Proportions

Abstract

Types, Categories, and Counts

…“Thinking is difficult, that’s why most people judge.”

— C.G. Jung

Setting up R Packages

library(tidyverse)
library(mosaic) # Our trusted friend
library(skimr)
library(vcd) # Michael Friendly's package, Visualizing Categorical Data
library(vcdExtra) # Categorical Data Sets

library(resampledata) # More datasets

library(GGally) # Correlation Plots
library(visStatistics) # Comprehensive all-in-one stats viz/test package
library(ca) # Correspondence Analysis, for use some day

library(ggmosaic) # Mosaic Plots
library(ggpubr) # Colours, Themes and new geometries in ggplot
## Making Tables
library(kableExtra) # html styled tables
library(gt)
library(tinytable)

Plot Theme

# https://stackoverflow.com/questions/74491138/ggplot-custom-fonts-not-working-in-quarto

# Chunk options
knitr::opts_chunk$set(
  fig.width = 7,
  fig.asp = 0.618, # Golden Ratio
  # out.width = "80%",
  fig.align = "center"
)
### Ggplot Theme
### https://rpubs.com/mclaire19/ggplot2-custom-themes

theme_custom <- function() {
  font <- "Roboto Condensed" # assign font family up front

  theme_classic(base_size = 14) %+replace% # replace elements we want to change

    theme(
      text = element_text(family = font),
      panel.grid.minor = element_blank(), # strip minor gridlines

      # text elements
      plot.title = element_text( # title
        family = font, # set font family
        # size = 20,               #set font size
        face = "bold", # bold typeface
        hjust = 0, # left align
        # vjust = 2                #raise slightly
        margin = margin(0, 0, 10, 0)
      ), plot.title.position = "plot",
      plot.subtitle = element_text( # subtitle
        family = font, # font family
        # size = 14,                #font size
        hjust = 0,
        margin = margin(2, 0, 5, 0)
      ),
      plot.caption = element_text( # caption
        family = font, # font family
        size = 8, # font size
        hjust = 1
      ), # right align

      axis.title = element_text( # axis titles
        family = font, # font family
        size = 10 # font size
      ),
      axis.text = element_text( # axis text
        family = font, # axis family
        size = 8
      ) # font size
    )
}

# Set graph theme
theme_set(new = theme_custom())

What graphs will we see today?

Variable #1	Variable #2	Chart Names	Chart Shape
Qual	Qual	Pies, and Mosaic Charts

What kind of Data Variables will we choose?

No	Pronoun	Answer	Variable/Scale	Example	What Operations?
3	How, What Kind, What Sort	A Manner / Method, Type or Attribute from a list, with list items in some " order" ( e.g. good, better, improved, best..)	Qualitative/Ordinal	Socioeconomic status (Low income, Middle income, High income),Education level (HighSchool, BS, MS, PhD),Satisfaction rating(Very much Dislike, Dislike, Neutral, Like, Very Much Like)	Median,Percentile

Introduction

To recall, a categorical variable is one for which the possible measured or assigned values consist of a discrete set of categories, which may be ordered or unordered. Some typical examples are:

• Gender, with categories “Male,” “Female.”
• Marital status, with categories “Never married,” “Married,” “Separated,” “Divorced,” “Widowed.”
• Fielding position (in baseball cricket), with categories “Slips,”Cover “,”Mid-off “Deep Fine Leg”, “Close-in”, “Deep”…
• Side effects (in a pharmacological study), with categories “None,” “Skin rash,” “Sleep disorder,” “Anxiety,” . . ..
• Political attitude, with categories “Left,” “Center,” “Right.”
• Party preference (in India), with categories “BJP” “Congress,” “AAP,” “TMC”…
• Treatment outcome, with categories “no improvement,” “some improvement,” or “marked improvement.”
• Age, with categories “0–9,” “10–19,” “20–29,” “30–39,” . . . .
• Number of children, with categories 0, 1, 2, . . . .

As these examples suggest, categorical variables differ in the number of categories: we often distinguish binary variables (or dichotomous variables) such as Gender from those with more than two categories (called polytomous variables).

Inspiration

(a) Obesity across the World

(b) Covid Deaths https://datatopics.worldbank.org/sdgatlas/goal-3-good-health-and-well-being?lang=en

Figure 1: Depicting Proportions

From Figure 1 (a), it is seen that Egypt, Qatar, and the United States are the only countries with a population greater than 1 million on this list. Poor food habits are once again a factor, with some cultural differences. In Egypt, high food inflation has pushed residents to low-cost high-calorie meals. To combat food insecurity, the government subsidizes bread, wheat flour, sugar and cooking oil, many of which are the ingredients linked to weight gain. In Qatar, a country with one of the highest per capita GDPs in the world, a genetic predisposition towards obesity and sedentary lifestyles worsen the impact of rich diets. And in the U.S., bigger portions are one of the many reasons cited for rampant adult and child obesity. For example, Americans ate 20% more calories in the year 2000 than they did in 1983. They consume 195 lbs of meat annually compared to 138 lbs in 1953. And their grain intake has increased 45% since 1970.

It’s worth noting however that this dataset is based on BMI values, which do not fully account for body types with larger bone and muscle mass.

From Figure 1 (b), according to World Bank, six countries (India, Russia, Indonesia, United States, Brazil, and Mexico) accounted for over 60 percent of the total additional deaths in the first two years of the pandemic.

How do these Chart(s) Work?

We saw with Bar Charts that when we deal with single Qual variables, we perform counts for each level of the variable. For a single Qual variable, even with multiple levels ( e.g. Education Status: High school, College, Post-Graduate, PhD), we can count the observations as with Bar Charts and plot Pies.

We can also plot Pie Charts when the number of levels in a single Qual variable are not too many. Almost always, a Bar chart is preferred. The problem is that humans are pretty bad at reading angles. This ubiquitous chart is much vilified in the industry and bar charts that we have seen earlier, are viewed as better options. On the other hand, pie charts are ubiquitous in design and business circles, and are very much accepted! Do also read this spirited defense of pie charts here. https://speakingppt.com/why-tufte-is-flat-out-wrong-about-pie-charts/

What if there are two Quals? Or even more? The answer is to take them pair-wise, make all combinations of levels for both and calculate counts for these. This is called a Contingency Table. Then we plot that table. We’ll see.

Categorical Data

From the {vcd package} vignette:

The first thing you need to know is that categorical data can be represented in three different forms in R, and it is sometimes necessary to convert from one form to another, for carrying out statistical tests, fitting models or visualizing the results.

• Case Data
• Frequency Data
• Cross-Tabular Count Data

Let us first see examples of each.

Case Form

From Michael Friendly Discrete Data Analysis and Visualization :

In many circumstances, data is recorded on each individual or experimental unit. Data in this form is called case data, or data in case form. Containing individual observations with one or more categorical factors, used as classifying variables. The total number of observations is nrow(X), and the number of variables is ncol(X).

R

class(Arthritis)

[1] "data.frame"

# Tibble as HTML for presentation
Arthritis %>%
  head(10) %>%
  kbl(
    caption = "Case Form: Arthritis Treatments
      and Effects<br> First 10 Observations",
    centering = TRUE
  ) %>%
  kable_classic_2(
    html_font = "Cambria",
    full_width = F
  ) %>%
  kable_styling(
    bootstrap_options =
      c("striped", "hover", "responsive")
  )

Case Form: Arthritis Treatments and Effects
First 10 Observations

ID	Treatment	Sex	Age	Improved
57	Treated	Male	27	Some
46	Treated	Male	29	None
77	Treated	Male	30	None
17	Treated	Male	32	Marked
36	Treated	Male	46	Marked
23	Treated	Male	58	Marked
75	Treated	Male	59	None
39	Treated	Male	59	Marked
33	Treated	Male	63	None
55	Treated	Male	63	None

web-r

1

The Arthritis data set has three factors and two integer variables. One of the three factors Improved is an ordered factor.

1. ID
2. Treatment: a factor; Placebo or Treated
3. Sex: a factor, M / F
4. Age: integer
5. Improved: Ordinal factor; None < Some < Marked

Each row in the Arthritis dataset is a separate case or observation.

Frequency Data Form

Data in frequency form has already been tabulated and aggregated by counting over the (combinations of) categories of the table variables. When the data are in case form, we can always trace any observation back to its individual identifier or data record, since each row is a unique observation or case; the reverse, with the Frequency Form is rarely possible.

Frequency Data is usually a data frame, with columns of categorical variables and at least one column containing frequency or count information.

R

str(GSS)

# Tibble as HTML for presentation
GSS %>%
  kbl(
    caption = "General Social Survey",
    centering = TRUE
  ) %>%
  kable_classic_2(
    html_font = "Cambria",
    full_width = F
  ) %>%
  kable_styling(
    bootstrap_options =
      c("striped", "hover", "responsive")
  )

'data.frame':   6 obs. of  3 variables:
 $ sex  : Factor w/ 2 levels "female","male": 1 2 1 2 1 2
 $ party: Factor w/ 3 levels "dem","indep",..: 1 1 2 2 3 3
 $ count: num  279 165 73 47 225 191

General Social Survey

sex	party	count
female	dem	279
male	dem	165
female	indep	73
male	indep	47
female	rep	225
male	rep	191

web-r

1

Respondents in the GSS survey were classified by sex and party identification. As can be seen, there is a count for every combination of the two categorical variables, sex and party.

Table form

Table Form Data can be a matrix, array or table object, whose elements are the frequencies in an n-way table. The variable names (factors) and their levels are given by dimnames(X).

HairEyeColor
class(HairEyeColor)

, , Sex = Male

       Eye
Hair    Brown Blue Hazel Green
  Black    32   11    10     3
  Brown    53   50    25    15
  Red      10   10     7     7
  Blond     3   30     5     8

, , Sex = Female

       Eye
Hair    Brown Blue Hazel Green
  Black    36    9     5     2
  Brown    66   34    29    14
  Red      16    7     7     7
  Blond     4   64     5     8

[1] "table"

HairEyeColor is a “two-way” table, consisting of two tables, one for Sex = Female and the other for Sex = Male. The total number of observations is sum(X). The number of dimensions of the table is length(dimnames(X)), and the table sizes are given by sapply(dimnames(X), length). The data looks like a n-dimensional cube and needs n-way tables to represent.

sum(HairEyeColor)

[1] 592

dimnames(HairEyeColor)

$Hair
[1] "Black" "Brown" "Red"   "Blond"

$Eye
[1] "Brown" "Blue"  "Hazel" "Green"

$Sex
[1] "Male"   "Female"

sapply(dimnames(HairEyeColor), length)

Hair  Eye  Sex 
   4    4    2 

A good way to think of tabular data is to think of a Rubik’s Cube.

Rubik’s Cube model for Multi-Table Data

TipRubik’s Cube and Categorical Data Tables

Each of the edges is an Ordinal Variable, each segment represents a level in the variable. So each face of the Cube represents two ordinal variables. Any segment is at the intersection of two (independent) levels of two variables, and the colour may be visualized as a count. This array of counts on a face is a 2D or 2-Way Table. ( More on this later )

Since we can only print 2D tables, we hold one face in front and the image we see is a 2-Way Table. Turning the Cube by 90 degrees gives us another face with 2 variables, with one variable in common with the previous face. If we consider two faces together, we get two 2-way tables, effectively allowing us to contemplate 3 categorical variables.

Multiple 2-Way tables can be flattened into a single long table that contains all counts for all combinations of categorical variables. This can be visualized as “opening up” and laying flat the Rubik’s cube, as with a cardboard model of it.

ftable(HairEyeColor)

            Sex Male Female
Hair  Eye                  
Black Brown       32     36
      Blue        11      9
      Hazel       10      5
      Green        3      2
Brown Brown       53     66
      Blue        50     34
      Hazel       25     29
      Green       15     14
Red   Brown       10     16
      Blue        10      7
      Hazel        7      7
      Green        7      7
Blond Brown        3      4
      Blue        30     64
      Hazel        5      5
      Green        8      8

Finally, we may need to convert the (multiple) tables into a data frame or tibble:

## Convert the two tables into a data frame
HairEyeColor %>%
  as_tibble()
# Tibble as HTML for presentation
HairEyeColor %>%
  as_tibble() %>% # Convert
  kbl(caption = "Hair Eye and Color") %>%
  kable_classic_2(html_font = "Cambria", full_width = F) %>%
  kable_styling(bootstrap_options = c("hover", "striped", "responsive"))

ABCDEFGHIJ0123456789

Hair <chr>	Eye <chr>	Sex <chr>	n <dbl>
Black	Brown	Male	32
Brown	Brown	Male	53
Red	Brown	Male	10
Blond	Brown	Male	3
Black	Blue	Male	11
Brown	Blue	Male	50
Red	Blue	Male	10
Blond	Blue	Male	30
Black	Hazel	Male	10
Brown	Hazel	Male	25

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Hair Eye and Color

Hair	Eye	Sex	n
Black	Brown	Male	32
Brown	Brown	Male	53
Red	Brown	Male	10
Blond	Brown	Male	3
Black	Blue	Male	11
Brown	Blue	Male	50
Red	Blue	Male	10
Blond	Blue	Male	30
Black	Hazel	Male	10
Brown	Hazel	Male	25
Red	Hazel	Male	7
Blond	Hazel	Male	5
Black	Green	Male	3
Brown	Green	Male	15
Red	Green	Male	7
Blond	Green	Male	8
Black	Brown	Female	36
Brown	Brown	Female	66
Red	Brown	Female	16
Blond	Brown	Female	4
Black	Blue	Female	9
Brown	Blue	Female	34
Red	Blue	Female	7
Blond	Blue	Female	64
Black	Hazel	Female	5
Brown	Hazel	Female	29
Red	Hazel	Female	7
Blond	Hazel	Female	5
Black	Green	Female	2
Brown	Green	Female	14
Red	Green	Female	7
Blond	Green	Female	8

Simple Plots for Categorical Data

We have already examined Bar Charts.

Pie Charts are discussed in here.

These are both good for single Qual variables. Bars are more suited when there are many levels and/or when there is more than one Qual variable, as discussed earlier.

Plotting Nested Proportions

When we want to visualize proportions based on Multiple Qual variables, we are looking at what Claus Wilke calls nested proportions: groups within groups. Making counts with combinations of levels for two Qual variables gives us a data structure called a Contingency Table, which we will use to build our plot for nested proportions. The Statistical tests for Proportions ( the ${\chi }^2$ test ) also needs Contingency Tables. The Frequency Table we encountered earlier is very close to being a full-fledged Contingency Table; one only needs to add the margin counts! So what is a Contingency Table?

Creating Contingency Tables

From Wolfram Alpha:

A contingency table, sometimes called a two-way frequency table, is a tabular mechanism with at least two rows and two columns used in statistics to present categorical data in terms of frequency counts. More precisely, an $r\times c$ contingency table shows the observed frequency of two variables the observed frequencies of which are arranged into $r$ rows and $c$ columns. The intersection of a row and a column of a contingency table is called a cell.

In this section we understand how to make Contingency Tables from each of the three forms. We will use vcd, mosaic and the tidyverse packages for our purposes. Then we will see how they can be visualized.

Using mosaic

I think this is the simplest and most elegant way of obtaining Contingency Tables:

data("GSS2002", package = "resampledata")
gss2002 <- GSS2002 %>%
  dplyr::select(Education, DeathPenalty) %>%
  tidyr::drop_na(., c(Education, DeathPenalty))
##
mosaic::tally(DeathPenalty ~ Education, data = gss2002) %>%
  addmargins()

            Education
DeathPenalty Left HS   HS Jr Col Bachelors Graduate  Sum
      Favor      117  511     71       135       64  898
      Oppose      72  200     16        71       50  409
      Sum        189  711     87       206      114 1307

Plotting this as an HTML table, we get:

DeathPenalty	Left HS	HS	Jr Col	Bachelors	Graduate	Sum
Favor	117	511	71	135	64	898
Oppose	72	200	16	71	50	409
Sum	189	711	87	206	114	1307

Figure 2: Contingency Table Picture

How was this computed?

So $117$ is the number of people who Left HS and Favor the death penalty, and $71$ is the count for Bachelors who Oppose the death penalty. And so on.

Using base R

# One Way Table ( one variable )
table(Arthritis$Treatment) # Contingency Table

Placebo Treated 
     43      41 

# 1-way Contingency Table
table(Arthritis$Treatment) %>% addmargins() # Contingency Table with margins

Placebo Treated     Sum 
     43      41      84 

# 2-Way Contingency Tables
# Choosing Treatment and Improved
table(Arthritis$Treatment, Arthritis$Improved) %>% addmargins()

         
          None Some Marked Sum
  Placebo   29    7      7  43
  Treated   13    7     21  41
  Sum       42   14     28  84

# Choosing Treatment and Sex
table(Arthritis$Sex, Arthritis$Improved) %>% addmargins()

        
         None Some Marked Sum
  Female   25   12     22  59
  Male     17    2      6  25
  Sum      42   14     28  84

We can use table() ( and also xtabs() ) to generate multi-dimensional tables too (More than 2-way) These will be printed out as a series of 2D tables, one for each value/level of the “third” parameter. We can then flatten this set of tables using ftable() and add margins to convert into a Contingency Table:

my_arth_table <- table(Arthritis$Treatment, Arthritis$Sex, Arthritis$Improved)
my_arth_table

, ,  = None

         
          Female Male
  Placebo     19   10
  Treated      6    7

, ,  = Some

         
          Female Male
  Placebo      7    0
  Treated      5    2

, ,  = Marked

         
          Female Male
  Placebo      6    1
  Treated     16    5

# Now flatten
ftable(my_arth_table)

                None Some Marked
                                
Placebo Female    19    7      6
        Male      10    0      1
Treated Female     6    5     16
        Male       7    2      5

ftable(my_arth_table) %>% addmargins()

             Sum
    19  7  6  32
    10  0  1  11
     6  5 16  27
     7  2  5  14
Sum 42 14 28  84

A bit strange that the column labels disappear in the ftable when margins are added…maybe need to investigate the FUN argument to add_margins().

Using vcd

The vcd ( Visualize Categorical Data ) package by Michael Friendly has a convenient function to create Contingency Tables: structable(); this function produces a ‘flat’ representation of a high-dimensional contingency table constructed by recursive splits (similar to the construction of mosaic charts/graphs). structable tends to render flat tables, of the kind that can be thought of as a “text representation” of the vcd::mosaic plot:

The arguments of structable are:

• a formula $y+p\sim x+z$ which shows which variables are to be included as columns and rows respectively on a table;
• a data argument, which can indicate a data frame from where the variables are drawn.

arth_vcd <- vcd::structable(data = Arthritis, Treatment ~ Improved)
arth_vcd
class(arth_vcd)
arth_vcd %>% addmargins()

         Treatment Placebo Treated
Improved                          
None                    29      13
Some                     7       7
Marked                   7      21
[1] "structable" "ftable"    
        Treatment
Improved Placebo Treated Sum
  None        29      13  42
  Some         7       7  14
  Marked       7      21  28
  Sum         43      41  84

# With Margins
arth_vcd %>%
  as.matrix() %>%
  addmargins()

        Treatment
Improved Placebo Treated Sum
  None        29      13  42
  Some         7       7  14
  Marked       7      21  28
  Sum         43      41  84

# HairEyeColor is in multiple table form
HairEyeColor
# structable flattens these into one, as for a mosaic chart
vcd::structable(HairEyeColor)
# As tibble
vcd::structable(HairEyeColor) %>% as_tibble()

, , Sex = Male

       Eye
Hair    Brown Blue Hazel Green
  Black    32   11    10     3
  Brown    53   50    25    15
  Red      10   10     7     7
  Blond     3   30     5     8

, , Sex = Female

       Eye
Hair    Brown Blue Hazel Green
  Black    36    9     5     2
  Brown    66   34    29    14
  Red      16    7     7     7
  Blond     4   64     5     8

             Eye Brown Blue Hazel Green
Hair  Sex                              
Black Male          32   11    10     3
      Female        36    9     5     2
Brown Male          53   50    25    15
      Female        66   34    29    14
Red   Male          10   10     7     7
      Female        16    7     7     7
Blond Male           3   30     5     8
      Female         4   64     5     8

ABCDEFGHIJ0123456789

Hair <fct>	Eye <fct>	Sex <fct>	Freq <dbl>
Black	Brown	Male	32
Brown	Brown	Male	53
Red	Brown	Male	10
Blond	Brown	Male	3
Black	Blue	Male	11
Brown	Blue	Male	50
Red	Blue	Male	10
Blond	Blue	Male	30
Black	Hazel	Male	10
Brown	Hazel	Male	25

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UCBAdmissions is already in Frequency Form i.e. a Contingency Table. But it is a set of (two-way) Contingency Tables:

UCBAdmissions
###
vcd::structable(UCBAdmissions)
###
structable(UCBAdmissions) %>%
  as.matrix() %>%
  addmargins()

, , Dept = A

          Gender
Admit      Male Female
  Admitted  512     89
  Rejected  313     19

, , Dept = B

          Gender
Admit      Male Female
  Admitted  353     17
  Rejected  207      8

, , Dept = C

          Gender
Admit      Male Female
  Admitted  120    202
  Rejected  205    391

, , Dept = D

          Gender
Admit      Male Female
  Admitted  138    131
  Rejected  279    244

, , Dept = E

          Gender
Admit      Male Female
  Admitted   53     94
  Rejected  138    299

, , Dept = F

          Gender
Admit      Male Female
  Admitted   22     24
  Rejected  351    317

              Gender Male Female
Admit    Dept                   
Admitted A            512     89
         B            353     17
         C            120    202
         D            138    131
         E             53     94
         F             22     24
Rejected A            313     19
         B            207      8
         C            205    391
         D            279    244
         E            138    299
         F            351    317

            Gender
Admit_Dept   Male Female  Sum
  Admitted_A  512     89  601
  Admitted_B  353     17  370
  Admitted_C  120    202  322
  Admitted_D  138    131  269
  Admitted_E   53     94  147
  Admitted_F   22     24   46
  Rejected_A  313     19  332
  Rejected_B  207      8  215
  Rejected_C  205    391  596
  Rejected_D  279    244  523
  Rejected_E  138    299  437
  Rejected_F  351    317  668
  Sum        2691   1835 4526

Important

Note that structable does not permit the adding of margins directly; it needs to be converted to a matrix for addmargins() to do its work.

Using tidyverse

So far these packages give Contingency Tables that are easy to see for humans; some of these structures are also capable being passed directly to commands such as stats::chisq.test() or janitor::chisq.test().

Often we need Contingency Tables that are in tibble form, and we need to perform some data processing using dplyr to get there. Doing this with the tidyverse set of packages may seem counter-intuitive and long-winded, but the workflow is easily understandable.

First we develop the counts:

diamonds %>% count(cut)
diamonds %>% count(clarity)
diamonds %>%
  group_by(cut, clarity) %>%
  dplyr::summarise(count = n())

ABCDEFGHIJ0123456789

cut <ord>	n <int>
Fair	1610
Good	4906
Very Good	12082
Premium	13791
Ideal	21551

5 rows

ABCDEFGHIJ0123456789

clarity <ord>	n <int>
I1	741
SI2	9194
SI1	13065
VS2	12258
VS1	8171
VVS2	5066
VVS1	3655
IF	1790

8 rows

ABCDEFGHIJ0123456789

cut <ord>	clarity <ord>	count <int>
Fair	I1	210
Fair	SI2	466
Fair	SI1	408
Fair	VS2	261
Fair	VS1	170
Fair	VVS2	69
Fair	VVS1	17
Fair	IF	9
Good	I1	96
Good	SI2	1081

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We need to have the individual levels of cut as rows and the individual levels of clarity as columns. This means that we need to pivot this from “long to wide”¹ to obtain a Contingency Table:

diamonds %>%
  group_by(cut, clarity) %>%
  dplyr::summarise(count = n()) %>%
  pivot_wider(
    id_cols = cut,
    names_from = clarity,
    values_from = count
  ) %>%
  # Now add the row and column totals using the `janitor` package
  janitor::adorn_totals(where = c("row", "col")) %>%
  # Recover to tibble since janitor gives a "tabyl" format
  # ( which can be useful too !)
  as_tibble() -> diamonds_ct
diamonds_ct

ABCDEFGHIJ0123456789

cut <ord>	I1 <int>	SI2 <int>	SI1 <int>	VS2 <int>
Fair	210	466	408	261
Good	96	1081	1560	978
Very Good	84	2100	3240	2591
Premium	205	2949	3575	3357
Ideal	146	2598	4282	5071
Total	741	9194	13065	12258

6 rows | 1-5 of 10 columns

### Another Way
diamonds %>%
  group_by(cut, clarity) %>%
  dplyr::summarise(count = n()) %>%
  pivot_wider(
    id_cols = cut,
    names_from = clarity,
    values_from = count
  ) %>%
  # Now add the row and column totals using the `dplyr` package
  # From: https://stackoverflow.com/a/67885521
  mutate("row_totals" = sum(across(where(is.integer)))) %>%
  ungroup() %>%
  add_row(cut = "col_total", summarize(., across(where(is.integer), sum)))

ABCDEFGHIJ0123456789

cut <chr>	I1 <int>	SI2 <int>	SI1 <int>	VS2 <int>
Fair	210	466	408	261
Good	96	1081	1560	978
Very Good	84	2100	3240	2591
Premium	205	2949	3575	3357
Ideal	146	2598	4282	5071
col_total	741	9194	13065	12258

6 rows | 1-5 of 10 columns

Now then, how does one plot a set of data that looks like this, a matrix? No column is a single variable, nor is each row a single observation, which is what we understand with the idea of tidy data.

Mosaic Plots

The answer is provided in the very shape of the data: we plot this as a set of tiles, where $$areaoftile\sim countareaoftile\sim count$$ We recursively partition off a (usually) square area into vertical and horizontal pieces whose area is proportional to the count at a specific combination of levels of the two Qual variables. So we might follow the process as shown below:

• Take the bottom row of per-column totals and create vertical rectangles with these widths
  
• Take the individual counts in the rows and partition each rectangle based in the counts in these rows.

(a) GSS Mosaic Chart Step #1

(b) GSS Mosaic Chart Step #2

Figure 3: Mosaic Chart for GSS Data

The first split shows the various levels of Education and their counts as widths. Order is alphabetical! This splitting corresponds to the bottom ROW of the Figure 2. HS is clearly the largest subgroup in Education.

In the second step, the columns from Figure 3 (a) are sliced horizontally into tiles, in proportion to the number of people in each Education category/level who support/do not support DeathPenalty. This is done in proportion to all the entries in each COLUMN, giving us Figure 3 (b).

Let us now make this plot with a variety of approaches.

Using vcd

The vcd::mosaic() function needs the data in contingency table form. We already built one using mosaic::tally() and that is easily plotted:

# Code used earlier
data("GSS2002", package = "resampledata")
gss2002 <- GSS2002 %>%
  # select two categorical variables from the dataset
  dplyr::select(Education, DeathPenalty) %>%
  drop_na(Education, DeathPenalty)
gss2002

ABCDEFGHIJ0123456789

Education <fct>	DeathPenalty <fct>
HS	Favor
Bachelors	Favor
HS	Favor
HS	Favor
HS	Favor
HS	Favor
HS	Favor
Jr Col	Favor
HS	Oppose
Bachelors	Favor

Next

123456

...

131

Previous

1-10 of 1,307 rows

# make a tally table
gss_table <- mosaic::tally(DeathPenalty ~ Education, data = gss2002)
gss_table %>% addmargins()

            Education
DeathPenalty Left HS   HS Jr Col Bachelors Graduate  Sum
      Favor      117  511     71       135       64  898
      Oppose      72  200     16        71       50  409
      Sum        189  711     87       206      114 1307

# gss_table is *not* a tibble, but a *table* object.

vcd::mosaic(gss_table,
  gp = shading_hsv,
  main = "mosaic::tally() + vcd::mosaic()"
)

There is also a command within vcd itself to create a Contingency Table, vcd::structable():

arthritis_table <- vcd::structable(~ Treatment + Improved,
  data = Arthritis
)
arthritis_table
vcd::mosaic(arthritis_table,
  gp = shading_max,
  main = "Arthritis Treatment Dataset"
)

          Improved None Some Marked
Treatment                          
Placebo              29    7      7
Treated              13    7     21

Using ggmosaic

ggmosaic takes a tibble with Qualitative variables, internally computes the counts/table, and plots the mosaic plot:

gss2002

ABCDEFGHIJ0123456789

Education <fct>	DeathPenalty <fct>
HS	Favor
Bachelors	Favor
HS	Favor
HS	Favor
HS	Favor
HS	Favor
HS	Favor
Jr Col	Favor
HS	Oppose
Bachelors	Favor

Next

123456

...

131

Previous

1-10 of 1,307 rows

# library(ggmosaic)
#
# Set graph theme
theme_set(new = theme_custom())
##
ggplot(data = gss2002) +
  ggmosaic::geom_mosaic(
    aes(
      x = product(DeathPenalty, Education),
      fill = DeathPenalty
    )
  ) +
  theme(legend.position = "top")

Warning: The `scale_name` argument of `continuous_scale()` is deprecated as of ggplot2
3.5.0.

Warning: The `trans` argument of `continuous_scale()` is deprecated as of ggplot2 3.5.0.
ℹ Please use the `transform` argument instead.

Warning: `unite_()` was deprecated in tidyr 1.2.0.
ℹ Please use `unite()` instead.
ℹ The deprecated feature was likely used in the ggmosaic package.
  Please report the issue at <https://github.com/haleyjeppson/ggmosaic>.

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Using ggformula

This needs quite some work, to convert the Contingency Table into a mosaic plot; perhaps not the most intuitive of methods either. This code has been developed using this Stackoverflow post.

# Reference
# https://stackoverflow.com/questions/19233365/how-to-create-a-marimekko-mosaic-plot-in-ggplot2


# Set graph theme
theme_set(new = theme_custom())

gss_summary <- gss2002 %>%
  dplyr::group_by(Education, DeathPenalty) %>%
  dplyr::summarise(count = n()) %>% # This is good for a chisq test

  # Data is still grouped by `Education`
  # Add two more columns to facilitate mosaic Plot
  # These two columns are quite unusual...
  mutate(
    edu_count = sum(count),
    edu_prop = count / sum(count)
  ) %>%
  ungroup()
gss_summary

ABCDEFGHIJ0123456789

Education <fct>	DeathPenalty <fct>	count <int>	edu_count <int>	edu_prop <dbl>
Left HS	Favor	117	189	0.6190476
Left HS	Oppose	72	189	0.3809524
HS	Favor	511	711	0.7187060
HS	Oppose	200	711	0.2812940
Jr Col	Favor	71	87	0.8160920
Jr Col	Oppose	16	87	0.1839080
Bachelors	Favor	135	206	0.6553398
Bachelors	Oppose	71	206	0.3446602
Graduate	Favor	64	114	0.5614035
Graduate	Oppose	50	114	0.4385965

1-10 of 10 rows

# This works but is not very intuitive...
gf_col(edu_prop ~ Education,
  data = gss_summary,
  width = ~edu_count, # Not typically used in a column chart
  fill = ~DeathPenalty,
  stat = "identity",
  position = "fill",
  color = "black"
) %>%
  gf_text(edu_prop ~ Education,
    label = ~ scales::percent(edu_prop),
    position = position_stack(vjust = 0.5)
  ) %>%
  gf_facet_grid(~Education,
    scales = "free_x",
    space = "free_x"
  ) %>%
  gf_theme(scale_fill_manual(values = c("orangered", "palegreen3")))

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Using visStatistics

visStatistics is a recent package that allows a very wide variety of statistical charts to be created automagically based on the variables chosen. Let us plot a mosaic chart directly with this package

visstat(gss2002$DeathPenalty, gss2002$Education)

Coloured Tiles: Actual and Expected Contingency Tables

We notice that the mosaic plots has coloured some tiles blue and some red. Why was this done? Consider the set of mosaic plots below:

vcd::mosaic(arthritis_table, gp = shading_max, legend = FALSE)
vcd::mosaic(arthritis_table, type = "expected")
vcd::assoc(arthritis_table)

Figure 4: Actual Contingency Table

Figure 5: Expected Contingency Table

Figure 6: Tile-Wise Differences

From an inspection of these plots, we see the (tile-wise) difference between situations when Qualitative variables are related to that when they not related.

The graph on the left show the mosaic plot of the actual Contingency Table.

The graph in the middle shows a similar but fictitious plot but with the cuts neatly horizontal or vertical. This mosaic would be what we would expect, if Education and the opinion on Death Penalty were independent!!

Clearly, there are differences in area of the corresponding tiles in the two mosaics, actual and expected, as shown in the graph on the right. Some differences are positive, and some negative. In the actual mosaic, Figure 4, tiles with large positive differences are coloured blue, and those with large negative differences are coloured red.

The higher the absolute values of these differences, the greater the effect of one Qual on the other. More when we get into Inference for Two Proportions.

Dataset: Titanic

Banzai!!! That was quite some journey! Let us end it by quickly looking at a sadly famous dataset:

data("titanic", package = "ggmosaic")
titanic

ABCDEFGHIJ0123456789

Class <fct>	Sex <fct>	Age <fct>	Survived <fct>
3rd	Male	Child	No
3rd	Male	Child	No
3rd	Male	Child	No
3rd	Male	Child	No
3rd	Male	Child	No
3rd	Male	Child	No
3rd	Male	Child	No
3rd	Male	Child	No
3rd	Male	Child	No
3rd	Male	Child	No

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There were 2201 passengers, as per this dataset.

Data Dictionary

NoteQuantitative Data

None.

NoteQualitative Data

• Survived: (chr) yes or no
• Class: (chr) Class of Travel, else “crew”
• Age: (chr) Adult, Child
• Sex: (chr) Male / Female.

Research Questions

NoteQ.1. What is the dependence of survived upon sex?

vcd::structable(Survived ~ Sex, data = titanic) %>%
  vcd::mosaic(gp = shading_max)

Note the huge imbalance in survived with sex: men have clearly perished in larger numbers than women. Which is why the colouring by the Pearson Residuals show large positive residuals for men who died, and large negative residuals for women who died.

So sadly Jack is far more likely to have died than Rose.

NoteQ.2. How does Survived depend upon Class?

vcd::structable(Survived ~ Class, data = titanic) %>%
  vcd::mosaic(gp = shading_max)

Crew has seen deaths in large numbers, as seen by the large negative residual for crew-survivals. First Class passengers have had speedy access to the boats and have survived in larger proportions than say second or third class. There is a large positive residual for first-class survivals.

Rose travelled first class and Jack was third class. So again the odds are stacked against him.

Balloon Plots

There is another visualization of Categorical Data, called a Balloon Plot. We will use the housetasks dataset from the package ggpubr.

Dataset: Who Does the Housework?

housetasks <- read.delim(
  system.file("demo-data/housetasks.txt",
    package = "ggpubr"
  ),
  row.names = 1
)
housetasks

ABCDEFGHIJ0123456789

	Wife <int>	Alternating <int>	Husband <int>	Jointly <int>
Laundry	156	14	2	4
Main_meal	124	20	5	4
Dinner	77	11	7	13
Breakfeast	82	36	15	7
Tidying	53	11	1	57
Dishes	32	24	4	53
Shopping	33	23	9	55
Official	12	46	23	15
Driving	10	51	75	3
Finances	13	13	21	66

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inspect(housetasks)

quantitative variables:  
         name   class min Q1 median Q3 max     mean       sd  n missing
1        Wife integer   0 10     32 77 156 46.15385 50.05971 13       0
2 Alternating integer   1 11     14 24  51 19.53846 16.26149 13       0
3     Husband integer   1  5      9 23 160 29.30769 44.97663 13       0
4     Jointly integer   2  4     15 57 153 39.15385 44.09808 13       0

We see that we have 13 observations.

Important

This data is already in Contingency Table form (without the margin totals)!

Data Dictionary

NoteQuantitative Data

• Freq: (int) No of times a task was carried out by specific people

NoteQualitative Data

• Who: (chr) Who carried out the task?
• Task: (chr) Task? Which task? Can’t you see I’m tired?

# Set graph theme
theme_set(new = theme_custom())
##
ggpubr::ggballoonplot(housetasks,
  fill = "value",
  ggtheme = theme_pubr()
) +
  scale_fill_viridis_c(option = "C") +
  labs(title = "A Balloon Plot for Categorical Data")

And repeat with the familiar HairEyeColor dataset:

# Set graph theme
theme_set(new = theme_custom())

df <- as_tibble(HairEyeColor)
df

ABCDEFGHIJ0123456789

Hair <chr>	Eye <chr>	Sex <chr>	n <dbl>
Black	Brown	Male	32
Brown	Brown	Male	53
Red	Brown	Male	10
Blond	Brown	Male	3
Black	Blue	Male	11
Brown	Blue	Male	50
Red	Blue	Male	10
Blond	Blue	Male	30
Black	Hazel	Male	10
Brown	Hazel	Male	25

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ggballoonplot(df,
  x = "Hair",
  y = "Eye", size = "n",
  fill = "n",
  ggtheme = theme_pubr()
) +
  scale_fill_viridis_c(option = "C") +
  labs(title = "Balloon Plot")

# Balloon Plot with facetting
ggballoonplot(df,
  x = "Hair",
  y = "Eye", size = "n",
  fill = "n",
  facet.by = "Sex",
  ggtheme = theme_pubr()
) +
  scale_fill_viridis_c(option = "C") +
  labs(
    title = "Balloon Plot with Facetting by Sex",
    subtitle = "Hair and Eye Color"
  )

Note the somewhat different syntax with ggballoonplot: the variable names are enclosed in quotes.

Balloon Plots work because they use color and size aesthetics to represent categories and counts respectively.

Wait, But Why?

• We can detect correlation between Quant variables using the scatter plots and regression lines
• And we can detect association between Qual variables using mosaics, sieves (which we did not see here, but is possible in R), and with balloon plots.
• Your project primary research data may be pure Qualitative too, as with a Questionnaire / Survey instrument.
• One such Qual variable therein will be your target variable
• You will need to justify whether the target variable is dependent upon the other Quals, and then to decide what to do about that.

AI Generated Summary and Podcast

This excerpt from a course on Data Analysis using Metaphors focuses on the importance of understanding and visualizing categorical data. It discusses different ways to represent categorical data in R, including case data, frequency data, and cross-tabular count data. The text also explores various visualization techniques like bar plots, pie charts, mosaic plots, and balloon plots. It emphasizes the use of contingency tables for analyzing relationships between categorical variables, illustrating how to create them and visualize them using R packages. Additionally, the text delves into the concept of Pearson residuals, which help to identify associations between categorical variables and highlight deviations from independence.

Conclusion

How are the bar plots for categorical data different from histograms? Why don’t “regular” scatter plots simply work for Categorical data? Discuss!

There are quite a few things we can do with Qualitative/Categorical data:

1. Make simple bar charts with colours and facetting
2. Make Contingency Tables for a $X^2$-test
3. Make Mosaic Plots to show how the categories stack up
4. Make Balloon Charts as an alternative
5. Then, draw your inferences and tell the story!

Your Turn

1. Take some of the categorical datasets from the vcd and vcdExtra packages and recreate the plots from this module. Go to https://vincentarelbundock.github.io/Rdatasets/articles/data.html and type “vcd” in the search box. You can directly load CSV files from there, using read_csv("url-to-csv").

2. Try the housetasks dataset that we used for Balloon Plots, to create a mosaic plot with Pearson Residuals.

NoteClothing and Intelligence Rating of Children!!

Are well-dressed students actually smarter?

NotePre-marital Sex and Divorce.

NoteAre Emily and Greg More Employable Than Lakisha and Jamal?

Are first names a basis for racial discrimination, in the US?

This dataset was generated as part of a landmark research study done by Marianne Bertrand and Senthil Mullainathan. Read the description therein to really understand how you can prove causality with a well-crafted research experiment.

AI Generated Summary and Podcast

This module focuses on the importance of understanding and visualizing categorical data. It discusses different ways to represent categorical data in R, including case data, frequency data, and cross-tabular count data. The text also explores various visualization techniques like bar plots, pie charts, mosaic plots, and balloon plots. It emphasizes the use of contingency tables for analyzing relationships between categorical variables, illustrating how to create them and visualize them using R packages. Additionally, the text delves into the concept of Pearson residuals, which help to identify associations between categorical variables and highlight deviations from independence.

References

1. Winston Chang (2024). R Graphics Cookbook. https://r-graphics.org

2. Nice Chi-square interactive story at https://statisticalstories.xyz/chi-square

3. Chittaranjan Andrade(July 22, 2015). Understanding Relative Risk, Odds Ratio, and Related Terms: As Simple as It Can Get. https://www.psychiatrist.com/jcp/understanding-relative-risk-odds-ratio-related-terms/

4. Mine Cetinkaya-Rundel and Johanna Hardin. An Introduction to Modern Statistics, Chapter 4. https://openintro-ims.netlify.app/explore-categorical.html
   

5. Using the strcplot command from vcd, https://cran.r-project.org/web/packages/vcd/vignettes/strucplot.pdf
   

6. Creating Frequency Tables with vcd, https://cran.r-project.org/web/packages/vcdExtra/vignettes/A_creating.html
   

7. Creating mosaic plots with vcd, https://cran.r-project.org/web/packages/vcdExtra/vignettes/D_mosaics.html
   

8. Michael Friendly, Corrgrams: Exploratory displays for correlation matrices. The American Statistician August 19, 2002 (v1.5). https://www.datavis.ca/papers/corrgram.pdf
   

9. Visualizing Categorical Data in R
   

10. H. Riedwyl & M. Schüpbach (1994), Parquet diagram to plot contingency tables. In F. Faulbaum (ed.), Softstat ’93: Advances in Statistical Software, 293–299. Gustav Fischer, New York.

R Package Citations

Package	Version	Citation
ggmosaic	0.3.3	Jeppson, Hofmann, and Cook (2021)
ggpubr	0.6.0	Kassambara (2023)
janitor	2.2.1	Firke (2024)
kableExtra	1.4.0	Zhu (2024)
resampledata	0.3.2	Chihara and Hesterberg (2018)
sjlabelled	1.2.0	Lüdecke (2022)
sjPlot	2.8.17	Lüdecke (2024)
tinytable	0.9.0	Arel-Bundock (2025)
vcd	1.4.13	Meyer, Zeileis, and Hornik (2006); Zeileis, Meyer, and Hornik (2007); Meyer et al. (2024)
vcdExtra	0.8.5	Friendly (2023)
visStatistics	0.1.7	Schilling (2025)

Arel-Bundock, Vincent. 2025. tinytable: Simple and Configurable Tables in “HTML,” “LaTeX,” “Markdown,” “Word,” “PNG,” “PDF,” and “Typst” Formats. https://doi.org/10.32614/CRAN.package.tinytable.

Chihara, Laura M., and Tim C. Hesterberg. 2018. Mathematical Statistics with Resampling and r. John Wiley & Sons Hoboken NJ. https://github.com/lchihara/MathStatsResamplingR?tab=readme-ov-file.

Firke, Sam. 2024. janitor: Simple Tools for Examining and Cleaning Dirty Data. https://doi.org/10.32614/CRAN.package.janitor.

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Footnotes

1. https://tidyr.tidyverse.org/articles/pivot.html