---
title: "ggplot2 ecosystem<br/>& designing visualizations"
subtitle: "Lecture 10"
author: "Dr. Colin Rundel"
footer: "Sta 523 - Fall 2022"
format:
  revealjs:
    theme: slides.scss
    transition: fade
    slide-number: true
    self-contained: true
execute: 
  echo: true
---

```{r setup, message=FALSE, warning=FALSE, include=FALSE}
options(
  htmltools.dir.version = FALSE, # for blogdown
  width=80
)

knitr::opts_chunk$set(
  fig.align = "center", fig.retina = 2, dpi = 150,
  out.width = "100%"
)

library(tidyverse)
library(palmerpenguins)
```


# The wider ggplot2 ecosystem


# ggthemes


## ggplot2 themes

:::: {.small}
```{r theme1}
g = ggplot( palmerpenguins::penguins, 
            aes(x=species, y=body_mass_g, fill=species)) + 
    geom_boxplot()
```

:::: {.columns}
::: {.column width='50%'}
```{r theme2, warning=FALSE, fig.height=5, fig.width=7, out.width="50%"}
g
```

```{r theme3, warning=FALSE, fig.height=5, fig.width=7, out.width="50%"}
g + theme_dark()
```
:::
::: {.column width='50%'}
```{r theme4, warning=FALSE, fig.height=5, fig.width=7, out.width="50%"}
g + theme_minimal()
```

```{r theme5, warning=FALSE, fig.height=5, fig.width=7, out.width="50%"}
g + theme_void()
```
:::
::::

::::

## ggthemes

:::: {.columns .small}
::: {.column width='50%'}
```{r theme6, warning=FALSE, fig.height=5, fig.width=7, out.width="50%"}
g + ggthemes::theme_economist() + 
  ggthemes::scale_fill_economist()
```

```{r theme7, warning=FALSE, fig.height=5, fig.width=7, out.width="50%"}
g + ggthemes::theme_fivethirtyeight() + 
  ggthemes::scale_fill_fivethirtyeight()
```
:::
::: {.column width='50%'}
```{r theme8, warning=FALSE, fig.height=5, fig.width=7, out.width="50%"}
g + ggthemes::theme_gdocs() +
  ggthemes::scale_fill_gdocs()
```

```{r theme9, warning=FALSE, fig.height=5, fig.width=7, out.width="50%"}
g + ggthemes::theme_wsj() +
  ggthemes::scale_fill_wsj()
```
:::
::::


## And for those who miss Excel

:::: {.columns .small}
::: {.column width='50%'}
```{r theme10, warning=FALSE, fig.height=5, fig.width=7, out.width="100%"}
g + ggthemes::theme_excel() +
  ggthemes::scale_fill_excel()
```
:::
::: {.column width='50%'}
```{r theme11, warning=FALSE, fig.height=5, fig.width=7, out.width="100%"}
g + ggthemes::theme_excel_new() +
  ggthemes::scale_fill_excel_new()
```
:::
::::


#

![](imgs/hex-ggrepel.png){fig-align="center" width="40%"}

## 

::: {.small}
```{r ggrepel1}
d = tibble(
  car = rownames(mtcars),
  weight = mtcars$wt,
  mpg = mtcars$mpg
) %>%
  filter(weight > 2.75, weight < 3.45)
```
:::

. . .

:::: {.columns .small}
::: {.column width='50%'}
```{r ggrepel2, out.width="65%", fig.width=5, fig.height=5}
#| code-line-numbers: "3-5"
ggplot(d, aes(x=weight, y=mpg)) +
  geom_point(color="red") +
  geom_text(
    aes(label = car)
  )
```
:::
::: {.column width='50%'}
```{r ggrepel3, out.width="65%", fig.width=5, fig.height=5}
#| code-line-numbers: "3-5"
ggplot(d, aes(x=weight, y=mpg)) +
  geom_point(color="red") +
  ggrepel::geom_text_repel(
    aes(label = car)
  )
```
:::
::::


##

::: {.small}
```{r ggrepel5, out.width="65%", fig.width=8, fig.height=5}
#| code-line-numbers: "|5,6" 
ggplot(d, aes(x=weight, y=mpg)) +
  geom_point(color="red") +
  ggrepel::geom_text_repel(
    aes(label = car),
    nudge_x = .1, box.padding = 1, point.padding = 0.6,
    arrow = arrow(length = unit(0.02, "npc")), segment.alpha = 0.25
  )
```
:::


#


![](imgs/patchwork_logo.png){fig-align="center" width="40%"}


## ggplot objects

```{r pw_plots}
library(patchwork)

p1 = ggplot(palmerpenguins::penguins) + 
  geom_boxplot(aes(x = island, y = body_mass_g))

p2 = ggplot(palmerpenguins::penguins) + 
  geom_boxplot(aes(x = species, y = body_mass_g))

p3 = ggplot(palmerpenguins::penguins) + 
  geom_point(aes(x = flipper_length_mm, y = body_mass_g, color = sex))

p4 = ggplot(palmerpenguins::penguins) + 
  geom_point(aes(x = bill_length_mm, y = body_mass_g, color = sex))
```

. . .

```{r}
class(p1)
```


##

```{r pw_plot1, fig.width=10, out.width="70%", warning=FALSE}
p1 + p2 + p3 + p4
```


##

```{r pw_plot2, fig.width=10, out.width="70%", warning=FALSE}
p1 + p2 + p3 + p4 + plot_layout(nrow=1)
```


##

```{r pw_plot3, fig.width=10, out.width="70%", warning=FALSE}
p1 / (p2 + p3 + p4)
```


##


```{r pw_plot4, fig.width=10, out.width="70%", warning=FALSE}
p1 + p2 + p3 + p4 + 
  plot_annotation(title = "Palmer Penguins", tag_levels = c("A"))
```


##

::: {.small}
```{r pw_plot5, fig.width=10, out.width="60%", warning=FALSE}
p1 + {
  p2 + {
    p3 + p4 + plot_layout(ncol = 1) + plot_layout(tag_level = 'new')
  }
} + 
  plot_layout(ncol = 1) +
  plot_annotation(tag_levels = c("1","a"), tag_prefix = "Fig ")
```
:::


# GGally

##

```{r ggally, message=FALSE, warning=FALSE, out.width="50%"}
GGally::ggpairs(palmerpenguins::penguins)
```


#

```{r echo=FALSE, fig.align="center", out.width="45%"}
knitr::include_graphics("imgs/hex-gganimate.png")
```


##

:::: {.columns .small}
::: {.column width='50%'}
```{r eval=FALSE}
#| code-line-numbers: "|19"
airq = airquality
airq$Month = month.name[airq$Month]

ggplot(
  airq, 
  aes(Day, Temp, group = Month)
) + 
  geom_line() + 
  geom_segment(
    aes(xend = 31, yend = Temp), 
    linetype = 2, 
    colour = 'grey'
  ) + 
  geom_point(size = 2) + 
  geom_text(
    aes(x = 31.1, label = Month), 
    hjust = 0
  ) + 
  gganimate::transition_reveal(Day) +
  coord_cartesian(clip = 'off') + 
  labs(
    title = 'Temperature in New York', 
    y = 'Temperature (°F)'
  ) + 
  theme_minimal() + 
  theme(plot.margin = margin(5.5, 40, 5.5, 5.5))
```
:::
::: {.column width='50%'}
```{r echo=FALSE}
knitr::include_graphics("imgs/gganim_weather.gif")
```
:::
::::

::: {.aside}
[github.com/thomasp85/gganimate](https://github.com/thomasp85/gganimate)
:::

## More extensions

::: {.center .large}
[exts.ggplot2.tidyverse.org/gallery/](https://exts.ggplot2.tidyverse.org/gallery/)
:::

```{r echo=FALSE, out.width="66%"}
knitr::include_graphics("imgs/ggplot2_exts.png")
```



# Why do we visualize?


## Asncombe's Quartet

```{r}
datasets::anscombe %>% as_tibble()
```


## Tidy anscombe

::: {.medium}
```{r}
(tidy_anscombe = datasets::anscombe %>%
  pivot_longer(everything(), names_sep = 1, names_to = c("var", "group")) %>%
  pivot_wider(id_cols = group, names_from = var, 
              values_from = value, values_fn = list(value = list)) %>% 
  unnest(cols = c(x,y)))
```
:::


##

::: {.medium}
```{r}
tidy_anscombe %>%
  group_by(group) %>%
  summarize(
    mean_x = mean(x), mean_y = mean(y), 
    sd_x = sd(x), sd_y = sd(y),
    cor = cor(x,y), .groups = "drop"
  )
```
:::


##

```{r fig.width=7, out.width="45%"}
ggplot(tidy_anscombe, aes(x = x, y = y, color = as.factor(group))) +
  geom_point(size=2) +
  facet_wrap(~group) +
  geom_smooth(method="lm", se=FALSE, fullrange=TRUE, formula = y~x) +
  guides(color="none")
```


## DatasauRus

::: {.small}
```{r datasaurus}
ggplot(
  datasauRus::datasaurus_dozen, 
  aes(x = x, y = y, color = dataset)
) +
  geom_point() +
  facet_wrap(~dataset) +
  guides(color="none")
```
:::


::: {.aside}
See [here](https://www.autodesk.com/research/publications/same-stats-different-graphs) for the original paper
:::

##

```{r echo=FALSE, fig.width=12, fig.height=5}
datasauRus::datasaurus_dozen %>%
  filter(dataset %in% c("bullseye", "dino", "star")) %>%
  ggplot(
    aes(
      x = x, y = y, 
      color = dataset
    )
  ) +
    geom_point() +
    facet_wrap(~dataset) +
    guides(color="none")
```


##

:::: {.columns .small}
::: {.column width='33%'}
```{r}
datasauRus::datasaurus_dozen
```
:::
::: {.column width='66%'}
```{r}
datasauRus::datasaurus_dozen %>%
  group_by(dataset) %>%
  summarize(mean_x = mean(x), mean_y = mean(y), 
            sd_x = sd(x), sd_y = sd(y), 
            cor = cor(x,y), .groups = "drop")
```
:::
::::

## Simpson's Paradox

```{r include=FALSE}
datasauRus::simpsons_paradox %>%
  ggplot(aes(x=x, y=y, color=dataset)) +
    geom_point() +
    facet_wrap(vars(dataset))

ctrs = matrix(
  c(
    25,15,
    38,29,
    48,58,
    59,75,
    80,83
  ),
  byrow=TRUE,
  ncol=2
)

simpsons = datasauRus::simpsons_paradox %>%
  filter(dataset == "simpson_2", x < 75) %>%
  select(-dataset) %>%
  mutate(., group = kmeans(., ctrs)$cluster %>% as.character()) 
```


```{r echo=FALSE} 
simpsons %>%
  ggplot(aes(x=x, y=y)) +
    geom_point() +
    geom_smooth(method="lm", se=FALSE, color="black", formula=y~x)
```


## Simpson's Paradox

```{r echo = FALSE} 
simpsons %>%
  ggplot(aes(x=x, y=y, color=group)) +
    geom_point() +
    geom_smooth(method="lm", se=FALSE, formula=y~x) +
    geom_smooth(method="lm", se=FALSE, color="black", formula=y~x) +
    guides(color = "none")
```


# Designing effective visualizations

## Gapminder

::: {.center .large}
[www.youtube.com/embed/OwII-dwh-bk](https://www.youtube.com/embed/OwII-dwh-bk)
:::


## Keep it simple


<br/>

:::: {.columns}
::: {.column width='50%'} 
```{r pie-3d, echo=FALSE, out.width="100%"}
knitr::include_graphics("imgs/pie-3d.jpg")
```
:::
::: {.column width='50%'}
<br/> <br/>
```{r pie-to-bar, echo=FALSE, out.width="100%"}
d <- tribble(
  ~category,                     ~value,
  "Cutting tools"                , 0.03,
  "Buildings and administration" , 0.22,
  "Labor"                        , 0.31,
  "Machinery"                    , 0.27,
  "Workplace materials"          , 0.17
)
ggplot(d, aes(x = fct_reorder(category, value), y = value)) +
  geom_col() +
  theme_minimal() +
  coord_flip() +
  labs(x = "", y = "")
```
:::
::::


## Judging relative area


::: {.aside}
From Data to Viz caveat collection - [The issue with pie chart](https://www.data-to-viz.com/caveat/pie.html)
:::


```{r echo=FALSE, out.width="75%"}
knitr::include_graphics("imgs/caveat_pie1.png")
```

. . .

```{r echo=FALSE, out.width="75%"}
knitr::include_graphics("imgs/caveat_pie2.png")
```


## Use color	to	draw	attention

<br/> <br/>

:::: {.columns}
::: {.column width='50%'}
```{r echo=FALSE, out.width="100%"}
d %>%
  mutate(category = str_replace(category, " ", "\n")) %>%
  ggplot(aes(x = category, y = value, fill = category)) +
    geom_col() +
    theme_minimal() +
    labs(x = "", y = "") +
    theme(legend.position = "none")
```
:::
::: {.column width='50%'}
```{r echo=FALSE, out.width="100%"}
ggplot(d, aes(x = fct_reorder(category, value), y = value, fill = category)) +
  geom_col() +
  theme_minimal() +
  coord_flip() +
  labs(x = "", y = "") +
  scale_fill_manual(values = c("red", rep("gray", 4))) +
  theme(legend.position = "none")
```
:::
::::


## Tell a story

<br/>

:::: {.columns}
::: {.column width='50%'}
```{r echo=FALSE, fig.align="center", out.width="98%"}
knitr::include_graphics("imgs/time-series-story-1.png")
```
:::
::: {.column width='50%'}
```{r echo=FALSE, fig.align="center", out.width="100%"}
knitr::include_graphics("imgs/time-series-story-2.png")
```
:::
::::


::: {.aside}
*Credit*: Angela Zoss and Eric Monson, Duke DVS
:::

## Leave out non-story details

<br/> <br/>

:::: {.columns}
::: {.column width='50%'}
```{r echo=FALSE, fig.align="center", out.width="100%"}
knitr::include_graphics("imgs/vis_inj1.png")
```
:::
::: {.column width='50%'}
```{r echo=FALSE, fig.align="center", out.width="96%"}
knitr::include_graphics("imgs/vis_inj2.png")
```
:::
::::


::: {.aside}
*Credit*: Angela Zoss and Eric Monson, Duke DVS
:::


## Ordering matter

:::: {.columns}
::: {.column width='50%'}
```{r echo=FALSE, fig.align="center", out.width="80%"}
knitr::include_graphics("imgs/vis_order1.png")
```
:::
::: {.column width='50%'}
```{r echo=FALSE, fig.align="center", out.width="80%"}
knitr::include_graphics("imgs/vis_order2.png")
```
:::
::::


::: {.aside}
*Credit*: Angela Zoss and Eric Monson, Duke DVS
:::


## Clearly indicate missing data

<br/>

```{r echo=FALSE, fig.align="center", out.width="100%"}
knitr::include_graphics("imgs/vis_missing.png")
```

::: {.aside}
http://ivi.sagepub.com/content/10/4/271, Angela Zoss and Eric Monson, Duke DVS
:::


## Reduce cognitive load

<br/>

```{r echo=FALSE, fig.align="center", out.width="100%"}
knitr::include_graphics("imgs/vis_text.png")
```

::: {.aside}
http://www.storytellingwithdata.com/2012/09/some-finer-points-of-data-visualization.html
:::

## Use descriptive titles

:::: {.columns}
::: {.column width='50%'}
```{r echo=FALSE, fig.align="center", out.width="80%"}
knitr::include_graphics("imgs/vis-title-1.png")
```
:::
::: {.column width='50%'}
```{r echo=FALSE, fig.align="center", out.width="80%"}
knitr::include_graphics("imgs/vis-title-2.png")
```
:::
::::

::: {.aside}
*Credit*: Angela Zoss and Eric Monson, Duke DVS
:::

## Annotate figures

<br/>

```{r echo=FALSE, fig.align="center", out.width="80%"}
knitr::include_graphics("imgs/vis_annotate.png")
```


::: {.aside}
https://bl.ocks.org/susielu/23dc3082669ee026c552b85081d90976
:::

## All of the data doesn't tell a story

```{r echo=FALSE, fig.align="center", out.width="60%"}
knitr::include_graphics("imgs/vis_nyt1.png")
```


::: {.aside}
[nytimes.com/interactive/2014/06/05/upshot/how-the-recession-reshaped-the-economy-in-255-charts.html](http://www.nytimes.com/interactive/2014/06/05/upshot/how-the-recession-reshaped-the-economy-in-255-charts.html)
:::

## All of the data doesn't tell a story


```{r echo=FALSE, fig.align="center", out.width="60%"}
knitr::include_graphics("imgs/vis_nyt2.png")
```


::: {.aside}
[nytimes.com/interactive/2014/06/05/upshot/how-the-recession-reshaped-the-economy-in-255-charts.html](http://www.nytimes.com/interactive/2014/06/05/upshot/how-the-recession-reshaped-the-economy-in-255-charts.html)
:::

## All of the data doesn't tell a story

```{r echo=FALSE, fig.align="center", out.width="60%"}
knitr::include_graphics("imgs/vis_nyt3.png")
```


::: {.aside}
[nytimes.com/interactive/2014/06/05/upshot/how-the-recession-reshaped-the-economy-in-255-charts.html](http://www.nytimes.com/interactive/2014/06/05/upshot/how-the-recession-reshaped-the-economy-in-255-charts.html)
:::

# Chart Remakes / Makeovers


## The Why Axis - Gender Gap


```{r echo=FALSE, fig.align="center", out.width="45%"}
knitr::include_graphics("imgs/vis_gap.jpg")
```

::: {.aside}
[thewhyaxis.info/gap-remake/](https://web.archive.org/web/20220121073030/thewhyaxis.info/gap-remake/)
:::


## The Why Axis - BLS


```{r echo=FALSE, fig.align="center", out.width="60%"}
knitr::include_graphics("imgs/vis_bls.gif")
```

::: {.aside}
[thewhyaxis.info/defaults/](https://web.archive.org/web/20210805020658/thewhyaxis.info/defaults/)
:::


## Other Resources

- Duke Library - Center for Data and Visualization Sciences - https://library.duke.edu/data/

- Tidy tuesday - https://github.com/rfordatascience/tidytuesday

- Flowing data - https://flowingdata.com/

- Twitter - #dataviz, #tidytuesday

- Books:
  - Wickham, Navarro, Pedersen. *ggplot2: Elegant Graphics for Data Analysis*. 3rd edition. Springer, 2021.
  - Wilke. *Fundamentals of Data Visualization*. O’Reilly Media, 2019.
  - Healy. *Data Visualization: A Practical Introduction*. Princeton University Press, 2018.
  - Tufte. *The visual display of quantitative information*. 2nd edition. Connecticut Graphics Press, 2015.

## Acknowledgments

Above materials are derived in part from the following sources:

* Visualization training materials developed by Angela Zoss and Eric Monson, [Duke DVS](http://libcms.oit.duke.edu/data/)