parallel_sets.qmd

# Parallel sets {#sec-parallel-sets}


```{r}
#| label: setup
#| message: false
#| warning: false
#| include: false
library(tidyverse)
library(lubridate)
library(scales)
library(knitr)
library(kableExtra)
library(colorblindr)
library(downlit)
# fonts ----
library(extrafont)
library(sysfonts)
source("_common.R")
# use font
showtext::showtext_auto()
# set theme
ggplot2::theme_set(theme_ggp2g(
    base_size = 12))
# pak::pak("thomasp85/ggforce")
library(ggforce)
```


```{r}
#| label: status
#| results: "asis"
#| echo: false
# status ----
# polish, dev, draft, complete
status("complete")
```

:::: {.callout-note collapse="false" icon=false}

<br>

```{r}
#| label: full_code_display
#| eval: true
#| echo: false
#| warning: false
#| message: false
#| out-height: '60%'
#| out-width: '60%'
#| fig-align: right
library(palmerpenguins) 
library(ggplot2)
library(ggforce)
peng_wide <- palmerpenguins::penguins |> 
  drop_na() |> 
  count(island, species, sex) |> 
  rename(value = n)
para_set_peng <- ggforce::gather_set_data(
                            data = peng_wide, 
                            x = 1:3)
labs_psets <- labs(
        title = "Categories of Palmer Penguins", 
        y = "Count", fill = "Sex")

ggp2_psets <- ggplot(data = para_set_peng, 
    mapping = aes(x = x, 
        id = id, 
        split = y, 
        value = value)) +
  geom_parallel_sets(aes(fill = sex), 
        alpha = 0.3, 
        axis.width = 0.07) 

ggp2_psets_axes <- ggp2_psets +
  geom_parallel_sets_axes(
        axis.width = 0.07) 

ggp2_psets_labs <- ggp2_psets_axes +
  geom_parallel_sets_labels(
        size = 2.0, 
        color = '#ffffff') +
  scale_x_continuous(
        breaks = c(1, 2, 3), 
        labels = c("Island", "Species", "Sex")) +
  theme(axis.title.x = element_blank())

ggp2_psets_labs +
    labs_psets
```

::: {style="font-size: 1.10em; color: #02577A;"}
**This graph requires:**
:::

::: {style="font-size: 1.05em; color: #282b2d;"}
**`r emo::ji("check")` three categorical variables**    
:::

::: {style="font-size: 1.05em; color: #282b2d;"}
**`r emo::ji("check")` a numeric variable of counts**
:::

::::

## Description

Parallel sets (also referred to as Sankey diagrams or Alluvial charts) show the counts of categorical variables connected via a two-sided parallel display (or 'sets'). Parallel sets can also be used to show different states of paired dependent relationships (such as input vs output), or time 1 vs time 2.

The height of the connecting bands *between* the categories on the `x` axis represent the relative counts for each discrete level (displayed on the `y` axis). The levels *within* each variable are represented with color. 

We can build parallel set diagrams with the [`ggforce` package](https://ggforce.data-imaginist.com/index.html).  

Also check out [alluvial charts.](alluvial_charts.qmd)

## Set up 

::: {style="font-size: 1.15em; color: #1e83c8;"}
**PACKAGES:**
:::

Install packages.


::: {style="font-size: 0.85em;"}
```{r}
#| label: pkg_code_parallel_sets
#| code-fold: show
#| eval: false
#| echo: true
#| warning: false
#| message: false
#| results: hide
# pak::pak("thomasp85/ggforce")
install.packages("palmerpenguins")
library(ggforce)
library(palmerpenguins)
library(ggplot2)
```
:::


::: {style="font-size: 1.15em; color: #1e83c8;"}
**DATA:**
:::

::: {.column-margin}
![Artwork by allison horst](www/lter_penguins.png){fig-align="right" width="100%" height="100%"}
:::


We're going to remove the missing values from `palmerpenguins::penguins`, count the categorical variables (`island`, `sex`, `species`), and rename the `n` column (produced by the `count()` function) to `value`.

  - `ggforce` has a special [`gather_set_data()`](https://ggforce.data-imaginist.com/reference/gather_set_data.html) function that *changes tidy data into a tidy(er) format*

::: {style="font-size: 0.85em;"}
```{r}
#| label: data_code_parallel_sets
#| code-fold: show
#| eval: true
#| echo: true
peng_wide <- palmerpenguins::penguins |> 
  drop_na() |> 
  count(island, species, sex) |> 
  rename(value = n)
para_set_peng <- ggforce::gather_set_data(
                            data = peng_wide, 
                            x = 1:3)
dplyr::glimpse(para_set_peng)
```
:::

## Grammar

::: {style="font-size: 1.15em; color: #1e83c8;"}
**CODE:**
:::

  - Create labels with `labs()`

  - Initialize the graph with `ggplot()` and provide `data`

  - Map `x` to `x`, `id` to `id`, `y` to `split`, and `value` to `value`

  - In the `geom_parallel_sets()` function, map `sex` to `fill` and manually set the `alpha` (opacity) and the `axis.width` 

  - In the `geom_parallel_sets_axes()` function, set the `axis.width` to the same value as the `geom_parallel_sets()` above

  - For labeling, adjust the `size` manually and set the `color` to something that stands out against the black vertical axes

  - Manually label the `x` axis with `scale_x_continuous()`, setting the `breaks` and `labels` to the variable names in the `peng_wide` dataset

  - Finally, remove the `x` title with `axis.title.x = element_blank()`

::: {style="font-size: 0.85em;"}
```{r}
#| label: code_graph_parallel_sets
#| code-fold: show
#| eval: false
#| echo: true 
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
labs_psets <- labs(
        title = "Categories of Palmer Penguins", 
        y = "Count", fill = "Sex")

ggp2_psets <- ggplot(data = para_set_peng, 
    mapping = aes(x = x, 
        id = id, 
        split = y, 
        value = value)) +
  geom_parallel_sets(aes(fill = sex), 
        alpha = 0.3, 
        axis.width = 0.07) 

ggp2_psets_axes <- ggp2_psets +
  geom_parallel_sets_axes(
        axis.width = 0.07) 

ggp2_psets_labs <- ggp2_psets_axes +
  geom_parallel_sets_labels(
        size = 2.0, 
        color = '#ffffff') +
  scale_x_continuous(
        breaks = c(1, 2, 3), 
        labels = c("Island", "Species", "Sex")) +
  theme(axis.title.x = element_blank())

ggp2_psets_labs +
    labs_psets
```
:::



::: {style="font-size: 1.15em; color: #1e83c8;"}
**GRAPH:**
:::

```{r}
#| label: create_graph_parallel_sets
#| eval: true
#| echo: false
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
labs_psets <- labs(
        title = "Categories of Palmer Penguins", 
        y = "Count", fill = "Sex")

ggp2_psets <- ggplot(data = para_set_peng, 
    mapping = aes(x = x, 
        id = id, 
        split = y, 
        value = value)) +
  geom_parallel_sets(aes(fill = sex), 
        alpha = 0.3, 
        axis.width = 0.07) 

ggp2_psets_axes <- ggp2_psets +
  geom_parallel_sets_axes(
        axis.width = 0.07) 

ggp2_psets_labs <- ggp2_psets_axes +
  geom_parallel_sets_labels(
        size = 2.0, 
        color = '#ffffff') +
  scale_x_continuous(
        breaks = c(1, 2, 3), 
        labels = c("Island", "Species", "Sex")) +
  theme(axis.title.x = element_blank())

ggp2_psets_labs +
    labs_psets
```

## More info

If the categories have long names, you can move the location of the labels *outside* the set. 

### Labeling sets

If the categories have long names, use the `angle`, `nudge_x`/`nudge_y` and `hjust`/`vjust` in `geom_parallel_sets_labels()` to adjust the size, location, and color of the labels. 

  - Manually setting the `limits` of the `x` axis in `scale_x_continuous()` will also give more room for the labels. 

::: {style="font-size: 0.85em;"}
```{r}
#| label: create_graph_parallel_sets_labs
#| eval: true
#| echo: true
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
ggp2_psets_axes + 
  geom_parallel_sets_labels(
      size = 3.2, 
      colour = '#000000',
      angle = 0, 
      nudge_x = 0.1, 
      hjust = 0) + 
  scale_x_continuous(
        limits = c(0.9, 3.2),
        breaks = c(1, 2, 3), 
        labels = c("Island", "Species", "Sex")) + 
  theme(axis.title.x = element_blank()) + 
    labs_psets
```
:::