Data visualization using ggplot2 and its

extensions

R-Ladies Tunis | useR! 2021 Conference | 7 July 2021

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Haifa Ben Messaoud

                
Amir Souissi

    Data Scientist

                      Consultant Data Scientist

Find us at...
   @rladiestunis

   @rladiestunis

   [email protected]

                  

    
Kaouthar Driss
                              
Mouna Belaid

Data Science Engineer

    Data Scientist

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 Outline
1) Data presentation using the peopleanalyticsdata package

2) One-variable visualization

Boxplot Viz

Barplot Viz

Density Histogram Viz

3) Two-variables visualization

Two categorical variables: geom_count,etc.

Two numeric variables: scatterplots, etc.

One categorical, one numeric: boxplots, etc.

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 Outline
4) Correlation Matrix for three or more variable Viz

Augmenting one- and two-variable visualization with color, and other aesthetic mappings

5) Graph appearance enhancement

How to add animation to a graph

How to make your graphs look professional

Adding RStudio logo

Graph export options

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 How to follow this workshop
Workshop materials are available at the following link

Prerequisites:

Basic proficiency in R
Some basic knowledge about different R data types & structures (character, numeric, data frame, etc.)

Possibility to communicate with Teacher Assistants for relevant questions about our training session

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 Learning goals 🚀
Get a clear understanding of the ggplot2 R package and some of its extensions: ggprism, ggstatsplot, gganimate, GGally and
patchwork

Design effective data visualization by choosing the appropriate ggplot2 geoms when selecting the data

Make some visualization enhancements using professional plots

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 What is the grammar of graphics?
Google defines a grammar as “the whole system and structure of a language or of languages in general, usually taken as
consisting of syntax and morphology (including inflections) and sometimes also phonology and semantics.”1

Others consider a grammar to be “the fundamental principles or rules of an art or science.2

Applied to visualizations, a grammar of graphics is a grammar used to describe and create a wide range of statistical graphics.3

The layered grammar of graphics approach is implemented in ggplot2, a widely used graphics library for R. All graphics in
this library are built using a layered approach, building layers up to create the final graphic.

The ggplot2 is an abbreviation of grammar of graphics plot. The ggplot2 is created by Hadley Wickham.

Hadley Wickham wrote a very interesting book ggplot2: elegant graphics for data analysis that shows you how to use ggplot2 to
create graphics that help you understand your data.

[1] Google

[2] Wickham, Hadley. (2010) “A Layered Grammar of Graphics”. Journal of Computational and Graphical Statistics, 19(1).

[3] Wilkinson, Leland. (2005). The Grammar of Graphics. (UChicago authentication required)

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 The components of graphics using ggplot2
- Data: is what we want to visualize. Data should be in a data.frame format to be used in ggplot2.

- Coordinate system (coord): A coord describes how data coordinates are mapped to the plane of the graphics. We normally use
Cartesian coordinates (default), but a number of others are available, including polar coordinates and map projections.

- Geoms: The geoms are the geometric objects that are drawn to represent the data such as points, lines, areas, polygons, etc.

- Aesthetics: Aesthetics are visual properties of geoms such as x and y positions, colors, shapes, transparency, etc.

- Scales: Scales map values in the data space to values in the aesthetic space whether it is color, size, or shape.

- Statistical transformation (stats): The stats summarize data in many useful ways. Examples binning and counting to create a
histogram and regression line for regression analysis.

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 Prior installation
install.packages(c('peopleanalyticsdata',
'ggplot2',
'summarytools',
'dplyr',
'ggprism',
'GGally',
'magick',
'patchwork',
'ggstatsplot',
'gganimate'))

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 Overview of the peopleanalyticsdata R package
Data sets for statistical inference modeling related to People Analytics.
Contains eleven data sets from the book 'Handbook of
Regression Modeling in People Analytics' by Keith McNulty (2020).

library(peopleanalyticsdata)
data(package = 'peopleanalyticsdata')

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 DT::datatable(sociological_data,
fillContainer = FALSE, options = list(autoWidth = TRUE, pageLength = 4, scrollX =

Show 4 entries Search:

annual_income_ppp average_wk_hrs education_months region job_type gender family_size work_d

Southern
1 66417 50 157 Unskilled F 5
Asia

Southern
2 55124 50 156 Unskilled F 5
Asia

Southern
3 55124 50 155 Unskilled F 5
Asia

Southern
4 54238 50 154 Unskilled F 5
Asia

Showing 1 to 4 of 2,618 entries Previous 1 2 3 4 5 … 655 Next

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 Data Frame Summary
Dimensions: 2618 x 9

Duplicates: 16

Freqs (% of
No Variable Stats / Values Graph Missing
Valid)
annual_income_ppp Mean (sd) : 76040.1 (20981.7)
min < med < max:
2863 < 82140 < 361 distinct 10
1
[integer] 119564
IQR (CV) : 27459 (0.3) values (0.4%)
average_wk_hrs Mean (sd) : 44.2 (5.9)
min < med < max:
30 < 43 < 55
IQR (CV) : 11 26 distinct 34
2
[integer] (0.1) values (1.3%)
education_months Mean (sd) : 179.3 (39.7)
min < med < max:
40 < 184 < 280
IQR (CV) 173 distinct 19
3
[integer] : 50 (0.2) values (0.7%)

Generated by summarytools 0.9.8 (R version 4.0.3)

2021-07-07

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 Boxplot
A boxplot aims to study the distribution. It can also show the distribution within multiple groups, along with the median, range,
and outliers.

The dark line inside the box represents the median. The top of box is 75% percentile and bottom of box is 25% percentile.

The end points of the lines (a.k.a whiskers) is at a distance of 1.5*IQR, where IQR or Inter Quartile Range is the distance
between 25th and 75th percentiles. The points outside the whiskers are marked as dots and are normally considered as extreme
points.

geom_boxplot()
Requires to specify the data data().
Requires the x and y aesthetic inside aes() while plotting one numeric and one categorical data visualization.
Can change appearance of the boxes with color, fill, alpha arguments.

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 One-variable visualization: Boxplot

ggplot(data = sociological_data)

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 One-variable visualization: Boxplot

ggplot(data = sociological_data) +
aes(x = gender,
y = annual_income_ppp)

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 One-variable visualization: Boxplot

ggplot(data = sociological_data) +
aes(x = gender,
y = annual_income_ppp) +
geom_boxplot()

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 One-variable visualization: Boxplot

ggplot(data = sociological_data) +
aes(x = gender,
y = annual_income_ppp) +
geom_boxplot() +
scale_x_discrete(labels = c('F' = 'Female',

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 One-variable visualization: Boxplot

ggplot(data = sociological_data) +
aes(x = gender,
y = annual_income_ppp,
fill = gender) +
geom_boxplot() +
scale_x_discrete(labels = c('F' = 'Female',
scale_fill_manual(name ='Gender',
labels = c('Female','Male
values = c('#FF1493' , '#

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 One-variable visualization: Boxplot

ggplot(data = sociological_data) +
aes(x = gender,
y = annual_income_ppp,
fill = gender) +
geom_boxplot() +
scale_x_discrete(labels = c('F' = 'Female',
scale_fill_manual(name ='Gender',
labels = c('Female','Male
values = c('#FF1493' , '#
ggtitle(label = 'Annual income by gender')
xlab(label = 'Gender') +
ylab(label = 'Annual income in USD')

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 One-variable visualization: Boxplot

ggplot(data = sociological_data) +
aes(x = gender,
y = annual_income_ppp,
fill = gender) +
geom_boxplot() +
scale_x_discrete(labels = c('F' = 'Female',
scale_fill_manual(name ='Gender',
labels = c('Female','Male
values = c('#FF1493' , '#
ggtitle(label = 'Annual income by gender')
xlab(label = 'Gender') +
ylab(label = 'Annual income in USD') +
theme_bw()

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 One-variable visualization: Boxplot - How to add
statistical details
To add statistical details to out boxplot, we will use ggstatsplot is an extension of ggplot2 package for creating graphics with
details from statistical tests included in the information-rich plots themselves.

In a typical exploratory data analysis workflow, data visualization and statistical modeling are two different phases: visualization
informs modeling, and modeling in its turn can suggest a different visualization method, and so on and so forth.

The central idea of ggstatsplot is simple: combine these two phases into one in the form of graphics with statistical details,
which makes data exploration simpler and faster.

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 One-variable visualization: Boxplot - How to add
statistical details
This function creates either a violin plot, a box plot, or a mix of two for between-group or between-condition comparisons with results
from statistical tests in the subtitle.

library(ggstatsplot)
ggbetweenstats(
data = sociological_data,
x = gender,
y = annual_income_ppp,
title = "Annual income by gender"
)

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 Barplot
A barplot displays the relationship between a numeric and a categorical variable.

A type of graph in which different amounts that are being compared are shown using rectangles that have different
lengths but the same width.

geom_bar()
Requires to specify data data().
Provides both x and y inside aes() where, x is either character or factor and y is numeric.
Specifies width of bars with the bins or binwidth argument
Sets stat=identity to make a bar chart create bars instead of a histogram.
Can change appearance of the bars with color, fill, alpha arguments.

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 One-variable visualization: Barplot

ggplot(data = sociological_data) +
aes(x = gender,
y = average_wk_hrs) +
geom_bar(stat = 'identity', binwidth = 0.5)

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 One-variable visualization: Barplot

ggplot(data = sociological_data) +
aes(x = gender,
y = average_wk_hrs) +
geom_bar(stat = 'identity', binwidth = 0.5)
scale_x_discrete(labels = c('F' = 'Female',

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 One-variable visualization: Barplot

ggplot(data = sociological_data) +
aes(x = gender,
y = average_wk_hrs,
fill = gender) +
geom_bar(stat='identity', binwidth = 0.5) +
scale_x_discrete(labels = c('F' = 'Female',
scale_fill_manual(name = 'Gender',
labels = c('Female','Male
values = c('#FF1493','#41

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 One-variable visualization: Barplot

ggplot(data = sociological_data) +
aes(x = gender,
y = average_wk_hrs,
fill = gender) +
geom_bar(stat='identity', binwidth = 0.5) +
scale_x_discrete(labels = c('F' = 'Female',
scale_fill_manual(name = 'Gender',
labels = c('Female','Male
values = c('#FF1493','#41
ggtitle(label = 'Average of working hours b
xlab(label = 'Gender') +
ylab(label = 'Average working hours')

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 One-variable visualization: Barplot

ggplot(data = sociological_data) +
aes(x = gender,
y = average_wk_hrs,
fill = gender) +
geom_bar(stat='identity', binwidth = 0.5) +
scale_x_discrete(labels = c('F' = 'Female',
scale_fill_manual(name = 'Gender',
labels = c('Female','Male
values = c('#FF1493','#41
ggtitle(label = 'Average of working hours b
xlab(label = 'Gender') +
ylab(label = 'Average working hours') +
scale_y_continuous(expand = c(0,0)) +
theme_bw()

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 One-variable visualization: Barplot

ggplot(data = sociological_data) +
aes(x = gender,
y = average_wk_hrs,
fill = gender) +
geom_bar(stat='identity', binwidth = 0.5) +
scale_x_discrete(labels = c('F' = 'Female',
scale_fill_manual(name = 'Gender',
labels = c('Female','Male
values = c('#FF1493','#41
ggtitle(label = 'Average of working hours b
xlab(label = 'Gender') +
ylab(label = 'Average working hours') +
scale_y_continuous(expand = c(0,0)) +
theme_bw() +
coord_flip()

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 Density Histogram
we attempt to visualize the underlying probability distribution of the data by drawing an appropriate continuous curve.

geom_histogram()
A histogram corresponds to a set of filled rectangles whose heights correspond to the counts and whose widths
correspond to the width of the variable bins.

In a density plot,

Requires to specify data data().

Requires the x aesthetic inside aes().
Used to change appearance of the bars with color, fill, alpha arguments.

geom_density()
Dedicated to change the appearance of the curve with size, col, lty arguments.

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 One-variable visualization: Density Histogram

ggplot(data = sociological_data) +
aes(x = education_months,
y = ..density..) +
geom_histogram()

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 One-variable visualization: Density Histogram

ggplot(data = sociological_data) +
aes(x = education_months,
y = ..density..) +
geom_histogram() +
geom_density(size = 1,
col = 'black',
lty = 2)

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 One-variable visualization: Density Histogram

ggplot(data = sociological_data) +
aes(x = education_months,
y = ..density..) +
geom_histogram() +
geom_density(size = 1,
col = 'black',
lty = 2) +
xlab(label = 'Education (months)') +
ylab(label = 'Density')

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 One-variable visualization: Density Histogram

ggplot(data = sociological_data) +
aes(x = education_months,
y = ..density..) +
geom_histogram(aes(color = gender,
fill = gender),
alpha = 0.4,
position = 'identity') +
geom_density(aes(color = gender),
size = 1,
lty = 2) +
xlab(label = 'Education (months)') +
ylab(label = 'Density') +
scale_fill_manual(values = c('#FF1493', '#4
scale_color_manual(values = c('#FF1493', '#

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 Scatterplot
A scatterplot aims to understand the nature of relationship between two dependant variables.

geom_point()
Requires to specify data data().
Requires the x and y aesthetic inside aes().

geom_smooth()
Draws a smoothing line (based on loess) by default, can be tweaked to draw the line of best fit by setting method='lm'.

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 Two-variable visualization : Scatterplot

ggplot(data = sociological_data) +
aes(x = annual_income_ppp,
y = education_months) +
geom_point()

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 Two-variable visualization : Scatterplot

ggplot(data = sociological_data) +
aes(x = annual_income_ppp,
y = education_months) +
geom_point(shape = 18,
color = '#88398a')

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 Two-variable visualization : Scatterplot

ggplot(data = sociological_data) +
aes(x = annual_income_ppp,
y = education_months) +
geom_point(shape = 18,
color = '#88398a') +
xlab(label = 'Annual income in USD') +
ylab(label = 'Education (months)')

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 Two-variable visualization : Scatterplot

ggplot(data = sociological_data) +
aes(x = annual_income_ppp,
y = education_months) +
geom_point(shape = 18,
color = '#88398a') +
xlab(label = 'Annual income in USD') +
ylab(label = 'Education (months)') +
geom_smooth(method = lm)

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 Two-variable visualization : Scatterplot

ggplot(data = sociological_data) +
aes(x = annual_income_ppp,
y = education_months) +
geom_point(shape = 18,
color = '#88398a') +
xlab(label = 'Annual income in USD') +
ylab(label = 'Education (months)') +
geom_smooth(method = lm,
linetype = 'dashed',
color = 'darkred',
fill = 'blue')

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 Two-variable visualization : Scatterplot

ggplot(data = sociological_data) +
aes(x = annual_income_ppp,
y = education_months,
color = job_type) +
geom_point(shape = 18) +
geom_smooth(method = lm,
linetype = 'dashed') +
xlab(label = 'Annual income in USD') +
ylab(label = 'Education (months)') +
scale_color_manual(name = 'Job type',
values = c('#E69F00','#5
theme(legend.position = "bottom")

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 Two-variable visualization : Scatterplot

library(ggpmisc)
library(dplyr)
sociological_data_S <- sociological_data
filter(job_type %i
p + theme(legend.position = "bottom",
text = element_text(size = 10))
stat_poly_eq(formula = y ~ x,
data = sociological_data
color='#E69F00',
rr.digits = 3,
aes(annual_income_ppp,
education_months,
label = paste('Skill
..eq.l
'~ital
..rr.l
sep =
eq.with.lhs = 'italic(ed
eq.x.rhs = '~italic(inc)
parse = TRUE,
label.y.npc = .95,
label.x.npc = .01)

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 Two-variable visualization : Scatterplot

library(ggpmisc)
library(dplyr)
sociological_data_U <- sociological_data
filter(job_type %i
p + theme(legend.position = "bottom",
text = element_text(size = 10))
stat_poly_eq(formula = y ~ x,
data = sociological_data
color='#56B4E9',
rr.digits = 3,
aes(annual_income_ppp,
education_months,
label = paste('Unski
..eq.l
'~ital
..rr.l
sep =
eq.with.lhs = 'italic(ed
eq.x.rhs = '~italic(inc)
parse = TRUE,
label.y.npc = .90,
label.x.npc = .01)

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 Correlation matrix
A correlation matrix is simply a table that displays the correlation coefficients for different numerix variables. The
matrix depicts the correlation between all the possible pairs of values in a table. It is a powerful tool to summarize a
large dataset and to identify and visualize patterns in the given data.

corr()
Calculates the correlation between two variables.

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 Three-variable visualization : Correlation matrix
DT::datatable(round(cor(sociological_data[,-c(4,5,6)]),3),
fillContainer = FALSE, options = list(autoWidth = TRUE, scrollX = TRUE))

Show 10 entries Search:

annual_income_ppp average_wk_hrs education_months family_size work_distance languages

annual_income_ppp 1 -0.595 0.773 0.231 -0.025 -

average_wk_hrs -0.595 1 -0.585 -0.247 0.083

education_months 0.773 -0.585 1 0.295 -0.044 -

family_size 0.231 -0.247 0.295 1 -0.093

work_distance -0.025 0.083 -0.044 -0.093 1

languages -0.018 0.063 -0.032 -0.06 0.938

Showing 1 to 6 of 6 entries Previous 1 Next

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 Three-variable visualization : Correlation matrix
library(GGally)
ggpairs(sociological_data, columns = 1:3)

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 Three-variable visualization : Correlation matrix
library(GGally)
ggpairs(sociological_data, columns = 1:3) +
theme_bw()

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 Three-variable visualization : Correlation matrix
library(GGally)
ggpairs(sociological_data, columns = 1:3,
lower = list(continuous = wrap('smooth',
method = 'lm',
color='grey')),
diag = list(continuous = wrap('barDiag')),
upper = list(continuous = wrap('cor', size = 5))) +
theme_bw()

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 Three-variable visualization : correlation matrix
library(GGally)
ggpairs(sociological_data,
columns = 1:3,
ggplot2::aes(colour = gender))

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 Graph appearance enhancement : changing the
theme

library(ggprism)

ggplot(data = sociological_data) +
aes(x = annual_income_ppp,
y = average_wk_hrs) +
geom_point(aes(color = factor(family_size))
xlab(label = 'Indivdual annual income (PPP
ylab(label = 'Average number of hours per w
scale_color_manual(name = 'Family size',
values = c('#1B9E77', '#
'#7570B3', '#
'#66A61E', '#
'#A6761D', '#
'#4267B2')) +
theme_prism(base_size = 12)

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 Graph appearance enhancement : making
animation

library(gganimate)

p <- ggplot(data = sociological_data) +

aes(x = annual_income_ppp,
y = average_wk_hrs) +
geom_point(aes(color = factor(family_siz
xlab(label = 'Indivdual annual income (P
ylab(label = 'Average number of hours pe
scale_color_manual(name = 'Family size',
values = c('#1B9E77', '#
'#7570B3', '#
'#66A61E', '#
'#A6761D', '#
'#4267B2')) +
theme_prism(base_size = 12)
anim <- p +
transition_states(family_size,
transition_length = 2,
state_length = 1)
anim

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 How to make your plot looks professional

library(ggprism)

ggplot(data = sociological_data) +
aes(x = annual_income_ppp,
y = education_months,
color = job_type) +
geom_point() +
ggtitle('Education and income by job type')
xlab(label = 'Annual income in USD') +
ylab(label = 'Total months spend in educati
labs(caption = 'Source : Sociological surve
scale_color_manual(name ='Job type',
labels = c('Skilled','Un
values = c('#E69F00','#5
theme_prism(base_size = 12) +
theme(legend.position = "bottom")

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 How to make your plot looks professional

library(magick)
library(ggprism)
ggplot(data = sociological_data) +
aes(x = annual_income_ppp,
y = education_months,
color = job_type) +
geom_point() +
ggtitle('Education and income by job type')
xlab(label = 'Annual income in USD') +
ylab(label = 'Total months spend in educati
labs(caption = 'Source : Sociological surve
scale_color_manual(name ='Job type',
labels = c('Skilled','Un
values = c('#E69F00','#5
theme_prism(base_size = 12) +
theme(legend.position = "bottom")
grid::grid.raster(image_read('figs/RStudio-Lo
x = 0.1,
y = 0.005,
just = c('left', 'bottom'),
width = unit(1, 'inches'))

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 How to lay out multiple plots
We will use patchwork package an extension of ggplot2 that combine two or more graphs together.

The + operator simply combines plots.

The | will place plots next to each other.

The / will place them on top of each other.

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 How to lay out multiple plots

library(patchwork)
p1 <- ggplot(data = sociological_data) +
aes(x = annual_income_ppp,
y = education_months) +
geom_point(shape = 18,
color = '#88398a') +
xlab(label = 'Annual income in USD') +
ylab(label = 'Education (months)')
p2 <- ggplot(data = sociological_data) +
aes(x = gender,
y = average_wk_hrs,
fill = gender) +
geom_bar(stat='identity', binwidth = 0.
scale_x_discrete(labels = c('F' = 'Fema
scale_fill_manual(name = 'Gender',
labels = c('Female','Male
values = c('#FF1493','#41
ggtitle(label = 'Average of working hou
xlab(label = 'Gender') +
ylab(label = 'Average working hours') +
scale_y_continuous(expand = c(0,0)) +
theme_bw()
p1 / p2

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 Graph export options
ggsave('figs/figure.jpeg', width = 8, height = 6, units = 'in', dpi = 600, limitsize = TRUE

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 Thanks!
   @rladiestunis

   @rladiestunus

   [email protected]

Slides created with remark.js and the R package xaringan

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