (5 ),labels = dollar) + # pretty_breaks() ! scale_y_continuous (name = "Gross" ,breaks = pretty_breaks (12 ),labels = dollar) # Pretty sick
PRO TIP: PACKAGE “SCALES” APPLICATIONS
The “scales” package has a host of amazing formatting functions. Commonly:
dollar() and dollar_format() for currencypercent() and percent format() for percentsnumber() and number_format() for numbers
These and other functions are incredibly useful, especially for cleaning.
YOUR TURN: STATS, COORDINATES, AND SCALES
Load the necessary packages with library().
In geom_point(), set “alpha = 0.3”
Add geom_smooth() with +
Add lims() with:
x = c(0, 10000)y = c(0, 50)
In scale_x_continuous(), add “label = name”
Add labs() with:
x = “Population Density”y = “College Educated (%)”
dc_light_exercise_example-05
The Faceting Layer
The faceting layer allows us to create facets , a.k.a small multiples or trellis charts.
All faceting functions begin with facet_
facet_wrap() creates a grid; facet_grid() creates side-by-sidesThere are other arguments, but the formula x ~ y (variables), is critical
Single-Variable Faceting: The formula x ~ y needs only one side.
You can replace the empty side with . or leave it blank.
ggplot (hancock,aes (x = net,y = gross)) + geom_point (alpha = 0.5 ) + geom_smooth (alpha = 0.5 ,method = "lm" ) + theme_minimal () + scale_x_continuous (name = "Net" ,breaks = pretty_breaks (3 ),labels = dollar) + scale_y_continuous (name = "Gross" ,breaks = pretty_breaks (3 ),labels = dollar) + facet_wrap (facets = ethnicity ~ .) # Only one side needed
Facet Grid: When you want side-by-side comparisons for all plots, use facet_grid():
ggplot (hancock,aes (x = net,y = gross)) + geom_point (alpha = 0.5 ) + geom_smooth (alpha = 0.5 ,method = "lm" ) + theme_minimal () + scale_x_continuous (name = "Net" ,breaks = pretty_breaks (3 ),labels = dollar) + scale_y_continuous (name = "Gross" ,breaks = pretty_breaks (3 ),labels = dollar) + facet_grid (facets = . ~ ethnicity, ) # Now with facet_grid() !
Modify facet_*() functions with arguments beyond the x ~ y formula.
rows = accepts the number of rows in a facet gridcols = accepts the number of columnslabeller = accepts new strip names
YOUR TURN: FACETING
Unfortunately, the R widget cannot visualize faceting (yet).
Open a new RStudio script. Copy and paste the below code.
Use a facet_*() function on variable cut.
dc_light_exercise_example-06
The Themes Layer
The themes layer allows you to customize ever pixel of non-data ink in your plot.
Function themes() is the workhorse function for this layer
themes() arguments are a large but consistent frameworkFunctions beginning with theme_ set premade themes
The themes layer adjusts every non-data pixel
Everything we’ve done so far, plus changing the facet strip labels:
ggplot (hancock,aes (x = net,y = gross)) + geom_point (alpha = 0.5 ,color = "grey30" ) + geom_smooth (alpha = 0.5 ,method = "lm" ) + theme_minimal () + scale_x_continuous (name = "Net" ,breaks = pretty_breaks (3 ),labels = dollar) + scale_y_continuous (name = "Gross" ,breaks = pretty_breaks (3 ),labels = dollar) + facet_wrap (facets = . ~ ethnicity) + theme (strip.text = element_text (face = "bold" ,color = "grey40" ,family = "Verdana" )) # The framework in action
So what the hell was that? There’s a whole consistent framework here!
There’s a few hierarchies of functions and arguments that we’ll look at below.
We’ve saved the above plot in object p, which we’ll use herein.
First Entering theme(): You’ll get hit with four short arguments:
line = modifies all lines in the plotrect = modifies all rectangles in the plottext = modifies all text in the plottitle = modifies just titles in the plot
Latter Arguments in theme(): More specific argument families for each element.
axis arguments for axis lines, ticks, and textlegend arguments for boxes, keys, spacing, text, and titlespanel arguments for overall plot spacing and grid linesplot arguments for tags, titles, and marginsstrip arguments for facet strip text and backgrounds
+ theme (axis.title = ...)
Once Argument is Selected: Arguments typically accept theme element functions:
All element functions begin with element_
element_rect() applies to rectangleselement_line() applies to lineselement_text() applies to textelement_blank() removes it
+ theme (axis.title = element_text (color = "gray50" ,face = "bold" ,size = 10 ))
YOUR TURN: CUSTOMIZING TITLE THEMES
Load package scales to help format our scales. In themes():
Change argument ‘x =’ in labs() to “Year”
Format the plot’s axes title color to “grey20”
Make the main title size 12 and “bold” face
Continue experimenting with modifications
dc_light_exercise_example-07
Interactive Charts with “plotly”
On a brief side note, you can make your “ggplot2” plots interactive with “plotly”.
Saving “ggplot” Objects: You can save plots as objects with assignment, or <-:
library (scales)library (ggplot2)<- ggplot (hancock, # Modified plot assigned to "p" with <- aes (x = net,y = gross)) + geom_point (alpha = 0.5 ,color = "grey30" ) + geom_smooth (alpha = 0.5 ,method = "lm" ) + theme_minimal () + scale_x_continuous (name = "Weekly Net" ,labels = dollar,breaks = pretty_breaks (3 )) + scale_y_continuous (name = "Weekly Gross" ,labels = dollar,breaks = pretty_breaks (4 )) + facet_wrap (facets = . ~ ethnicity)
Plotlify! Once loaded, use function ggplotly() on your ggplot oject :
library (plotly) ggplotly (p) # Insert your ggplot object!
Sweet. Not perfect - but with a bit of TLC it’d be right as rain.
Combining Plots
Overlaying one plot ontop of another is simply a matter of adding geoms .
Needed within those geoms may be new calls to aes().
Let’s begin with a simple jitter plot of net distributed by ethnicity:
ggplot (hancock,aes (x = net,y = ethnicity)) + geom_jitter (height = 0.3 ,alpha = 0.3 ,color = "steelblue" ) + theme_minimal ()
Overlay plots by adding additional geom . Here, we add geom_boxplot():
ggplot (hancock,aes (x = ethnicity,y = net)) + geom_jitter (height = 0.3 ,alpha = 0.3 ,color = "steelblue" ) + coord_flip () + theme_minimal () + geom_boxplot (height = 0.3 , # Simply add the new geom fill = "transparent" , # Modify attributes accordingly color = "grey50" )
The Final Product: A plot overlay with some finishing touches:
library (extrafont)ggplot (hancock,aes (x = reorder (ethnicity, net),y = net)) + geom_jitter (height = 0.3 ,alpha = 0.4 ,color = "dodgerblue" ) + coord_flip () + theme_minimal () + geom_boxplot (height = 0.2 ,fill = "transparent" ,color = "grey50" ) + labs (title = "Distribution of weekly net by ethnicity" ,subtitle = "Hancock Airport, 2018" ,x = NULL ,y = "Weekly Net" ,caption = "Source: Syracuse Regional Airport Authority" ) + scale_y_continuous (labels = dollar) + theme (text = element_text (family = "Calibri Light" ),axis.title.x = element_text (vjust = - 1 ,color = "grey20" ),plot.caption = element_text (vjust = - 1 ,color = "grey60" ),plot.subtitle = element_text (vjust = 1 ,color = "grey30" ),plot.title = element_text (vjust = 2 ,color = "grey10" ),axis.text.x = element_text (colour = "grey10" ),axis.text.y = element_text (colour = "grey10" ))
Package “ggplot2” Extensions
We used a “ggplot2” extension in the introduction to this chapter: “GGally” .
You can find a list of every single extension at the ggplot2 extensions gallery
Further Resources
To review the practice data from Hancock Airport, get the raw data URL here .
There’s a lot to master here - but it’s worth it. These can help:
