Recreating (more) data visualizations from the book “Knowledge is Beautiful”: Part II

June 22, 2018
By

(This article was first published on Stories by Matt.0 on Medium, and kindly contributed to R-bloggers)

In part II of this series I continue to recreate some of the visualizations from the book “Knowledge is Beautiful” by David McCandless in R.

David McCandless is author of two bestselling infographics books and gives a great TED talk about data visualization. His second book Knowledge is Beautiful , published in 2015, contains 196 beautiful infographics which took 15,832 hours to complete.

If you haven’t checked out Part I of the series yet, please do.

Passwords

This visualization is a scatter-plot of commonly used passwords arranged along the x-axis, from left-to-right, according to the first character in the password [A to Z] and then [0 to 9]. Passwords are color-coded according to the category, sized according to the strength of the password, and the frequency of use along the y-axis.

In the last post I downloaded the data as an excel from the Google Docs and loaded the appropriate sheet with the read_excel() function from the readxl package.

Frustratingly, data can sometimes be distributed within PDFs. For example, Rafael Irizarry, walks through a new calculation of excess mortality in Puerto Rico after the devastating Hurricane Maria in 2017, using newly released data from the Puerto Rico government. Irizarry’s post comes with the data but it’s sadly in PDF form.

The tabulizer library provides R bindings to the Tabula java library and can be used to extract tables from PDF documents.

The dataset is located here: bit.ly/KIB_Passwords. Let’s import it:

# Download tabular data from a pdf spanning multiple pages
library(tabulizer)
passwords <- "~/passwords.pdf"
# The table spreads across five pages
pages <- c(1:5)
df_total <- data.frame()
for (i in pages) {
out <- extract_tables(passwords, page = i)
out <- as.data.frame(out)
colnames(out) <- c("rank","password","category", "online_crack", "offline_crack", "rank_alt", "strength","font_size")
out <- out[-1,1:8]
df_total <- rbind(df_total, out)
}

The data requires a bit of cleaning before continuing.

df_total <- na.omit(df_total)
df_total$rank <- as.numeric(df_total$rank)

Along the x-axis passwords are binned according to the first character of the password. We can use grepl inside dplyr ‘s mutate() function to create new column binning each password.

# make a group for passwords beginning in A-Z and through 0-9
df_total <- df_total %>%
mutate(group = case_when(grepl("^A", password, ignore.case = TRUE) ~ "A",
grepl("^B", password, ignore.case = TRUE) ~ "B",
grepl("^C", password, ignore.case = TRUE) ~ "C",
grepl("^D", password, ignore.case = TRUE) ~ "D",
grepl("^E", password, ignore.case = TRUE) ~ "E",
grepl("^F", password, ignore.case = TRUE) ~ "F",
grepl("^G", password, ignore.case = TRUE) ~ "G",
grepl("^H", password, ignore.case = TRUE) ~ "H",
grepl("^I", password, ignore.case = TRUE) ~ "I",
grepl("^J", password, ignore.case = TRUE) ~ "J",
grepl("^K", password, ignore.case = TRUE) ~ "K",
grepl("^L", password, ignore.case = TRUE) ~ "L",
grepl("^M", password, ignore.case = TRUE) ~ "M",
grepl("^N", password, ignore.case = TRUE) ~ "N",
grepl("^O", password, ignore.case = TRUE) ~ "O",
grepl("^P", password, ignore.case = TRUE) ~ "P",
grepl("^Q", password, ignore.case = TRUE) ~ "Q",
grepl("^R", password, ignore.case = TRUE) ~ "R",
grepl("^S", password, ignore.case = TRUE) ~ "S",
grepl("^T", password, ignore.case = TRUE) ~ "T",
grepl("^U", password, ignore.case = TRUE) ~ "U",
grepl("^V", password, ignore.case = TRUE) ~ "V",
grepl("^W", password, ignore.case = TRUE) ~ "W",
grepl("^X", password, ignore.case = TRUE) ~ "X",
grepl("^Y", password, ignore.case = TRUE) ~ "Y",
grepl("^Z", password, ignore.case = TRUE) ~ "Z",
grepl("^0", password, ignore.case = TRUE) ~ "0",
grepl("^1", password, ignore.case = TRUE) ~ "1",
grepl("^2", password, ignore.case = TRUE) ~ "2",
grepl("^3", password, ignore.case = TRUE) ~ "3",
grepl("^4", password, ignore.case = TRUE) ~ "4",
grepl("^5", password, ignore.case = TRUE) ~ "5",
grepl("^6", password, ignore.case = TRUE) ~ "6",
grepl("^7", password, ignore.case = TRUE) ~ "7",
grepl("^8", password, ignore.case = TRUE) ~ "8",
grepl("^9", password, ignore.case = TRUE) ~ "9"))
# get rid of NA's
df_total <- na.omit(df_total)

The default is that 0–9 comes before A-Z but the McCandless visualization puts A-Z before 0–9, so let’s rearrange that.

df_total$group <- factor(df_total$group, levels = c("A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S", "T", "U" , "V", "W", "X", "Y", "Z", "1", "2", "3", "4", "5", "6", "7", "8", "9"))

Time to recreate the data visualization. We use geom_text() to display the passwords, sized according to the password strength, and color coordinated to the themes and colors used by McCandless

library(ggplot2)
library(extrafont) # For the Georgia font
ggplot(df_total, aes(x = group, y = rank)) +
geom_text(aes(label = password, color=category, size = font_size, alpha = 0.95)) +
# add the custom colors
scale_color_manual(values=c("#477080", "#A3968A", "#C08B99", "#777C77", "#C8AB6D", "#819DAB", "#C18A6F", "#443F36", "#6A9577", "#BF655A")) +
scale_y_continuous(position = "right", breaks = c(1,10,50,100,250,500)) +
scale_x_discrete(breaks = c("A","Z","1","9")) +
scale_y_reverse() +
labs(title = "Top 500 Passwords", subtitle = "Is yours here?", caption = "Source: bit.ly/KIB_Passwords") +
labs(x = NULL, position = "top") +
theme(legend.position = "none",
panel.background = element_blank(),
plot.title = element_text(size = 13,
family = "Georgia",
face = "bold", lineheight = 1.2), plot.subtitle = element_text(size = 10,
family = "Georgia"),
plot.caption = element_text(size = 5,
hjust = 0.99, family = "Georgia"),
axis.text = element_text(family = "Georgia"))

The data set McCandless made contains a lot of information on how passwords are cracked if your interested in learning more. It also has some tips on selecting a password. However, the TLDR can be excellently explained by this xkcd comic:

In the top frame, the Tr0ub4dor&3 password is easier for password cracking software to guess because it has less entropy than correcthorsebatterystaple and also more difficult for a human to remember, leading to insecure practices like writing the password down on a post-it attached to the monitor. So you should always convert a memorable sentence into a memorable password rather than a random alpha-numeric.

A Teaspoon of Sugar

The Sugar dataset visualization is a circular barplot that shows the number of teaspoons of sugar found in common beverages. This graph uses the coord_polaroption of ggplot2 (to simplify the post I’ve excluded the data munging code and instead provided a .csv file ready for plotting).

sugar <- read.csv("sugar.csv")
# Re-order the factors the way they appear in the data frame
names <- sugar$drinks
names
sugar$drinks <- factor(sugar$drinks, levels = rev(sugar$drinks), ordered = TRUE)
# Create a custom color palette
custompalette <- c("#C87295", "#CE7E9C", "#CE7E9C", "#C3C969", "#B77E94", "#693945", "#63645D", "#F9D9E0", "#B96E8E", "#18090E", "#E1E87E", "#B47E8F", "#B26F8B", "#B47E8F", "#B26F8B", "#B47E8F", "#B26F8B", "#9397A0", "#97B7C4", "#9AA24F", "#6B4A4F", "#97A053", "#B7BB6B", "#97A053", "#B7BB6B", "#97A053", "#B7BB6B", "#97A053", "#B7BB6B",
"#CED97B", "#E4E89C", "#C87295", "#CE7E9C")
ggplot(sugar, aes(x = drinks, y = teaspoons, fill = drinks)) +
geom_bar(width = 0.75, stat = "identity") +
coord_polar(theta = "y") +
xlab("") + ylab("") +
labs(title = "Teaspoons", caption = "Source: bit.ly/KIB_Sugar") +
# Increase ylim to avoid having a complete circle and set custom breaks to range of teaspoons
scale_y_continuous(limits = c(0,65), breaks=seq(0,26,1)) +
scale_fill_manual(values = custompalette) +
theme(legend.position = "none",
axis.text.y = element_blank(),
axis.text.x = element_text(color = "white", family = "Georgia"),
axis.ticks = element_blank(),
panel.background = element_rect(fill = "black", color = NA),
plot.title = element_text(color = "white",
size = 13,
family = "Georgia",
face = "bold", lineheight = 1.2),
plot.caption = element_text(size = 5,
hjust = 0.99,
color = "white",
family = "Georgia"),
panel.grid.major.y = element_line(color = "grey48", size = 0.05, linetype = "dotted"),
panel.grid.minor.y = element_blank(),
panel.grid.major.x = element_blank())

It would probably be best to manually add labels besides the bars as opposed to adjusting hjust in axis.text.y = .

Although I think the visualization is aesthetically pleasing, I would be remiss not to mention that these kinds of graphics should ultimately be avoided because it is hard/misleading to discern differences between groups (here is a good link explaining in depth why).

Speaking of good data visualization practices, most people will tell you to avoid pie charts, dynamite plots, etc. yet I see them every day in academic publications, government reports, etc.

Who knows, your employer may ask you to produce a bespoke infographic with a corporate logo in the background. Well, your in luck!

David McCandless included one pieplot in the book which I thought would be useful to reproduce; if only to show how to include background images in plots.

Who owns the Arctic?

Under international law, the high seas including the North Pole and the region of the Arctic Ocean surrounding it, are not owned by any country. However, territorial claims, which extend to the continental shelf in the Arctic fall under Canada, Russia, Denmark, Norway, USA and Iceland.

Although there’s lots of information in the dataset I couldn’t find the raw numbers he used for this visualization. Therefore, I’ll just give a ballpark estimate for numbers in this example.

library(magick)
# use image under Creative Commons Attribution-Share Alike 3.0 Unported license.
img <- image_read("https://upload.wikimedia.org/wikipedia/commons/9/91/Arctic_Ocean_location_map.svg")
bitmap <- img[[1]]
bitmap[4,,] <- as.raw(as.integer(bitmap[4,,]) * 0.4)
taster <- image_read(bitmap)
# custom pallete
my_palette <- c("#ADDFEA","#E3E9A3", "#FFD283", "#CAC3CF", "#62465F", "#B8E29B")
# Make data frame
df <- data.frame(
country = c("USA", "Russia", "Norway", "Iceland", "Denmark", "Canada"),
percentage = c(10,46,13,5,18,18))
# Re-order the factors the way they appear in the data frame
df$country <- factor(df$country, levels = c("USA", "Canada", "Denmark", "Iceland", "Norway", "Russia"), ordered = TRUE)
g <- ggplot(df, aes(x = "", y=percentage, fill = country)) +
geom_bar(width = 1, stat = "identity") +
coord_polar("y", start=0) +
scale_y_continuous(breaks = c(105,25,53,62,75,90),labels = c("USA", "Russia", "Norway", "Iceland", "Denmark", "Canada")) +
xlab("") + ylab("") +
labs(title = "Who owns the Arctic?", caption = "Source: bit.ly/KIB_PolePosition") +
scale_fill_manual(values = my_palette) +
theme(legend.position = "none",
axis.text.y = element_blank(),
axis.text.x = element_text(color = c("#ADDFEA","#B8E29B", "#62465F", "#CAC3CF", "#FFD283", "#E3E9A3"), family = "Georgia", size = 7.6),
axis.ticks = element_blank(),
panel.background = element_blank(),
axis.line = element_blank(),
plot.title = element_text(size = 13,
family = "Georgia",
face = "bold", lineheight = 1.2),
plot.caption = element_text(size = 5,
hjust = 0.99,
vjust = 15,
family = "Georgia"),
panel.grid.minor = element_blank(),
panel.grid.major = element_blank())
# You need to fiddle with the settings in RStudio and then Export to PDF, JPG, TIFF, etc.
library(grid)
grid.newpage()
g
grid.draw(rasterGrob(width = 0.34, height = 0.666, image=taster, just = "centre", hjust = 0.46, vjust = 0.47))

For more weird but (sometimes) useful, plots see Xenographics.

Reproducible code and content for this series can be found on Github

Hope you enjoyed this post and stay tuned for Part III!


Recreating (more) data visualizations from the book “Knowledge is Beautiful”: Part II was originally published in Towards Data Science on Medium, where people are continuing the conversation by highlighting and responding to this story.

To leave a comment for the author, please follow the link and comment on their blog: Stories by Matt.0 on Medium.

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