alluvial_charts.qmd

# Alluvial charts {#sec-alluvial-charts}

```{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 = 11))
# pak::pak("corybrunson/ggalluvial")
```

```{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(ggalluvial)
library(palmerpenguins) 
library(ggplot2)
library(patchwork)

peng_wide <- penguins |> 
  drop_na() |> 
  count(year, island, sex, species) |> 
  mutate(year = factor(year)) |> 
  rename(freq = n)

labs_alluvial <- ggtitle(label = "Palmer Penguins", 
    subtitle = "Stratified by year, island and species")
labs_alluvial_y <- ylab("Frequency") 
labs_alluvial_fill <- labs(fill = "Sex")

ggp2_alluvial_w <- ggplot(data = peng_wide,
  aes(axis1 = year, axis2 = island,
      axis3 = species, y = freq)) +
  scale_x_discrete(
    limits = c("Year", "Island", "Species"),
    expand = c(0.1, 0.07)) +
  geom_alluvium(aes(fill = sex)) +
  geom_stratum() +
  geom_text(stat = "stratum", 
    aes(label = after_stat(stratum)),
      size = 3)

ggp2_alluvial_w + 
  theme(legend.position = "bottom") +
  labs_alluvial + 
  labs_alluvial_y + 
  labs_alluvial_fill
```

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

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

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

::::

## Description 

An alluvial graph displays the changes in composition or flow over time or across multiple categories. 

We can build alluvial charts in `ggplot2` with the [`ggalluvial` package:](https://corybrunson.github.io/ggalluvial/). 

See also: [parallel sets](parallel_sets.qmd)

## Set up

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

Install packages.


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


Below we create a wide example of the `penguins` data (as `peng_wide`).

::: {style="font-size: 0.85em;"}
```{r}
#| label: data_code_alluvial
#| code-fold: show
#| eval: true
#| echo: true
peng_wide <- penguins |> 
  tidyr::drop_na() |> 
  dplyr::count(year, island, sex, species) |> 
  dplyr::mutate(year = factor(year)) |> 
  dplyr::rename(freq = n)
dplyr::glimpse(peng_wide)
```
:::

## Grammar

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



  - Create labels with `labs()` (with `ggtitle()`, `ylab()`, and `labs()`)

  - Add `scale_x_discrete()` with the `limits` set to `"Year"`, `"Island"` and `"Species"`, and `expand` to `0.1` and `0.07`

  - Add `geom_alluvium()` with `fill` set to the `sex` variable and `geom_stratum()`

  - Add `geom_text()`, with `stat` set to `stratum` and label set to `after_stat(stratum)` (*inside* `aes()`) 

::: {style="font-size: 0.85em;"}
```{r}
#| label: code_graph_alluvial
#| code-fold: show
#| eval: false
#| echo: true 
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
labs_alluvial <- ggtitle(label = "Palmer Penguins", 
    subtitle = "Stratified by year, island and species")
labs_alluvial_y <- ylab("Frequency") 
labs_alluvial_fill <- labs(fill = "Sex")

ggp2_alluvial_w <- ggplot(data = peng_wide,
  aes(axis1 = year, axis2 = island,
      axis3 = species, y = freq)) +
  scale_x_discrete(
    limits = c("Year", "Island", "Species"),
    expand = c(0.1, 0.07)) +
  geom_alluvium(aes(fill = sex)) +
  geom_stratum() +
  geom_text(stat = "stratum", 
    aes(label = after_stat(stratum)),
      size = 3)

ggp2_alluvial_w + 
  theme(legend.position = "bottom")
  labs_alluvial + 
  labs_alluvial_y + 
  labs_alluvial_fill
```
:::

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

The `ggalluvial` functions can handle wide or long data. 

```{r}
#| label: create_graph_alluvial
#| eval: true
#| echo: false
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
labs_alluvial <- ggtitle(label = "Palmer Penguins", 
    subtitle = "Stratified by year, island and species")
labs_alluvial_y <- ylab("Frequency") 
labs_alluvial_fill <- labs(fill = "Sex")

ggp2_alluvial_w <- ggplot(data = peng_wide,
  aes(axis1 = year, axis2 = island,
      axis3 = species, y = freq)) +
  scale_x_discrete(
    limits = c("Year", "Island", "Species"),
    expand = c(0.1, 0.07)) +
  geom_alluvium(aes(fill = sex)) +
  geom_stratum() +
  geom_text(stat = "stratum", 
    aes(label = after_stat(stratum)),
      size = 3)

ggp2_alluvial_w + 
  theme(legend.position = "bottom") +
  labs_alluvial + 
  labs_alluvial_y + 
  labs_alluvial_fill
```

## More info

The `ggalluvial` package can also help reshape data with the `to_lodes_form()` function.

### `to_lodes_form()` 

Below we create `peng_lodes` from the `penguins` dataset using the `to_lodes_form()` from the `ggalluvial` package.

::: {style="font-size: 0.85em;"}
```{r}
#| label: data_code_alluvial_lf
#| eval: true
#| echo: true
peng_lodes <- penguins |> 
  dplyr::select(Year = year, Island = island, 
         Species = species, Sex = sex) |> 
  tidyr::drop_na() |> 
  dplyr::count(Year, Island, Species, Sex) |> 
  dplyr::mutate(Year = factor(Year)) |> 
  dplyr::rename(Freqency = n) |> 
  ggalluvial::to_lodes_form(key = "Measure", axes = 1:3) 
glimpse(peng_lodes)
```
:::

Create labels with `labs()`

  - Map `Measure` to `x`, `Frequency` to `y`, `stratum` to `stratum`, `alluvium` to `alluvium`, and `label` to `stratum`.

  - Add the `geom_alluvium()` and map `Sex` to `fill`  

  - Add the `geom_stratum()` and set the `width` to `0.45`  

  - Add `geom_text()` and set `stat` to `"stratum"`

::: {style="font-size: 0.85em;"}
```{r}
#| label: create_graph_alluvial_lf
#| code-fold: true
#| eval: true
#| echo: true
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
labs_alluvial <- ggtitle(label = "Palmer Penguins", 
    subtitle = "Stratified by year, island and species")

ggp2_alluvial_lf <- ggplot(
    data = peng_lodes,
    aes(x = Measure,
        y = Freqency,
        stratum = stratum,
        alluvium = alluvium,
        label = stratum)) +
    ggalluvial::geom_alluvium(aes(fill = Sex)) +
    ggalluvial::geom_stratum(width = 0.45) +
    geom_text(stat = "stratum", size = 2.5)

ggp2_alluvial_lf +
    labs_alluvial +
    theme_ggp2g(base_size = 13)
```
:::

### `geom_flow()` 

If you'd like to arrange the date or time variable across the `x`, you can use the `ggalluvial::geom_flow()` with `ggalluvial::geom_stratum()`. 

  - First create `peng_alluvial`, a subset of `palmerpenguins::penguins_raw` with all variables turned to factors. 

::: {style="font-size: 0.85em;"}
```{r}
#| label: peng_alluvial
#| eval: true
#| echo: true
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
peng_alluvial <- palmerpenguins::penguins_raw |> 
  janitor::clean_names() |> 
  dplyr::mutate(year = lubridate::year(date_egg),
         year = factor(year),
         individual_id = factor(individual_id),
         island = factor(island)) |> 
  dplyr::select(year, individual_id, island)
dplyr::glimpse(peng_alluvial)
```
:::

  - Create labels with `labs()`

  - Initiate graph with `data`

  - Map the `year` to the `x`, `island` to `stratum`, `individual_id` to `alluvium`, `island` to `fill`, and `island` to `label`.

  - Add `scale_fill_brewer()`, and set the `type` to `"qual"` and choose a `palette`

  - Add the `geom_flow()`, with `stat` set to `"alluvium"`, `lode.guidance` set to `"frontback"`, and `color` to `"#A9A9A9"`

::: {style="font-size: 0.85em;"}
```{r}
#| label: ggp2_alluvial_flow
#| code-fold: true
#| eval: true
#| echo: true
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
# labels
labs_alluvial <- labs(
  title = "Penguin measurements across three years")
# add geom_flow() 
ggp2_alluvial_flow <- ggplot(data = peng_alluvial,
  mapping = aes(x = year, stratum = island, 
    alluvium = individual_id, 
    fill = island, label = island)) +
  scale_fill_brewer(type = "qual", palette = "Pastel2") +
  geom_flow(stat = "alluvium",
    lode.guidance = "frontback",
    color = "#A9A9A9")

ggp2_alluvial_flow
```

  - Add `ggalluvial::geom_stratum()`

```{r}
#| label: ggp2_alluvial_geom_stratum
#| code-fold: true
#| eval: true
#| echo: true
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
# add geom_stratum()
ggp2_alluvial_stratum <- ggp2_alluvial_flow +
  geom_stratum() 
ggp2_alluvial_stratum
```
:::

### `legend.position`

Move legend to bottom with `theme(legend.position = "bottom")`

::: {style="font-size: 0.85em;"}
```{r}
#| label: ggp2_alluvial_legend_position
#| code-fold: true
#| eval: true
#| echo: true
#| warning: false
#| message: false
#| out-height: '100%'
#| out-width: '100%'
#| layout-nrow: 1
#| column: page-inset-right
ggp2_alluvial_stratum + 
  labs_alluvial + 
  theme(legend.position = "bottom")
```
:::